HIV Life Cycle (Homo sapiens)

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62, 6915, 19, 31, 37, 48...922210728, 39126116, 787, 27, 73, 8488, 109243, 13, 40, 45, 66...44, 898, 32, 46, 69, 71...353, 10, 29, 68, 75...8, 10918, 47, 493, 14, 30, 53, 102...22, 1032, 50, 912659, 38, 6383593907, 2734, 887, 27, 51, 558513, 17, 33, 42, 52...8, 109520, 23, 70, 74, 9922, 79, 11092111, 13, 19, 861, 254, 2256, 59, 101886, 23, 7435, 64, 993520, 35, 9988, 108356518, 47, 76, 808826, 3521, 7735, 67, 1008858TFIIE [nucleoplasm]TFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase IIholoenzyme complex(phosphorylated)[nucleoplasm]linear duplex viralDNA [cytosol]TFIIH [nucleoplasm]HIV-1 processiveelongation complex[nucleoplasm]Ran-GDP[nucleoplasm]CD4:Envgp120:CCR5,CXCR4:complex[plasma membrane]TFIIF [nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]NTP [nucleoplasm]TFIIH [nucleoplasm]HIV-1 promoter:TFIIDcomplex[nucleoplasm]ubiquitin [plasmamembrane]Nucleocapsid[extracellularregion]Elongin Complex[nucleoplasm]Nucleocapsid[extracellularregion]Trimeric ENVprecursor[endoplasmicreticulum membrane]IN bound to sticky3' ends of viral DNA[nucleoplasm]gp41 homotrimer[viral envelope]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]phospho-DSIF complex[nucleoplasm]Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD (phospho-NELF phosphoDSIF) [nucleoplasm]gp41 homotrimer[viral envelope]p6 protein [cytosol]RNA Pol II(hypophosphorylated)complex bound toDSIF protein[nucleoplasm]TFIIF [nucleoplasm]TFIIH [nucleoplasm]RT [cytosol]HIV-1 transcriptioncomplex containing 4nucleotide longtranscript[nucleoplasm]CCR5, CXCR4 [plasmamembrane]gp120 homotrimer[cytosol]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTP[cytosol]RT [extracellularregion]CAK [nucleoplasm]gp120 homotrimer[cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]HIV-1 RNA homodimer[extracellularregion]IN bound to sticky3' ends of viral DNA[nucleoplasm]RTC with extendingsecond-strand DNA[cytosol]Matrix [cytosol]RNA Pol II(hypophosphorylated):cappedpre-mRNA complex[nucleoplasm]TFIIF [nucleoplasm]TFIIE [nucleoplasm]Nuclear Pore Complex(NPC) [nuclearenvelope]RTC with degradedRNA template andminus sssDNA[cytosol]Virion with exposedcoreceptor bindingsites [extracellularregion]p6 protein [cytosol]Matrix [cytosol]linear duplex viralDNA [nucleoplasm]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTP[nucleoplasm]p6 protein [cytosol]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RT [cytosol]Virion withCD4:gp120 bound toCCR5/CXCR4[extracellularregion]HIV-1 RNA homodimer[cytosol]RT [extracellularregion]viral DNA:Kuproteins:XRCC4:DNAligase IV complex[nucleoplasm]CD4:Env gp120 withexposed coreceptorbinding site [plasmamembrane]Cap Binding Complex(CBC) [nucleoplasm]Nucleocapsid[cytosol]Cap Binding Complex(CBC) [nucleoplasm]TFIID [nucleoplasm]CD4:Envgp120/gp41insertioncomplex:CCR5/CXCR4[plasma membrane]NELF complex[nucleoplasm]P-TEFb complex[nucleoplasm]RT [cytosol]gp41 homotrimer withhairpin structureformation [viralenvelope]RTC with minussssDNA:tRNAprimer:RNA template[cytosol]TFIIF [nucleoplasm]HIV-1 transcriptioncomplex containing 3nucleotide longtranscript[nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]gp120 homotrimer[viral envelope]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]p6 protein[nucleoplasm]Rev-bound HIV-1 mRNA[cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]HIV-1promoter:TFIID:TFIIA:TFIIB:PolII:TFIIF complex*[nucleoplasm]minus sssDNA primerfor minus strand DNAextension [cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]minus sssDNA:tRNAprimer generated byRNAse-H [cytosol]Matrix [cytosol]Elongin Complex[nucleoplasm]RNA Pol II(hypophosphorylated):cappedpre-mRNA complex[nucleoplasm]p6 protein [cytosol]FACT complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]minus sssDNA:RNAtemplate:tRNA primer[cytosol]CAK [nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]TFIIF [nucleoplasm]Trimeric ENVprecursor [Golgimembrane]Ku70:Ku80heterodimer[nucleoplasm]monoubiquitinatedN-myristoyl GAG(P04591) protein[plasma membrane]TFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]HIV-1 earlyelongation complexwithhyperphosphorylatedPol II CTD[nucleoplasm]Assembling HIVvirion [plasmamembrane]viral DNA with 3'sticky ends[nucleoplasm]viral DNA with 3'sticky ends[cytosol]monoubiquitinatedN-myristoyl GAG(P04591) protein[cytosol]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]TFIIH [nucleoplasm]TFIIF [nucleoplasm]p6 protein[extracellularregion]TFIIF [nucleoplasm]Rev-bound HIV-1 mRNA[nucleoplasm]Env oligomer withgp41 hairpinstructure formation[viral envelope]Matrix [cytosol]RTC (ReverseTranscriptionComplex) with RNAtemplate [cytosol]CHMP4 [cytosol]RT [cytosol]Env oligomer withgp120(exposed)[plasma membrane]XRCC4:DNA ligase IVcomplex[nucleoplasm]p6 protein [cytosol]CD4:Env gp120/gp41fusion peptidecomplex:CCR5 [plasmamembrane]Elongin B:C complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]DSIF complex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]gp41 homotrimer[cytosol]HIV-1 transcriptioncomplex containing4-9 nucleotide longtranscript[nucleoplasm]Elongin B:C complex[nucleoplasm]FACT complex[nucleoplasm]NELF complex[nucleoplasm]p6 protein[extracellularregion]FACT complex[nucleoplasm]Matrix [cytosol]CD4:Env gp120/gp41hairpin complex[plasma membrane]Elongin Complex[nucleoplasm]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTP[cytosol]viral DNA with 3'sticky ends[nucleoplasm]p6 protein [cytosol]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]HIV-1 Tat-containingpaused processiveelongation complex[nucleoplasm]Elongin B:C complex[nucleoplasm]RanBP1:Ran-GTP:CRM1:Rev-boundmRNA complex[cytosol]NELF complex[nucleoplasm]CD4:Env gp120 withexposed coreceptorbinding site [plasmamembrane]RNA template:tRNAprimer [cytosol]Elongin Complex[nucleoplasm]DSIF complex[nucleoplasm]TFIID [nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]TFIIF [nucleoplasm]TFIIH [nucleoplasm]FACT complex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]p6 protein [cytosol]DSIF complex[nucleoplasm]CAK [nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]DSIF complex[nucleoplasm]CCR5/CXCR4:CD4:Envgp120 (secondconformation change)complex [plasmamembrane]phospho-NELF complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(phosphorylated)[nucleoplasm]P-TEFb complex[nucleoplasm]Elongin B:C complex[nucleoplasm]RT [cytosol]viral PIC proteins[nucleoplasm]CCR5, CXCR4 [plasmamembrane]CAK [nucleoplasm]CD4:Env gp120/gp41fusion peptidecomplex [plasmamembrane]Rev multimer-boundHIV-1 mRNA[nucleoplasm]TFIIF [nucleoplasm]gp120 homotrimer[viral envelope]TFIIH [nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RNA polymerase II(phosphorylated):TFIIFcomplex[nucleoplasm]NELF complex[nucleoplasm]Cap Binding Complex(CBC) [nucleoplasm]CD4:Env gp120/gp41insertion complex[plasma membrane]Elongin B:C complex[nucleoplasm]DSIF complex[nucleoplasm]HIV-1 transcriptioncomplex containing 9nucleotide longtranscript[nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]TFIIF [nucleoplasm]HIV-1 openpre-initiationcomplex[nucleoplasm]p6 protein [cytosol]p6 protein [cytosol]NELF complex[nucleoplasm]1-LTR form ofcircular viral DNA[nucleoplasm]HIV-1 RNA homodimer[extracellularregion]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]Elongin Complex[nucleoplasm]p6 protein[extracellularregion]RT [cytosol]DSIF complex[nucleoplasm]NELF complex[nucleoplasm]gp41 homotrimer[viral envelope]Matrix [nucleoplasm]minus sssDNA primertransferred to 3'-end of viral RNAtemplate [cytosol]Rev multimer-boundHIV-1 mRNA:CRM1complex[nucleoplasm]HIV-1 RNA homodimer[cytosol]TFIIE [nucleoplasm]Ku70:Ku80heterodimer[nucleoplasm]Integrated provirus[nucleoplasm]CAK [nucleoplasm]Rev multimer-boundHIV-1 mRNA [cytosol]Env oligomer withgp41(fusionpeptide)/gp120(released)[viral envelope]TFIIF [nucleoplasm]endoplasmic reticulum membraneRNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]gp120 homotrimer[cytosol]RNA Polymerase IIholoenzyme complex(hypophosphorylated):TFIIFcomplex[nucleoplasm]HIV-1 Polymerase II(phosphorylated):TFIIF:cappedpre-mRNA[nucleoplasm]viral DNA bound withIntegrase [cytosol]Nup62 Complex[nuclear envelope]p6 protein [cytosol]p6 protein [cytosol]Autointegrated viralDNA as an invertedcircle [nucleoplasm]Ku70:Ku80heterodimer[nucleoplasm]gp120 homotrimerafter secondconformation change[viral envelope]Rev-bound HIV-1 mRNA[nucleoplasm]Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD[nucleoplasm]Cap Binding Complex(CBC) [nucleoplasm]NTP [nucleoplasm]p6 protein[nucleoplasm]Nup107 Complex[nuclear envelope]RT [extracellularregion]HIV-1 elongationcomplex containingTat [nucleoplasm]Trimeric gp120:gp41oligomer [viralenvelope]CAK [nucleoplasm]IN:viral DNA boundto host genomic DNAwith staggered ends[nucleoplasm]Vps/Vta1 [cytosol]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RNA Pol II(hypophosphorylated):cappedpre-mRNA complex[nucleoplasm]RT [cytosol]Matrix [cytosol]Elongin B:C complex[nucleoplasm]HIV-1 closedpre-initiationcomplex[nucleoplasm]TFIIF [nucleoplasm]NTP [nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]gp41 homotrimer[viral envelope]ESCRT-I [endosomemembrane]HIV-1 RNA homodimer[extracellularregion]CCR5, CXCR4 [plasmamembrane]RNA Polymerase IIholoenzyme complex(phosphorylated)[nucleoplasm]Integrated provirus[nucleoplasm]HIV-1 RNA homodimer[extracellularregion]TFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]Matrix [cytosol]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]HIV-1 RNA homodimer[extracellularregion]CAK [nucleoplasm]TFIIE [nucleoplasm]Matrix [cytosol]TFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]TFIID [nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RNA Pol II(hypophosphorylated)complex bound toDSIF protein[nucleoplasm]Rev multimer-boundHIV-1 mRNA[nucleoplasm]TFIIE [nucleoplasm]TFIIF [nucleoplasm]monoubiquitinatedN-myristoyl GAG(P04591) protein[plasma membrane]HIV-1 abortedelongation complexafter arrest[nucleoplasm]linear duplex viralDNA [cytosol]gp120 homotrimerafter secondconformation change[viral envelope]P-TEFb complex[nucleoplasm]ESCRT-III [cytosol]gp41 homotrimer[viral envelope]viral PIC proteins[nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]p6 protein[extracellularregion]TFIIH [nucleoplasm]CAK [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]NELF complex[nucleoplasm]Matrix [nucleoplasm]Matrix [cytosol]CD4:Env gp120(second conformationchange) complex[plasma membrane]RT [cytosol]DSIF complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(phosphorylated)[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]Nucleocapsid[extracellularregion]Cap Binding Complex(CBC) [nucleoplasm]TFIIF [nucleoplasm]TFIID [nucleoplasm]CAK [nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]Elongin B:C complex[nucleoplasm]RNA polymerase II(phosphorylated):TFIIFcomplex[nucleoplasm]Trimeric gp120:gp41oligomer [viralenvelope]Rev multimer-boundHIV-1 mRNA[nucleoplasm]Aborted HIV-1 earlyelongation complex[nucleoplasm]CAK [nucleoplasm]TFIIF [nucleoplasm]TFIIH [nucleoplasm]HIV-1 earlyelongation complexwithhyperphosphorylatedPol II CTD[nucleoplasm]CCR5, CXCR4 [plasmamembrane]TFIIE [nucleoplasm]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTP[nucleoplasm]gp41 homotrimer[viral envelope]Matrix [nucleoplasm]p6 protein [cytosol]P-TEFb complex[nucleoplasm]TFIIA [nucleoplasm]Nucleocapsid[extracellularregion]Rev multimer-boundHIV-1 mRNA:CRM1complex[nucleoplasm]HIV-1 transcriptioncomplex[nucleoplasm]RT [cytosol]Elongin B:C complex[nucleoplasm]linear duplex viralDNA [nucleoplasm]Ran:GTP [cytosol]HIV-1 Tat-containingarrested processiveelongation complex[nucleoplasm]TFIIH [nucleoplasm]Elongin B:C complex[nucleoplasm]RT [cytosol]CAK [nucleoplasm]Cap Binding Complex(CBC) [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]TFIIH [nucleoplasm]ubiquitin [plasmamembrane]HIV-1 Tat-containingprocessiveelongation complex[nucleoplasm]CAK [nucleoplasm]TFIIE [nucleoplasm]HIV-1promoter:TFIID:TFIIA:TFIIBcomplex[nucleoplasm]DSIF complex[nucleoplasm]HIV-1 transcriptioncomplex containingtranscript to +30[nucleoplasm]TFIIH [nucleoplasm]NELF complex[nucleoplasm]Elongin Complex[nucleoplasm]Virion BuddingComplex [plasmamembrane]TFIIH [nucleoplasm]IN:viral DNA boundto host genomic DNA [nucleoplasm]HIV-1 RNA homodimer[extracellularregion]ESCRT-III [cytosol]Nup107 Complex[nuclear envelope]p6 protein[nucleoplasm]cytosolRNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]early endosome membraneRNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]DSIF complex[nucleoplasm]Cap Binding Complex(CBC) [nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]Matrix [cytosol]NELF complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]RTC with minusstrand DNA synthesisinitiated from3'-end [cytosol]Trimeric gp120:gp41oligomer [plasmamembrane]TFIIE [nucleoplasm]TFIID [nucleoplasm]IN bound to sticky3' ends of viral DNAin PIC [cytosol]TFIIF [nucleoplasm]IN bound to sticky3' ends of viral DNAin PIC [nucleoplasm]Golgi membraneTFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]TFIIH [nucleoplasm]TFIIH [nucleoplasm]phospho-DSIF complex[nucleoplasm]ESCRT-I [endosomemembrane]minus sssDNA primertransferred to 3'-end of viral RNAtemplate [cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]TFIID [nucleoplasm]TFIIF [nucleoplasm]CHMP4 [cytosol]DSIF complex[nucleoplasm]Vps/Vta1 [cytosol]CAK [nucleoplasm]TFIIF [nucleoplasm]XRCC4:DNA ligase IVcomplex[nucleoplasm]DSIF complex[nucleoplasm]p6 protein [cytosol]CAK [nucleoplasm]RNA Pol II(hypophosphorylated):cappedpre-mRNA complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]gp120 homotrimerwith exposedcoreceptor bindingsites [viralenvelope]TFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]minus sssDNA primerfor minus strand DNAextension [cytosol]CHMP2 [cytosol]Trimeric gp120:gp41oligomer [plasmamembrane]DSIF complex[nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]Immature HIV virion[extracellularregion]NTP [nucleoplasm]TFIIE [nucleoplasm]NELF complex[nucleoplasm]CD4:Env gp120/gp41hairpincomplex:CCR5/CXCR4[plasma membrane]TFIIF [nucleoplasm]RT [extracellularregion]Ran:GTP [cytosol]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]linear duplex viralDNA [nucleoplasm]RT [cytosol]TFIIF [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]TFIIA [nucleoplasm]TFIIA [nucleoplasm]gp120 homotrimerafter secondconformation change[viral envelope]Mature HIV virion[extracellularregion]CAK [nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]DSIF complex[nucleoplasm]Matrix [cytosol]viral PIC proteins[nucleoplasm]NTP [nucleoplasm]TFIIF [nucleoplasm]DSIF complex[nucleoplasm]TFIIF [nucleoplasm]CHMP2 [cytosol]RTC with extendingminus strand DNA[cytosol]Elongin B:C complex[nucleoplasm]Integrationintermediate[nucleoplasm]uncoated viralcomplex [cytosol]TFIIF [nucleoplasm]Elongin Complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]Ku70:Ku80heterodimer[nucleoplasm]RNA polymerase II(phosphorylated):TFIIFcomplex[nucleoplasm]TFIIA [nucleoplasm]TFIIA [nucleoplasm]DSIF complex[nucleoplasm]RTC with duplex DNAcontainingdiscontinuous plusstrand flap[cytosol]TFIIH [nucleoplasm]Crm1:Ran GTPase:GTP[cytosol]Ku proteins bound toviral DNA[nucleoplasm]FACT complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hypophosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]TFIIA [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]Virion withfusogenicallyactivated gp41[extracellularregion]Matrix [cytosol]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]RTC with integrationcompetent viral DNA[cytosol]NELF complex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]Cap Binding Complex(CBC) [nucleoplasm]Ku proteins bound toviral DNA[nucleoplasm]RTC with tRNAprimer:RNA template[cytosol]Elongin B:C complex[nucleoplasm]Ub [cytosol]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]Elongin B:C complex[nucleoplasm]Matrix [cytosol]RNA Pol II withphosphorylated CTD:CE complex[nucleoplasm]HIV-1 Polymerase II(phosphorylated):TFIIF:cappedpre-mRNA[nucleoplasm]ubiquitin [plasmamembrane]TFIIH [nucleoplasm]P-TEFb(CyclinT1:Cdk9)-containingelongation complexwith separated anduncleaved transcript[nucleoplasm]RNA Polymerase IIholoenzyme complex(hypophosphorylated):TFIIFcomplex[nucleoplasm]RT [extracellularregion]Elongin Complex[nucleoplasm]RNA Pol II withphosphorylated CTD:CE complex withactivated GT[nucleoplasm]TFIIF [nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]TFIIF [nucleoplasm]FACT complex[nucleoplasm]Virion with CD4bound to gp120[extracellularregion]RT [cytosol]CAK [nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]viral PIC proteins[nucleoplasm]p6 protein[nucleoplasm]gp41 homotrimer withfusion peptideinserted intomembrane [viralenvelope]Encapsidated viralcore [cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]Rev-bound HIV-1 mRNA[nucleoplasm]HIV-1 initiationcomplex withphosphodiester-PPiintermediate[nucleoplasm]Nup62 Complex[nuclear envelope]NTP [nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]TFIIF [nucleoplasm]TFIIH [nucleoplasm]TFIIF [nucleoplasm]Ran:GTP [cytosol]FACT complex[nucleoplasm]Elongin Complex[nucleoplasm]Ran GTPase:GDP[cytosol]HIV-1 PromoterEscape Complex[nucleoplasm]TFIIE [nucleoplasm]NELF complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]TFIIH [nucleoplasm]Elongin Complex[nucleoplasm]Nucleocapsid[extracellularregion]Rev multimer-boundHIV-1 mRNA[nucleoplasm]TFIIH [nucleoplasm]Ran-GTP[nucleoplasm]Matrix [cytosol]NELF complex[nucleoplasm]p6 protein[nucleoplasm]FACT complex[nucleoplasm]RT [extracellularregion]Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD (phospho-NELF phosphoDSIF) [nucleoplasm]linear duplex viralDNA [nucleoplasm]TFIIF [nucleoplasm]DSIF complex[nucleoplasm]RNA Pol II(hypophosphorylated)complex bound toDSIF protein[nucleoplasm]TFIIH [nucleoplasm]FACT complex[nucleoplasm]IN bound to sticky3' ends of viral DNA[cytosol]Matrix [cytosol]HIV-1 cappedpre-mRNA:CBC:RNA PolII (phosphorylated)complex[nucleoplasm]NELF complex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]RTC with annealedcomplementary PBSseqments in +sssDNAand -strand DNA[cytosol]Ku proteins bound toviral DNA[nucleoplasm]TFIID [nucleoplasm]TFIID [nucleoplasm]DSIF:NELF:earlyelongation complexafter limitednucleotide addition[nucleoplasm]RNA Pol II(hypophosphorylated)complex bound toDSIF protein[nucleoplasm]HIV-1 elongationcomplex[nucleoplasm]Nucleocapsid[cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]Matrix [cytosol]TFIIH [nucleoplasm]CAK [nucleoplasm]HIV-1 transcriptioncomplex containingextruded transcriptto +30 [nucleoplasm]Rev-bound HIV-1 mRNA[nucleoplasm]gp41 homotrimer withhairpin structureformation [viralenvelope]minus sssDNA primerfor minus strand DNAextension [cytosol]TFIIF [nucleoplasm]Viral coresurrounded by Matrixlayer [cytosol]TFIIF [nucleoplasm]p6 protein [cytosol]TFIIF [nucleoplasm]phospho-NELF complex[nucleoplasm]TFIIH [nucleoplasm]TFIIF [nucleoplasm]TFIIH [nucleoplasm]TFIIH [nucleoplasm]NELF complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]gp120 homotrimerafter secondconformation change[viral envelope]Autointegrated viralDNA as smallercircles[nucleoplasm]Nucleocapsid[extracellularregion]RNA Polymerase IIholoenzyme complex(hypophosphorylated):TFIIFcomplex[nucleoplasm]CAK [nucleoplasm]nucleoplasmP-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]RT [cytosol]HIV-1 pausedprocessiveelongation complex[nucleoplasm]HIV-1 Tat-containingaborted elongationcomplex after arrest[nucleoplasm]RNA Polymerase IIholoenzyme complex(hypophosphorylated):TFIIFcomplex[nucleoplasm]HIV-1 RNA homodimer[cytosol]CCR5, CXCR4 [plasmamembrane]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]RNA Pol II(hypophosphorylated):cappedpre-mRNA complex[nucleoplasm]P-TEFb complex[nucleoplasm]CE:Pol II CTD:Spt5complex[nucleoplasm]Ran-GTP[nucleoplasm]Matrix [nucleoplasm]Early elongationcomplex withseparated abortedtranscript[nucleoplasm]CAK [nucleoplasm]Matrix [cytosol]Nucleocapsid[extracellularregion]NELF complex[nucleoplasm]NTP [nucleoplasm]RNA PolymearseII:NTP:TFIIF complex[nucleoplasm]NTP [nucleoplasm]HIV-1 transcriptioncomplex containing11 nucleotide longtranscript[nucleoplasm]IN bound to sticky3' ends of viral DNA[nucleoplasm]Trimeric gp120:gp41oligomer [cytosol]p6 protein[extracellularregion]HIV-1 arrestedprocessiveelongation complex[nucleoplasm]P-TEFb complex[nucleoplasm]Matrix [cytosol]RT [cytosol]PIC (PreIntegrationComplex) [cytosol]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]p6 protein [cytosol]TFIIH [nucleoplasm]RNA Polymerase IIholoenzyme complex(hypophosphorylated):TFIIFcomplex[nucleoplasm]Nuclear Pore Complex(NPC) [nuclearenvelope]HIV-1 transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30[nucleoplasm]RT [cytosol]p6 protein [cytosol]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]CD4:Env gp120/gp41hairpincomplex:CCR5/CXCR4[plasma membrane]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]CAK [nucleoplasm]FACT complex[nucleoplasm]HIV-1 RNA homodimer[cytosol]RT [extracellularregion]gp120 homotrimerafter secondconformation change[viral envelope]NTP [nucleoplasm]CAK [nucleoplasm]Elongin Complex[nucleoplasm]phospho-NELF complex[nucleoplasm]minus sssDNA primerfor minus strand DNAextension [cytosol]TFIIE [nucleoplasm]Ran-GTP[nucleoplasm]DSIF complex[nucleoplasm]DSIF complex[nucleoplasm]RNA polymerase II(phosphorylated):TFIIFcomplex[nucleoplasm]TFIID [nucleoplasm]CAK [nucleoplasm]TFIIA [nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]Virion with gp41fusion peptide ininsertion complex[extracellularregion]p6 protein [cytosol]TFIIF [nucleoplasm]TFIIF [nucleoplasm]gp41 homotrimer[cytosol]FACT complex[nucleoplasm]Matrix [cytosol]Virion with gp41exposed [extracellularregion]p6 protein[extracellularregion]CAK [nucleoplasm]RTC with nickedminus sssDNA:tRNAprimer:RNA template[cytosol]Matrix [nucleoplasm]DSIF complex[nucleoplasm]Tat:P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]RTC with minussssDNA transferredto 3'-end of viralRNA template[cytosol]HIV-1 initiationcomplex[nucleoplasm]RTC with extensiveRNase-H digestion[cytosol]FACT complex[nucleoplasm]ubiquitin [endosomemembrane]TFIIH [nucleoplasm]gp41 homotrimer[cytosol]Elongin B:C complex[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]p6 protein [cytosol]TFIIF [nucleoplasm]TFIIF [nucleoplasm]Env oligomer withgp41 hairpinstructure formation[viral envelope]RT [cytosol]RNA Polymerase IIholoenzyme complex(phosphorylated)[nucleoplasm]Nucleocapsid[cytosol]nicked minussssDNA:RNAtemplate:tRNA primer[cytosol]linear duplex viralDNA [cytosol]RNA Pol II(hypophosphorylated)complex bound toDSIF protein[nucleoplasm]monoubiquitinatedN-myristoyl GAG(P04591) protein[extracellularregion]Env oligomer withgp41(inserted)/gp120(released)[viral envelope]p6 protein[extracellularregion]2-LTR form ofcircular viral DNA[nucleoplasm]Rev-bound HIV-1 mRNA[cytosol]HIV-1 RNA homodimer[extracellularregion]TFIID [nucleoplasm]Env oligomer withgp120(secondconformation change)[viral envelope]CAK [nucleoplasm]DSIF:NELF:earlyelongation complex[nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]CAK [nucleoplasm]TFIIA [nucleoplasm]RNA Polymerase IIholoenzyme complex(phosphorylated)[nucleoplasm]HIV-1 RNA homodimer[extracellularregion]Crm1:Ran GTPase:GTP[cytosol]linear duplex viralDNA [nucleoplasm]CD4:Env gp120/gp41hairpin complex[plasma membrane]Nucleocapsid[extracellularregion]TFIIA [nucleoplasm]TFIIA [nucleoplasm]Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD andphospho-NELF[nucleoplasm]RNA polymerase II(phosphorylated):TFIIFcomplex[nucleoplasm]monoubiquitinatedN-myristoyl GAG(P04591) protein[endosome membrane]CCR5, CXCR4 [plasmamembrane]CAK [nucleoplasm]viral DNA bound withIntegrase in PIC[cytosol]RT [cytosol]p6 protein [cytosol]TFIIF [nucleoplasm]p6 protein[extracellularregion]RTC without viralRNA template[cytosol]Rev multimer-boundHIV-1 mRNA:CRM1complex[nucleoplasm]Env oligomer withgp120(exposed)[plasma membrane]RNA Polymerase IIholoenzyme complex(hyperphosphorylated)[nucleoplasm]viral DNA with 3'sticky ends[nucleoplasm]HIV-1 RNA homodimer[cytosol]p6 protein [cytosol]RNA Pol II(hypophosphorylated):cappedpre-mRNA complex[nucleoplasm]Rev-bound HIV-1 mRNA[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]HIV-1 RNA homodimer[extracellularregion]RNA polymerase II(phosphorylated):TFIIFcomplex[nucleoplasm]RNA Polymerase IIholoenzyme complex(hyperphosphorylated):TFIIFcomplex[nucleoplasm]Virion with gp41forming hairpinstructure[extracellularregion]Rev multimer-boundHIV-1 mRNA [cytosol]gp41 homotrimer withexposed fusionpeptide [viralenvelope]DSIF complex[nucleoplasm]gp120 homotrimer[viral envelope]RNA Polymerase II(unphosphorylated):TFIIFcomplex[nucleoplasm]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTP:NPC[nuclear envelope]Cap Binding Complex(CBC) [nucleoplasm]Tat-containingelongation complexprior to separation[nucleoplasm]RT [extracellularregion]Elongin Complex[nucleoplasm]NELF complex[nucleoplasm]RT [cytosol]TFIIF [nucleoplasm]gp120 homotrimerwith exposedcoreceptor bindingsites [viralenvelope]CD4:gp120:gp41membrane complex[plasma membrane]TFIIF [nucleoplasm]Trimeric gp120:gp41oligomer [viralenvelope]FACT complex[nucleoplasm]NELF complex[nucleoplasm]RT [cytosol]TFIIF [nucleoplasm]P-TEFb complex[nucleoplasm]P-TEFb(CyclinT1:Cdk9) complex[nucleoplasm]Elongin Complex[nucleoplasm]RNA Polymerase IIholoenzyme complex(unphosphorylated)[nucleoplasm]TFIIF [nucleoplasm]POLR2J [nucleoplasm]MA (P04591) protein[cytosol]NELFB [nucleoplasm]ATP [nucleoplasm]CCNH [nucleoplasm]POLR2F(1-127)[nucleoplasm]REV (P04618) protein[nucleoplasm]CTP [nucleoplasm]POLR2J [nucleoplasm]POLR2F(1-127)[nucleoplasm]POLR2I [nucleoplasm]UBC(305-380)[endosome membrane]GAG-POL Polyprotein(P04585)IN (Integrase)(P04585) protein[extracellularregion]CDK7 [nucleoplasm]NUP107 [nuclearenvelope]POLR2I [nucleoplasm]CDK7 [nucleoplasm]POLR2C [nucleoplasm]POLR2J [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]p51 (RT)[extracellularregion]NELFCD [nucleoplasm]NUP50 [nucleoplasm]POLR2D(2-142)[nucleoplasm]ELL [nucleoplasm]GTF2F2(2-249)[nucleoplasm]VPR (P69726) protein[extracellularregion]CTDP1 [nucleoplasm]TAF4 [nucleoplasm]UBC(533-608)[endosome membrane]HIV-1 transcriptioncomplex containingtranscript to +30POLR2H [nucleoplasm]TFIIHNELFA(2-528)[nucleoplasm]GTF2F2(2-249)[nucleoplasm]TAF11 [nucleoplasm]TFIIDCCNH [nucleoplasm]RTC with extendingsecond-strand DNAPOLR2J [nucleoplasm]SUPT4H1[nucleoplasm]N-myristoyl GAG(P04591) proteinTAF10 [nucleoplasm]Encapsidated viralcoreCCNH [nucleoplasm]POLR2K [nucleoplasm]POLR2J [nucleoplasm]GTF2E1 [nucleoplasm]POLR2G [nucleoplasm]POLR2J [nucleoplasm]Virion with gp41forming hairpinstructureVPU (P05919) protein[cytosol]VPR (P69726) protein[cytosol]p51 (RT) [cytosol]PSIP1 [nucleoplasm]GTF2H4 [nucleoplasm]GTF2H4 [nucleoplasm]POLR2G [nucleoplasm]GTF2E2 [nucleoplasm]TAF13 [nucleoplasm]POLR2E [nucleoplasm]UBC(1-76) [plasmamembrane]GTF2F2(2-249)[nucleoplasm]NELF complexPOLR2J [nucleoplasm]POLR2G [nucleoplasm]RNGTTPSIP1 [cytosol]MA (P04591) protein[cytosol]NELFA(2-528)[nucleoplasm]CDK7 [nucleoplasm]CCNT1 [nucleoplasm]CDK7 [nucleoplasm]NELFA(2-528)[nucleoplasm]Virion withCD4:gp120 bound toCCR5/CXCR4GTP [cytosol]POLR2L [nucleoplasm]PR (Protease)(P04585) protein[cytosol]POLR2F(1-127)[nucleoplasm]p51 (RT)[extracellularregion]DSIF:NELF:earlyelongation complexN-myristoyl GAG(P04591) protein[cytosol]NCBP2 [nucleoplasm]POLR2B [nucleoplasm]UBC(153-228) [plasmamembrane]other viral genomicRNAUTP [nucleoplasm]NC (P04591) protein[extracellularregion]GTF2B [nucleoplasm]TAF10 [nucleoplasm]BANF1 [cytosol]SUPT4H1[nucleoplasm]NC (P04585) protein[cytosol]POLR2D(2-142)[nucleoplasm]GAG-POL Polyprotein(P04585) [plasmamembrane]NUP85 [nuclearenvelope]POLR2F(1-127)[nucleoplasm]UBC(457-532) [plasmamembrane]POLR2B [nucleoplasm]POLR2C [nucleoplasm]TAF1 [nucleoplasm]POLR2E [nucleoplasm]SUPT4H1[nucleoplasm]GTF2H4 [nucleoplasm]ERCC3 [nucleoplasm]POLR2C [nucleoplasm]CCNT1 [nucleoplasm]MNAT1 [nucleoplasm]MA (P04585) protein[cytosol]GTP [nucleoplasm]TAF13 [nucleoplasm]Surface proteingp120 (P04578)[cytosol]POLR2G [nucleoplasm]CHMP4A [cytosol]HIV-1 RNA template[cytosol]GTF2F1(2-517)[nucleoplasm]UBC(153-228) [plasmamembrane]POLR2D(2-142)[nucleoplasm]CDK7 [nucleoplasm]BANF1 [cytosol]HIV-1 transcriptioncomplexTBP [nucleoplasm]GTF2F1(2-517)[nucleoplasm]TCEB2 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]VIF (P69723) proteinVirion with gp41fusion peptide ininsertion complexPOLR2L [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]p6 (P04585) protein[cytosol]RTC with degradedRNA template andminus sssDNAPOLR2L [nucleoplasm]CTDP1 [nucleoplasm]POLR2A [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]POLR2A [nucleoplasm]POLR2D(2-142)[nucleoplasm]POLR2L [nucleoplasm]POLR2F(1-127)[nucleoplasm]MNAT1 [nucleoplasm]GTF2H3 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]POLR2L [nucleoplasm]TAF6 [nucleoplasm]p-S5-POLR2A[nucleoplasm]POLR2L [nucleoplasm]PSIP1 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]p6 (P04591) protein[extracellularregion]HIV-1 processiveelongation complexPOLR2L [nucleoplasm]POLR2H [nucleoplasm]UBC(457-532) [plasmamembrane]SUPT4H1[nucleoplasm]DSIF:NELF:earlyelongation complexafter limitednucleotide additionPOLR2K [nucleoplasm]ERCC2 [nucleoplasm]ERCC3 [nucleoplasm]POLR2E [nucleoplasm]POLR2C [nucleoplasm]PPIA [cytosol]ATP [nucleoplasm]GTF2F1(2-517)[nucleoplasm]VPU (P05919)Nup45 [nuclearenvelope]POLR2J [nucleoplasm]Tat (P04608)[nucleoplasm]ERCC3 [nucleoplasm]CTP [nucleoplasm]CDK9 [nucleoplasm]TAF5 [nucleoplasm]RTC with extensiveRNase-H digestionPOLR2L [nucleoplasm]GTF2H2 [nucleoplasm]POLR2G [nucleoplasm]NC (P04585) protein[extracellularregion]VPS4B [cytosol]REV (P04618) protein[cytosol]IN (Integrase)(P04585) protein[extracellularregion]POLR2E [nucleoplasm]POLR2K [nucleoplasm]POLR2I [nucleoplasm]POLR2H [nucleoplasm]RAN [cytosol]N-myristoyl GAG(P04591) protein[extracellularregion]POLR2K [nucleoplasm]VPR (P69726) protein[nucleoplasm]CDK7 [nucleoplasm]Early elongationcomplex withseparated abortedtranscriptCDK7 [nucleoplasm]GAG-POL Polyprotein(P04585)[extracellularregion]POLR2L [nucleoplasm]POLR2J [nucleoplasm]POLR2L [nucleoplasm]MA (P04591) protein[cytosol]VPU (P05919) protein[cytosol]IN (Integrase)(P04585) protein[cytosol]VIF (P69723) protein[cytosol]POLR2D(2-142)[nucleoplasm]VPU (P05919) protein[nucleoplasm]POLR2E [nucleoplasm]GTF2A1(275-376)[nucleoplasm]UBC(381-456) [plasmamembrane]XRCC4 [nucleoplasm]Transmembraneprotein gp41 [viralenvelope]MA (P04591) protein[cytosol]MA (P04591) protein[nucleoplasm]PR (Protease)(P04585) protein[cytosol]POLR2K [nucleoplasm]POLR2B [nucleoplasm]NELFB [nucleoplasm]POLR2C [nucleoplasm]POLR2D(2-142)[nucleoplasm]UBB(1-76) [plasmamembrane]HIV-1 pausedprocessiveelongation complexTCEB3 [nucleoplasm]TAF10 [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]Reversetranscriptase/ribonucleaseH [cytosol]p6 (P04585) protein[cytosol]IN (Integrase)(P04585) protein[nucleoplasm]POLR2E [nucleoplasm]VPR (P69726) protein[cytosol]GTP [nucleoplasm]POLR2H [nucleoplasm]NUP37 [nuclearenvelope]p-NELFE[nucleoplasm]TAF4B [nucleoplasm]Cap Binding Complex(CBC)MNAT1 [nucleoplasm]POLR2J [nucleoplasm]Surface proteingp120 (P04578)[cytosol]PSIP1 [cytosol]Transmembraneprotein gp41 [viralenvelope]POLR2B [nucleoplasm]CCNH [nucleoplasm]GTF2F1(2-517)[nucleoplasm]HIV-1 mRNA[nucleoplasm]RPS27A(1-76)[cytosol]POLR2K [nucleoplasm]SSRP1 [nucleoplasm]REV (P04618) protein[cytosol]FACT complexCE:Pol II CTD:Spt5complexGTF2A1(1-274)[nucleoplasm]GTF2H4 [nucleoplasm]Transmembraneprotein gp41 [viralenvelope]POLR2J [nucleoplasm]CCNT1 [nucleoplasm]NCBP2 [nucleoplasm]POLR2E [nucleoplasm]CDK9 [nucleoplasm]HIV-1 transcriptioncomplex containingextruded transcriptto +30HMGA1 [cytosol]ATP [nucleoplasm]TAF5 [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]PPIA [cytosol]NELFA(2-528)[nucleoplasm]POLR2E [nucleoplasm]MA (P04591) protein[cytosol]NELFE [nucleoplasm]POLR2G [nucleoplasm]POLR2A [nucleoplasm]ERCC3 [nucleoplasm]UBC(381-456)[endosome membrane]IntegrationintermediatePOLR2F(1-127)[nucleoplasm]NELFA(2-528)[nucleoplasm]viral PIC proteinsviral RNA templatedegraded by RNase-H(initial) [cytosol]GTF2H4 [nucleoplasm]POLR2I [nucleoplasm]CCNT2 [nucleoplasm]VPU (P05919) protein[extracellularregion]TCEB1 [nucleoplasm]UBB(153-228) [plasmamembrane]POLR2F(1-127)[nucleoplasm]IN (Integrase)(P04585) protein[cytosol]HIV-1 mRNA[nucleoplasm]GTP [nucleoplasm]NELFCD [nucleoplasm]POLR2G [nucleoplasm]CTDP1 [nucleoplasm]POLR2B [nucleoplasm]PPIA [cytosol]NELFB [nucleoplasm]GTF2F2(2-249)[nucleoplasm]p-S5-POLR2A[nucleoplasm]IN bound to sticky3' ends of viral DNAin PICGTF2H1(2-548)[nucleoplasm]CDK9 [nucleoplasm]UBC(153-228)[endosome membrane]MA (P04591) protein[nucleoplasm]POLR2C [nucleoplasm]PSIP1 [cytosol]CDK9 [nucleoplasm]NUP153 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]POLR2C [nucleoplasm]PPIA [extracellularregion]UBA52(1-76)[endosome membrane]Surface proteingp120 [viralenvelope]TAF12 [nucleoplasm]ERCC3 [nucleoplasm]CCNT1 [nucleoplasm]TCEB1 [nucleoplasm]POLR2H [nucleoplasm]POLR2B [nucleoplasm]GTF2H1(2-548)[nucleoplasm]IN bound to sticky3' ends of viral DNAin PICp-SUPT5H[nucleoplasm]GTF2H1(2-548)[nucleoplasm]TAF13 [nucleoplasm]POLR2F(1-127)[nucleoplasm]GTF2H1(2-548)[nucleoplasm]p-SUPT5H[nucleoplasm]TAF11 [nucleoplasm]CDK7 [nucleoplasm]POLR2E [nucleoplasm]VPR (P69726) protein[extracellularregion]UBC(229-304) [plasmamembrane]CDK7 [nucleoplasm]POLR2F(1-127)[nucleoplasm]VPU (P05919) protein[cytosol]NC (P04591) protein[extracellularregion]POLR2L [nucleoplasm]VPS37B [endosomemembrane]p6 (P04585)[nucleoplasm]NELFB [nucleoplasm]p-SUPT5H[nucleoplasm]RAE1 [nuclearenvelope]ERCC3 [nucleoplasm]p6 (P04585) protein[cytosol]Ran-GDPPOLR2G [nucleoplasm]ERCC3 [nucleoplasm]TFIIHUBA52(1-76)[cytosol]TAF4 [nucleoplasm]NCBP1 [nucleoplasm]UBC(1-76) [plasmamembrane]IN (Integrase)(P04585) protein[cytosol]POLR2B [nucleoplasm]ERCC2 [nucleoplasm]ATPp-S5-POLR2A[nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]MA (P04591) protein[cytosol]POLR2E [nucleoplasm]p6 (P04585) protein[cytosol]p6 (P04585) protein[cytosol]ADPVPS37A [endosomemembrane]VPU (P05919) protein[nucleoplasm]POLR2B [nucleoplasm]p-SUPT5H[nucleoplasm]ERCC2 [nucleoplasm]p51 (RT) [cytosol]CCNH [nucleoplasm]TAF10 [nucleoplasm]CDK9 [nucleoplasm]POLR2E [nucleoplasm]p51 (RT) [cytosol]GTF2A1(275-376)[nucleoplasm]HIV-1 Polymerase II(phosphorylated):TFIIF:cappedpre-mRNAp6 (P04585) protein[cytosol]POLR2H [nucleoplasm]IN (Integrase)(P04585) proteinp-SUPT5H[nucleoplasm]RAE1 [nuclearenvelope]POLR2D(2-142)[nucleoplasm]SSRP1 [nucleoplasm]PR (Protease)(P04585) protein[extracellularregion]CCNT1 [nucleoplasm]UBA52(1-76) [plasmamembrane]VPU (P05919) protein[nucleoplasm]POLR2J [nucleoplasm]TCEB3 [nucleoplasm]TAF4 [nucleoplasm]POLR2K [nucleoplasm]MNAT1 [nucleoplasm]TAF5 [nucleoplasm]p6 (P04591)[nucleoplasm]POLR2F(1-127)[nucleoplasm]POLR2E [nucleoplasm]POLR2G [nucleoplasm]TAF10 [nucleoplasm]p6 (P04585) protein[extracellularregion]POLR2C [nucleoplasm]NUP93 [nuclearenvelope]p-S2,S5-POLR2A[nucleoplasm]POLR2C [nucleoplasm]Transmembraneprotein gp41 [viralenvelope]UBC(609-684)[cytosol]POLR2I [nucleoplasm]GTF2H4 [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]VTA1 [cytosol]POLR2F(1-127)[nucleoplasm]NCBP1 [nucleoplasm]POLR2F(1-127)[nucleoplasm]VPU (P05919) protein[extracellularregion]PR (Protease)(P04585) protein[extracellularregion]TAF12 [nucleoplasm]POLR2B [nucleoplasm]TFIIDReversetranscriptase/ribonucleaseH [cytosol]Reversetranscriptase/ribonucleaseH [cytosol]POLR2B [nucleoplasm]1-LTR form ofcircular viral DNAGTF2H2 [nucleoplasm]p-S5-POLR2A[nucleoplasm]POLR2C [nucleoplasm]NELFE [nucleoplasm]VPU (P05919) protein[cytosol]POLR2E [nucleoplasm]CHMP3(2-222)[cytosol]ELL [nucleoplasm]PR (Protease)(P04585) protein[extracellularregion]TFIIHMNAT1 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]p-SUPT5H[nucleoplasm]NUP62 [nuclearenvelope]POLR2G [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]NELFCD [nucleoplasm]GTF2F1(2-517)[nucleoplasm]GTF2H2 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]Tat (P04608)[nucleoplasm]POLR2G [nucleoplasm]HIV-1 RNA[extracellularregion]SSRP1 [nucleoplasm]CCNT1 [nucleoplasm]MatrixNELFCD [nucleoplasm]CD4:Env gp120/gp41hairpincomplex:CCR5/CXCR4XRCC5 [nucleoplasm]GTF2H4 [nucleoplasm]p6 (P04585) protein[cytosol]HMGA1 [cytosol]GlycosylatedEnvelopeglycoprotein gp160[Golgi membrane]RTC with tRNAprimer:RNA templateTrimeric ENVprecursorNC (P04591) protein[cytosol]p6 (P04585) protein[cytosol]POLR2I [nucleoplasm]PPIA [cytosol]POLR2A [nucleoplasm]GTF2H2 [nucleoplasm]GTF2A2 [nucleoplasm]IN (Integrase)(P04585) protein[nucleoplasm]Tat (P04608)TAF10 [nucleoplasm]GTF2A1(1-274)[nucleoplasm]TFIIHREV (P04618) protein[cytosol]Tat (P04608)[nucleoplasm]POLR2K [nucleoplasm]POLR2F(1-127)[nucleoplasm]ERCC2 [nucleoplasm]HMGA1 [nucleoplasm]NCBP1 [nucleoplasm]POLR2J [nucleoplasm]Virion with exposedcoreceptor bindingsitesNTPSUPT16H[nucleoplasm]BANF1 [cytosol]VIF (P69723) protein[nucleoplasm]UBB(77-152) [plasmamembrane]POLR2K [nucleoplasm]TBP [nucleoplasm]NUPL1-2 [nuclearenvelope]NUP210 [nuclearenvelope]TCEB3 [nucleoplasm]POLR2B [nucleoplasm]POLR2I [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]GTF2F1(2-517)[nucleoplasm]HIV-1 transcriptioncomplex containing 3nucleotide longtranscriptPOLR2D(2-142)[nucleoplasm]POLR2B [nucleoplasm]POLR2L [nucleoplasm]Reversetranscriptase/ribonucleaseH [extracellularregion]POLR2J [nucleoplasm]POLR2I [nucleoplasm]HIV-1 closedpre-initiationcomplexSurface proteingp120 [viralenvelope]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPGTF2F1(2-517)[nucleoplasm]NELFA(2-528)[nucleoplasm]GTF2H4 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]GTF2H3 [nucleoplasm]GTF2H3 [nucleoplasm]TAF4B [nucleoplasm]GTF2F1(2-517)[nucleoplasm]XPO1 [cytosol]p6 (P04591) protein[extracellularregion]TAF4B [nucleoplasm]CCNH [nucleoplasm]TAF12 [nucleoplasm]GTF2A1(1-274)[nucleoplasm]p51 (RT) [cytosol]Surface proteingp120 [viralenvelope]MA (P04585) protein[cytosol]MNAT1 [nucleoplasm]CTDP1 [nucleoplasm]CDK9 [nucleoplasm]ERCC3 [nucleoplasm]TCEA1 [nucleoplasm]GTF2H3 [nucleoplasm]VIF (P69723) protein[cytosol]POLR2C [nucleoplasm]VPU (P05919) protein[cytosol]GTF2A1(1-274)[nucleoplasm]POLR2J [nucleoplasm]POLR2C [nucleoplasm]POLR2F(1-127)[nucleoplasm]POLR2C [nucleoplasm]GTF2F1(2-517)[nucleoplasm]NELFB [nucleoplasm]POLR2H [nucleoplasm]TAF6 [nucleoplasm]VPU (P05919) protein[extracellularregion]GTF2H2 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]CTP [nucleoplasm]PPIAPOLR2I [nucleoplasm]p-SUPT5H[nucleoplasm]VPR (P69726) protein[cytosol]PPiPOLR2C [nucleoplasm]TAF12 [nucleoplasm]CHMP6(2-201)[cytosol]viral RNA templateextensively digestedexcept in PPT region[cytosol]UBC(381-456) [plasmamembrane]TAF11 [nucleoplasm]UBC(381-456) [plasmamembrane]RPS27A(1-76) [plasmamembrane]POLR2I [nucleoplasm]MNAT1 [nucleoplasm]POLR2F(1-127)[nucleoplasm]VPU (P05919) protein[cytosol]VPU (P05919) protein[cytosol]CTDP1 [nucleoplasm]POLR2H [nucleoplasm]POLR2F(1-127)[nucleoplasm]MA (P04591) protein[cytosol]POLR2E [nucleoplasm]TCEA1 [nucleoplasm]myristoylated NefProtein(UniProt:P04601)[cytosol]Reversetranscriptase/ribonucleaseH [extracellularregion]POLR2E [nucleoplasm]POLR2B [nucleoplasm]POLR2I [nucleoplasm]MA (P04585) protein[cytosol]p6 (P04591)[nucleoplasm]SUPT4H1[nucleoplasm]POLR2K [nucleoplasm]p6 (P04585) protein[extracellularregion]p-SUPT5H[nucleoplasm]POLR2J [nucleoplasm]POLR2H [nucleoplasm]p6 (P04591)[nucleoplasm]GTF2E2 [nucleoplasm]REV (P04618) protein[cytosol]SUPT4H1[nucleoplasm]CHMP4B [cytosol]POLR2F(1-127)[nucleoplasm]VIF (P69723) protein[cytosol]CHMP4C [cytosol]CCNT1 [nucleoplasm]POLR2B [nucleoplasm]POLR2K [nucleoplasm]POLR2L [nucleoplasm]POLR2J [nucleoplasm]ATP [nucleoplasm]NELFB [nucleoplasm]HIV-1 RNA homodimerGTF2BPOLR2B [nucleoplasm]GTF2F2(2-249)[nucleoplasm]TCEB1 [nucleoplasm]SUPT4H1[nucleoplasm]HIV-1 template DNAwith firsttranscriptdinucleotide, openedto +8 positionPOLR2B [nucleoplasm]GTF2E1 [nucleoplasm]p6 (P04585) protein[extracellularregion]VPU (P05919) protein[extracellularregion]UBC(609-684) [plasmamembrane]CCNH [nucleoplasm]ELL [nucleoplasm]POLR2I [nucleoplasm]Virion withfusogenicallyactivated gp41TAF1 [nucleoplasm]POLR2I [nucleoplasm]REV (P04618) protein[nucleoplasm]Tat (P04608)[nucleoplasm]POLR2G [nucleoplasm]POLR2D(2-142)[nucleoplasm]NC (P04591) protein[extracellularregion]MNAT1 [nucleoplasm]GTF2H2 [nucleoplasm]CCNT1 [nucleoplasm]XPO1 [nucleoplasm]NC (P04591) protein[extracellularregion]Reversetranscriptase/ribonucleaseH [extracellularregion]IN (Integrase)(P04585) protein[cytosol]ERCC2 [nucleoplasm]p6 (P04585)[nucleoplasm]p6 (P04585)[nucleoplasm]CHMP4A [cytosol]p51 (RT)[extracellularregion]POLR2G [nucleoplasm]GTF2H1(2-548)[nucleoplasm]POLR2K [nucleoplasm]GTF2H3 [nucleoplasm]PSIP1 [nucleoplasm]RAN [nucleoplasm]GTP [cytosol]Reversetranscriptase/ribonucleaseH [cytosol]POLR2G [nucleoplasm]POLR2J [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]REV (P04618) proteinMA (P04585) protein[cytosol]POLR2H [nucleoplasm]NUP188(2-1749)[nuclear envelope]POLR2J [nucleoplasm]NELFB [nucleoplasm]p6 (P04591) protein[cytosol]PPiPOLR2L [nucleoplasm]NELFCD [nucleoplasm]POLR2E [nucleoplasm]NC (P04591) protein[cytosol]CHMP7 [cytosol]CDK9 [nucleoplasm]POLR2H [nucleoplasm]TAF1 [nucleoplasm]POLR2K [nucleoplasm]CDK7 [nucleoplasm]POLR2A [nucleoplasm]VPU (P05919) protein[extracellularregion]CDK9 [nucleoplasm]POLR2E [nucleoplasm]SSRP1 [nucleoplasm]POLR2E [nucleoplasm]p6 (P04591) protein[cytosol]p6 (P04591) protein[cytosol]PPIA [cytosol]CDK7 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]NELFCD [nucleoplasm]POLR2J [nucleoplasm]GTF2H3 [nucleoplasm]POLR2C [nucleoplasm]p-SUPT5H[nucleoplasm]CCNT1 [nucleoplasm]VIF (P69723) protein[cytosol]ERCC2 [nucleoplasm]VPS4A(1-437)[cytosol]POLR2G [nucleoplasm]POLR2F(1-127)[nucleoplasm]POLR2K [nucleoplasm]VPS4A(1-437)[cytosol]POLR2B [nucleoplasm]CCNH [nucleoplasm]POLR2G [nucleoplasm]Immature HIV virionGTF2H2 [nucleoplasm]POLR2F(1-127)[nucleoplasm]REV (P04618) protein[nucleoplasm]TCEA1RTC (ReverseTranscriptionComplex) with RNAtemplatePOLR2D(2-142)[nucleoplasm]GTF2A1(1-274)[nucleoplasm]POLR2E [nucleoplasm]POLR2D(2-142)[nucleoplasm]XPO1 [cytosol]VIF (P69723) protein[cytosol]Ku proteins bound toviral DNAGTF2F2(2-249)[nucleoplasm]POM121 [nuclearenvelope]GTF2H2 [nucleoplasm]POLR2I [nucleoplasm]POLR2D(2-142)[nucleoplasm]POLR2D(2-142)[nucleoplasm]p6 (P04585) protein[extracellularregion]GTF2H2 [nucleoplasm]NELFB [nucleoplasm]POLR2K [nucleoplasm]POLR2C [nucleoplasm]POLR2B [nucleoplasm]NC (P04591) protein[extracellularregion]p-S5-POLR2A[nucleoplasm]GTP [cytosol]Viral coresurrounded by MatrixlayerPOLR2C [nucleoplasm]GTF2F2(2-249)[nucleoplasm]POLR2B [nucleoplasm]REV (P04618) protein[nucleoplasm]p-SUPT5HPOLR2G [nucleoplasm]VIF (P69723) protein[extracellularregion]NELFE [nucleoplasm]CTP [nucleoplasm]POLR2E [nucleoplasm]GTF2H1(2-548)[nucleoplasm]REV (P04618) protein[cytosol]POLR2G [nucleoplasm]REV (P04618) protein[cytosol]NELFE [nucleoplasm]GTF2H3 [nucleoplasm]GTF2E2 [nucleoplasm]p-SUPT5H[nucleoplasm]GTF2H4 [nucleoplasm]Rev-multimerPOLR2H [nucleoplasm]MNAT1 [nucleoplasm]GTF2H3 [nucleoplasm]HIV-1 elongationcomplex containingTatRNA Pol II withphosphorylated CTD:CE complex withactivated GTREV (P04618) protein[extracellularregion]HIV-1 cappedpre-mRNA:CBC:RNA PolII (phosphorylated)complexCTDP1 [nucleoplasm]FEN1UBC(381-456)[cytosol]POLR2L [nucleoplasm]UBB(77-152)[cytosol]TAF1 [nucleoplasm]POLR2H [nucleoplasm]GTF2A1(275-376)[nucleoplasm]POLR2C [nucleoplasm]p6 (P04591) protein[cytosol]RNA Polymerase II(unphosphorylated):TFIIFcomplexNCBP1 [nucleoplasm]TAF12 [nucleoplasm]p-SUPT5H[nucleoplasm]POLR2I [nucleoplasm]GTF2H3 [nucleoplasm]TAF4 [nucleoplasm]MA (P04591) protein[cytosol]POLR2J [nucleoplasm]POLR2L [nucleoplasm]GDP [nucleoplasm]TAF4 [nucleoplasm]CDK7 [nucleoplasm]VPU (P05919) protein[cytosol]SUPT4H1[nucleoplasm]HMGA1 [cytosol]POLR2D(2-142)[nucleoplasm]POLR2A [nucleoplasm]GTF2F1(2-517)[nucleoplasm]HMGA1 [nucleoplasm]GTF2A2 [nucleoplasm]GTF2E2 [nucleoplasm]ELLREV (P04618) protein[extracellularregion]Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD (phospho-NELF phosphoDSIF)XRCC5 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]GDP [cytosol]IN (Integrase)(P04585) protein[cytosol]POLR2D(2-142)[nucleoplasm]POLR2J [nucleoplasm]POLR2B [nucleoplasm]POLR2D(2-142)[nucleoplasm]CDK9 [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]GTF2F2(2-249)[nucleoplasm]ERCC3 [nucleoplasm]POLR2L [nucleoplasm]POLR2E [nucleoplasm]SEH1L-2 [nuclearenvelope]POLR2E [nucleoplasm]GTF2H2 [nucleoplasm]VPU (P05919) protein[cytosol]p6 (P04591) protein[cytosol]POLR2J [nucleoplasm]CXCR4 [plasmamembrane]VPS28 [endosomemembrane]TCEB1 [nucleoplasm]ERCC2 [nucleoplasm]UBC(457-532)[endosome membrane]Reversetranscriptase/ribonucleaseH [cytosol]NUP153 [nucleoplasm]POLR2K [nucleoplasm]ERCC2 [nucleoplasm]POLR2C [nucleoplasm]POLR2I [nucleoplasm]POLR2D(2-142)[nucleoplasm]CTDP1 [nucleoplasm]POLR2J [nucleoplasm]TCEB3 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]GTF2F1(2-517)[nucleoplasm]PPIA [extracellularregion]p6 (P04585)[nucleoplasm]POLR2G [nucleoplasm]UBC(533-608) [plasmamembrane]TAF13 [nucleoplasm]POLR2A [nucleoplasm]Vps/Vta1POLR2F(1-127)[nucleoplasm]CCNT2 [nucleoplasm]RNA Pol II(hypophosphorylated)complex bound toDSIF proteinCDK9 [nucleoplasm]MA (P04591) protein[cytosol]GTP [nucleoplasm]p51 (RT) [cytosol]Tat (P04608)[nucleoplasm]REV (P04618) protein[extracellularregion]NCBP1 [nucleoplasm]SSRP1 [nucleoplasm]ERCC2 [nucleoplasm]NELFE [nucleoplasm]p51 (RT)[extracellularregion]PR (Protease)(P04585) protein[extracellularregion]POLR2I [nucleoplasm]p51 (RT) [cytosol]POLR2B [nucleoplasm]NELFE [nucleoplasm]CCNT1 [nucleoplasm]POLR2H [nucleoplasm]TAF9 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]NCBP2 [nucleoplasm]TCEB1 [nucleoplasm]GTF2H1(2-548)[nucleoplasm]TAF13 [nucleoplasm]POLR2D(2-142)[nucleoplasm]POLR2C [nucleoplasm]POLR2K [nucleoplasm]POLR2K [nucleoplasm]POLR2B [nucleoplasm]p51 (RT)[extracellularregion]VTA1 [cytosol]POLR2H [nucleoplasm]NELFCD [nucleoplasm]GTF2F2(2-249)[nucleoplasm]NELFE [nucleoplasm]POLR2K [nucleoplasm]GTF2E2 [nucleoplasm]NUP133 [nuclearenvelope]GTF2A1(275-376)[nucleoplasm]RNA Pol II(hypophosphorylated):cappedpre-mRNA complexUBC(305-380) [plasmamembrane]GTF2H1(2-548)[nucleoplasm]GTF2F2(2-249)[nucleoplasm]GTF2F2(2-249)[nucleoplasm]POLR2G [nucleoplasm]POLR2K [nucleoplasm]CCR5 [plasmamembrane]POLR2I [nucleoplasm]GTF2F1(2-517)[nucleoplasm]POLR2K [nucleoplasm]MA (P04585) protein[cytosol]GTF2H4 [nucleoplasm]NC (P04585) protein[cytosol]CCNT1 [nucleoplasm]Multimeric capsidcoatPOLR2H [nucleoplasm]PPIA [cytosol]PPIA [cytosol]SSRP1 [nucleoplasm]DSIF complexp6 (P04591) protein[cytosol]POLR2J [nucleoplasm]ELL [nucleoplasm]POLR2A [nucleoplasm]NTPESCRT-IIIRNGTT [nucleoplasm]PPIA [cytosol]p6 (P04585) protein[cytosol]N-myristoyl GAG[plasma membrane]SSRP1 [nucleoplasm]NUP35 [nuclearenvelope]CTDP1 [nucleoplasm]PiPOLR2D(2-142)[nucleoplasm]TAF12 [nucleoplasm]VPR (P69726) protein[nucleoplasm]TCEA1 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]UBC(77-152)[cytosol]GTP [nucleoplasm]GTF2E1 [nucleoplasm]IN (Integrase)(P04585) protein[extracellularregion]CCR5 [plasmamembrane]NUP205(2-2012)[nuclear envelope]POLR2F(1-127)[nucleoplasm]POLR2H [nucleoplasm]POLR2H [nucleoplasm]POLR2J [nucleoplasm]CDK7 [nucleoplasm]TAF4B [nucleoplasm]CDK9 [nucleoplasm]MA (P04591) protein[cytosol]GTF2F1(2-517)[nucleoplasm]POLR2B [nucleoplasm]NELFB [nucleoplasm]CDK9 [nucleoplasm]HIV-1 unspliced RNAELL [nucleoplasm]TAF6 [nucleoplasm]PPIA [cytosol]p-S2,S5-POLR2A[nucleoplasm]POLR2G [nucleoplasm]TBP [nucleoplasm]RanBP1:Ran-GTP:CRM1:Rev-boundmRNA complexUBC(305-380)[cytosol]POLR2K [nucleoplasm]p6 (P04591) protein[cytosol]CCNT2 [nucleoplasm]VPU (P05919) protein[cytosol]PiNELFCD [nucleoplasm]CHMP2B [cytosol]CHMP7 [cytosol]p6 (P04585) protein[extracellularregion]NELFCD [nucleoplasm]POLR2J [nucleoplasm]CHMP6(2-201)[cytosol]RTC with nickedminus sssDNA:tRNAprimer:RNA templatePOLR2E [nucleoplasm]POLR2B [nucleoplasm]HIV-1 RNA[extracellularregion]PPiRPS27A(1-76)[endosome membrane]POLR2J [nucleoplasm]NC (P04591) protein[cytosol]CDK9 [nucleoplasm]TCEA1 [nucleoplasm]POLR2H [nucleoplasm]TAF9 [nucleoplasm]POLR2C [nucleoplasm]GTF2H2 [nucleoplasm]SUPT4H1[nucleoplasm]NUP160 [nuclearenvelope]RAN [nucleoplasm]UTP [nucleoplasm]POLR2A [nucleoplasm]ERCC3 [nucleoplasm]POLR2B [nucleoplasm]Ran-GTPIN (Integrase)(P04585) protein[extracellularregion]p-S5-POLR2A[nucleoplasm]IN (Integrase)(P04585) protein[cytosol]GTF2E1 [nucleoplasm]CDK7 [nucleoplasm]POLR2D(2-142)[nucleoplasm]VPR (P69726) protein[cytosol]POLR2D(2-142)[nucleoplasm]POLR2D(2-142)[nucleoplasm]POLR2H [nucleoplasm]GTF2H3 [nucleoplasm]HIV-1 RNA template[cytosol]POLR2F(1-127)[nucleoplasm]SUPT4H1[nucleoplasm]POLR2C [nucleoplasm]CDK9 [nucleoplasm]REV (P04618) protein[cytosol]IN (Integrase)(P04585) proteinCCNH [nucleoplasm]REV (P04618) protein[nucleoplasm]POLR2L [nucleoplasm]GTF2H4 [nucleoplasm]PPiGTF2H4 [nucleoplasm]UBC(609-684)[endosome membrane]POLR2K [nucleoplasm]GTF2F1(2-517)[nucleoplasm]p6 (P04585) protein[cytosol]TSG101(2-390)[endosome membrane]POLR2D(2-142)[nucleoplasm]POLR2F(1-127)[nucleoplasm]p-S5-POLR2A[nucleoplasm]Surface proteingp120 [viralenvelope]POLR2I [nucleoplasm]VIF (P69723) protein[extracellularregion]CDK7 [nucleoplasm]VPS37D [endosomemembrane]HIV-1 PromoterEscape ComplexTCEB2 [nucleoplasm]CD4 [plasmamembrane]NELFCD [nucleoplasm]UBC(457-532)[cytosol]POLR2G [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]p6 (P04591) protein[cytosol]TCEB3 [nucleoplasm]POLR2F(1-127)[nucleoplasm]VPR (P69726) protein[cytosol]p-S5-POLR2A[nucleoplasm]POLR2A [nucleoplasm]REV (P04618) protein[cytosol]POLR2B [nucleoplasm]VPU (P05919) protein[extracellularregion]PPiPOLR2K [nucleoplasm]UBB(1-76) [plasmamembrane]p-SUPT5H[nucleoplasm]TAF1 [nucleoplasm]POLR2H [nucleoplasm]NELFB [nucleoplasm]RNGTT [nucleoplasm]VIF (P69723) protein[cytosol]RTC with annealedcomplementary PBSseqments in +sssDNAand -strand DNAp6 (P04585) protein[cytosol]TAF13 [nucleoplasm]VPR (P69726) protein[cytosol]POLR2H [nucleoplasm]GTF2F2(2-249)[nucleoplasm]UBC(305-380) [plasmamembrane]p6 (P04585) protein[extracellularregion]GTF2E1 [nucleoplasm]ERCC2 [nucleoplasm]MA (P04585) protein[cytosol]myristoylated NefProtein(UniProt:P04601)[extracellularregion]CDK9 [nucleoplasm]NELFA(2-528)[nucleoplasm]TAF5 [nucleoplasm]POLR2F(1-127)[nucleoplasm]GTF2H3 [nucleoplasm]MA (P04585) protein[cytosol]NELFA(2-528)[nucleoplasm]POLR2D(2-142)[nucleoplasm]HIV-1 RNA template[cytosol]CCNH [nucleoplasm]TFIIHPOLR2F(1-127)[nucleoplasm]POLR2A [nucleoplasm]NUP50 [nucleoplasm]GTF2E1 [nucleoplasm]POLR2L [nucleoplasm]Rev multimer-boundHIV-1 mRNA:CRM1complexGTF2H3 [nucleoplasm]VPR (P69726) protein[extracellularregion]ERCC3 [nucleoplasm]NELFE [nucleoplasm]CHMP2B [cytosol]IN (Integrase)(P04585) protein[extracellularregion]Tat:P-TEFb(CyclinT1:Cdk9) complexTCEA1 [nucleoplasm]NELFB [nucleoplasm]POLR2L [nucleoplasm]p-S5-POLR2A[nucleoplasm]p6 (P04585) protein[cytosol]RNA Polymerase II(unphosphorylated):TFIIFcomplexTCEB1 [nucleoplasm]TAF6 [nucleoplasm]NUP133 [nuclearenvelope]POLR2J [nucleoplasm]TFIIAPOLR2B [nucleoplasm]ERCC2 [nucleoplasm]GTF2H4 [nucleoplasm]SUPT4H1[nucleoplasm]PPIA [cytosol]CDK9 [nucleoplasm]TCEB3 [nucleoplasm]POLR2J [nucleoplasm]GTF2H1(2-548)[nucleoplasm]p51 (RT) [cytosol]NELFE [nucleoplasm]TSG101(2-390)[endosome membrane]dNTPTCEB2 [nucleoplasm]TAF10 [nucleoplasm]HIV-1 mRNA[nucleoplasm]GTF2A1(1-274)[nucleoplasm]GTF2H4 [nucleoplasm]NUP155 [nuclearenvelope]TAF5 [nucleoplasm]POLR2A [nucleoplasm]TCEB1 [nucleoplasm]CCNT1 [nucleoplasm]POLR2L [nucleoplasm]UBA52(1-76) [plasmamembrane]GTF2H1(2-548)[nucleoplasm]POLR2C [nucleoplasm]VPU (P05919) protein[extracellularregion]RAN [nucleoplasm]TFIIHRTC with minussssDNA:tRNAprimer:RNA templateNUP93 [nuclearenvelope]Envelopeglycoprotein gp160[endoplasmicreticulum membrane]POLR2E [nucleoplasm]POLR2C [nucleoplasm]POLR2J [nucleoplasm]NELFA(2-528)[nucleoplasm]Tat (P04608)[nucleoplasm]p-SUPT5H[nucleoplasm]POLR2K [nucleoplasm]GTF2H3 [nucleoplasm]CHMP4C [cytosol]POLR2H [nucleoplasm]p51 (RT) [cytosol]p-S5-POLR2A[nucleoplasm]HIV-1 RNA template[cytosol]TFIIHERCC3 [nucleoplasm]RANBP1(2-201)SUPT4H1[nucleoplasm]POLR2I [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]NUP43 [nuclearenvelope]Cap Binding Complex(CBC)CTDP1 [nucleoplasm]VPR (P69726) protein[extracellularregion]MA (P04591) protein[cytosol]NELFA(2-528)[nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]CCNT1 [nucleoplasm]REV (P04618) protein[cytosol]TAF4B [nucleoplasm]GTF2H3 [nucleoplasm]PPIA [extracellularregion]POLR2E [nucleoplasm]CCNT2 [nucleoplasm]POLR2E [nucleoplasm]GTF2H3 [nucleoplasm]TFIIAPOLR2K [nucleoplasm]POLR2G [nucleoplasm]ERCC3 [nucleoplasm]NELFA(2-528)[nucleoplasm]TCEB2 [nucleoplasm]POLR2L [nucleoplasm]POLR2I [nucleoplasm]RANBP2 [cytosol]VIF (P69723) protein[cytosol]GTF2F1(2-517)[nucleoplasm]POLR2A [nucleoplasm]ERCC2 [nucleoplasm]p51 (RT) [cytosol]FURINPOLR2L [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]POLR2F(1-127)[nucleoplasm]TCEA1 [nucleoplasm]POLR2D(2-142)[nucleoplasm]ERCC2 [nucleoplasm]POLR2D(2-142)[nucleoplasm]SUPT16H[nucleoplasm]CTDP1 [nucleoplasm]POLR2C [nucleoplasm]VIF (P69723) protein[nucleoplasm]VIF (P69723) protein[cytosol]IN (Integrase)(P04585) protein[cytosol]uncoated viralcomplexUBC(1-76) [plasmamembrane]HIV-1 Tat-containingarrested processiveelongation complexNELFCD [nucleoplasm]Nuclear Pore Complex(NPC)TAF6 [nucleoplasm]p-S5-POLR2A[nucleoplasm]AAAS [nuclearenvelope]GTF2H3 [nucleoplasm]NUP98-5 [nuclearenvelope]VIF (P69723) protein[cytosol]POLR2L [nucleoplasm]POLR2H [nucleoplasm]GTF2F1(2-517)[nucleoplasm]ERCC2 [nucleoplasm]CCNT2 [nucleoplasm]POLR2G [nucleoplasm]TAF11 [nucleoplasm]Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD andphospho-NELFGTF2A1(275-376)[nucleoplasm]GTF2H2 [nucleoplasm]POLR2K [nucleoplasm]VPU (P05919)CCNH [nucleoplasm]CDK7 [nucleoplasm]GTF2A1(275-376)[nucleoplasm]CD4 [plasmamembrane]CCNT1 [nucleoplasm]IN (Integrase)(P04585) protein[nucleoplasm]TAF5 [nucleoplasm]POLR2A [nucleoplasm]POLR2I [nucleoplasm]Transmembraneprotein gp41 [viralenvelope]POLR2J [nucleoplasm]POLR2D(2-142)[nucleoplasm]VPS28 [endosomemembrane]UBB(1-76) [endosomemembrane]SUPT16H[nucleoplasm]POLR2I [nucleoplasm]UBB(153-228)[cytosol]REV (P04618) protein[extracellularregion]TCEB1 [nucleoplasm]NELFCD [nucleoplasm]GTF2F2(2-249)[nucleoplasm]ELL [nucleoplasm]CHMP3(2-222)[cytosol]CD4 [plasmamembrane]GTF2H4 [nucleoplasm]POLR2C [nucleoplasm]VPU (P05919) protein[cytosol]GTF2F2(2-249)[nucleoplasm]CTDP1 [nucleoplasm]POLR2B [nucleoplasm]IN (Integrase)(P04585) protein[nucleoplasm]PPIA [extracellularregion]NELFA(2-528)[nucleoplasm]TAF11 [nucleoplasm]Transmembraneprotein gp41 [viralenvelope]POLR2B [nucleoplasm]GTF2H2 [nucleoplasm]CCNH [nucleoplasm]GTF2H4 [nucleoplasm]NELFB [nucleoplasm]NUPL2 [cytosol]Tat (P04608)[nucleoplasm]HIV-1 RNA[extracellularregion]GTP [nucleoplasm]NCBP1 [nucleoplasm]CTP [nucleoplasm]viral RNA templatedegraded by RNase-H(initial) [cytosol]SUPT4H1[nucleoplasm]TBP [nucleoplasm]TAF12 [nucleoplasm]VIF (P69723) protein[cytosol]RAN [cytosol]REV (P04618) protein[extracellularregion]RPS27A(1-76) [plasmamembrane]HIV-1 RNA template[cytosol]POLR2E [nucleoplasm]POLR2C [nucleoplasm]NUP210 [nuclearenvelope]Tat (P04608)[nucleoplasm]UBB(153-228) [plasmamembrane]POLR2K [nucleoplasm]XPO1p51 (RT)[extracellularregion]POLR2K [nucleoplasm]POLR2I [nucleoplasm]PPIA [extracellularregion]TAF6 [nucleoplasm]GTF2H2 [nucleoplasm]POLR2B [nucleoplasm]SSRP1 [nucleoplasm]NUP205(2-2012)[nuclear envelope]BANF1 [nucleoplasm]CD4 [plasmamembrane]PPIA [extracellularregion]GTF2F2(2-249)[nucleoplasm]monoubiquitinatedN-myristoyl GAG(P04591) proteinPOLR2I [nucleoplasm]GTF2F1(2-517)[nucleoplasm]POLR2I [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]ELL [nucleoplasm]GTF2H2 [nucleoplasm]POLR2C [nucleoplasm]GTF2H1(2-548)[nucleoplasm]NELFCD [nucleoplasm]TAF12 [nucleoplasm]NC (P04591) protein[extracellularregion]MA (P04585) protein[cytosol]TCEB3 [nucleoplasm]IN (Integrase)(P04585) protein[extracellularregion]LIG4 [nucleoplasm]GTF2H2 [nucleoplasm]GTF2E2 [nucleoplasm]CCNH [nucleoplasm]POLR2L [nucleoplasm]NUP160 [nuclearenvelope]Ran GTPase:GDPGTF2H2 [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]VPR (P69726) protein[extracellularregion]HIV-1 openpre-initiationcomplexPOLR2J [nucleoplasm]REV (P04618) protein[cytosol]POLR2K [nucleoplasm]TBP [nucleoplasm]NELFA(2-528)[nucleoplasm]MNAT1 [nucleoplasm]CCNH [nucleoplasm]NELFA(2-528)[nucleoplasm]GTF2F1(2-517)[nucleoplasm]GTF2H2 [nucleoplasm]CTDP1 [nucleoplasm]RNMT [nucleoplasm]GTF2H2 [nucleoplasm]GTF2A1(1-274)[nucleoplasm]GTF2F2(2-249)[nucleoplasm]CCNH [nucleoplasm]p6 (P04585) protein[cytosol]P-TEFb complexVIF (P69723) protein[extracellularregion]MA (P04591) protein[cytosol]ADPPOLR2C [nucleoplasm]CHMP2A [cytosol]POLR2L [nucleoplasm]HMGA1 [nucleoplasm]SUPT16H[nucleoplasm]VPR (P69726) protein[cytosol]NC (P04585) protein[extracellularregion]GTF2A2 [nucleoplasm]CDK7 [nucleoplasm]NCBP2 [nucleoplasm]REV (P04618) protein[cytosol]Reversetranscriptase/ribonucleaseH [cytosol]GTF2H4 [nucleoplasm]REV (P04618) proteinCXCR4 [plasmamembrane]GTF2F1(2-517)[nucleoplasm]GTF2H1(2-548)[nucleoplasm]GTF2E2 [nucleoplasm]XRCC4:DNA ligase IVcomplexNELFB [nucleoplasm]HIV-1 Tat-containingprocessiveelongation complexRAN [cytosol]POLR2I [nucleoplasm]GTF2E1 [nucleoplasm]PPIAHIV-1 transcriptioncomplex containing 9nucleotide longtranscriptVPU (P05919) protein[cytosol]PPiTAF1 [nucleoplasm]p51 (RT) [cytosol]GTF2E2 [nucleoplasm]GTF2H1(2-548)[nucleoplasm]POLR2C [nucleoplasm]TFIIESEH1L-2 [nuclearenvelope]GTF2F1(2-517)[nucleoplasm]POLR2G [nucleoplasm]GTF2H1(2-548)[nucleoplasm]TCEA1 [nucleoplasm]VPS4B [cytosol]TAF5 [nucleoplasm]GTP [nucleoplasm]POLR2K [nucleoplasm]ERCC3 [nucleoplasm]GTF2H1(2-548)[nucleoplasm]ELL [nucleoplasm]NC (P04585) protein[extracellularregion]UBB(1-76) [plasmamembrane]GTF2H4 [nucleoplasm]TAF6 [nucleoplasm]CCNH [nucleoplasm]POLR2A [nucleoplasm]GTF2H3 [nucleoplasm]REV (P04618) protein[nucleoplasm]POLR2L [nucleoplasm]PR (Protease)(P04585) protein[extracellularregion]GTF2E1 [nucleoplasm]NUP37 [nuclearenvelope]TAF9 [nucleoplasm]TFIIEGTF2H4 [nucleoplasm]PR (Protease)(P04585) protein[extracellularregion]GTF2E2 [nucleoplasm]POLR2G [nucleoplasm]POLR2C [nucleoplasm]GTF2E1 [nucleoplasm]Rev multimer-boundHIV-1 mRNAp6 (P04591) protein[cytosol]tRNA-Lysine3RAN [nucleoplasm]REV (P04618) protein[cytosol]POLR2K [nucleoplasm]CDK7 [nucleoplasm]POLR2A [nucleoplasm]ADPNTPVPR (P69726) protein[cytosol]VPR (P69726) protein[nucleoplasm]MA (P04585) protein[cytosol]GTP [nucleoplasm]NELFE [nucleoplasm]POLR2D(2-142)[nucleoplasm]VIF (P69723) protein[cytosol]RANBP1(2-201)GAG Polyprotein(P04591)VIF (P69723) protein[cytosol]VPR (P69726) protein[cytosol]MYS-CoASurface proteingp120 [viralenvelope]Virion BuddingComplexMA (P04585) protein[cytosol]POLR2K [nucleoplasm]POLR2D(2-142)[nucleoplasm]UBC(533-608) [plasmamembrane]POLR2E [nucleoplasm]ERCC3 [nucleoplasm]CTDP1 [nucleoplasm]GDPUBC(609-684) [plasmamembrane]Transmembraneprotein gp41 [viralenvelope]PPIA [cytosol]CDK9 [nucleoplasm]POLR2C [nucleoplasm]NC (P04585) protein[extracellularregion]RNA Polymerase II(unphosphorylated):TFIIFcomplexCXCR4 [plasmamembrane]POLR2J [nucleoplasm]POLR2C [nucleoplasm]GTF2F1(2-517)[nucleoplasm]GTF2H2 [nucleoplasm]TAF1 [nucleoplasm]POLR2F(1-127)[nucleoplasm]POLR2E [nucleoplasm]REV (P04618) protein[cytosol]p6 (P04585) protein[cytosol]NELFCD [nucleoplasm]GTF2F2(2-249)[nucleoplasm]POLR2L [nucleoplasm]NELFA(2-528)[nucleoplasm]Transmembraneprotein gp41 [viralenvelope]POLR2L [nucleoplasm]CHMP5 [cytosol]PPIA [cytosol]SUPT4H1[nucleoplasm]UBC(229-304)[endosome membrane]ERCC2 [nucleoplasm]2-LTR form ofcircular viral DNAp6 (P04591)[nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]viral DNA bound withIntegrase in PICGTF2F2(2-249)[nucleoplasm]POLR2F(1-127)[nucleoplasm]ERCC3 [nucleoplasm]Ku70:Ku80heterodimerVIF (P69723) protein[extracellularregion]POLR2K [nucleoplasm]GTF2A2 [nucleoplasm]POLR2I [nucleoplasm]p6 (P04585) protein[cytosol]POLR2L [nucleoplasm]XRCC4 [nucleoplasm]NELFA(2-528)[nucleoplasm]CDK7 [nucleoplasm]RAN [cytosol]p-S2,S5-POLR2A[nucleoplasm]POLR2C [nucleoplasm]POLR2K [nucleoplasm]MNAT1 [nucleoplasm]GTF2H2 [nucleoplasm]SUPT16H[nucleoplasm]p6 (P04591) protein[cytosol]VIF (P69723) protein[cytosol]POLR2G [nucleoplasm]UBC(1-76) [endosomemembrane]GTF2F2(2-249)[nucleoplasm]POLR2C [nucleoplasm]MA (P04585) protein[cytosol]POLR2I [nucleoplasm]p6 (P04591) protein[extracellularregion]POLR2B [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]NCBP2 [nucleoplasm]MNAT1 [nucleoplasm]TAF4 [nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplexPOLR2I [nucleoplasm]p51 (RT) [cytosol]POLR2H [nucleoplasm]POLR2I [nucleoplasm]p6 (P04591) protein[cytosol]NEDD4L(2-975)[cytosol]GTP [nucleoplasm]UTP [nucleoplasm]GTF2A2 [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]LIG1PSIP1SUPT16H[nucleoplasm]MNAT1 [nucleoplasm]GTF2E1 [nucleoplasm]SUPT16H[nucleoplasm]MA (P04591) protein[nucleoplasm]POLR2H [nucleoplasm]Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPMA (P04585) protein[cytosol]p51 (RT) [cytosol]NELFE [nucleoplasm]POLR2I [nucleoplasm]RCC1CDK9 [nucleoplasm]POLR2F(1-127)[nucleoplasm]TAF5 [nucleoplasm]NELFE [nucleoplasm]POLR2L [nucleoplasm]POLR2I [nucleoplasm]NC (P04585) protein[cytosol]TCEA1 [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]POLR2C [nucleoplasm]VPR (P69726) protein[cytosol]Tat (P04608)[nucleoplasm]GTF2B [nucleoplasm]POLR2K [nucleoplasm]GTF2F2(2-249)[nucleoplasm]VPR (P69726) protein[cytosol]UBC(229-304)[cytosol]TAF6 [nucleoplasm]POLR2D(2-142)[nucleoplasm]HIV-1 arrestedprocessiveelongation complexGTF2F1(2-517)[nucleoplasm]POLR2B [nucleoplasm]GTF2F1(2-517)[nucleoplasm]NELFA(2-528)[nucleoplasm]VIF (P69723) protein[extracellularregion]POLR2C [nucleoplasm]NELFB [nucleoplasm]UBB(153-228) [plasmamembrane]ERCC3 [nucleoplasm]Virion with CD4bound to gp120VPU (P05919) protein[cytosol]CCNH [nucleoplasm]CCNH [nucleoplasm]TCEB1 [nucleoplasm]NELFCD [nucleoplasm]VPS37C [endosomemembrane]CDK9 [nucleoplasm]POLR2D(2-142)[nucleoplasm]Surface proteingp120 [viralenvelope]NUP54 [nuclearenvelope]UBC(609-684) [plasmamembrane]N-myristoyl GAG(P04591) protein[endosome membrane]GTF2F1(2-517)[nucleoplasm]RNA Pol II withphosphorylated CTD:CE complexNELFB [nucleoplasm]POLR2D(2-142)[nucleoplasm]POLR2H [nucleoplasm]POLR2E [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]TBP [nucleoplasm]GTF2H1(2-548)[nucleoplasm]SUPT4H1[nucleoplasm]GTF2F2(2-249)[nucleoplasm]TAF13 [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]VIF (P69723) protein[extracellularregion]POLR2I [nucleoplasm]UBC(229-304) [plasmamembrane]HIV-1 templateDNA:4-9 nucleotidetranscript hybridPOLR2E [nucleoplasm]POLR2G [nucleoplasm]GTF2H2 [nucleoplasm]Trimeric gp120:gp41oligomerPOLR2F(1-127)[nucleoplasm]RTGTF2A1(1-274)[nucleoplasm]p6 (P04591) protein[cytosol]GTF2F2(2-249)[nucleoplasm]HIV-1 RNA[extracellularregion]POLR2E [nucleoplasm]POLR2B [nucleoplasm]TAF1 [nucleoplasm]GTF2B [nucleoplasm]NELFA(2-528)[nucleoplasm]POM121 [nuclearenvelope]UBC(77-152)[endosome membrane]SSRP1 [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]myristoylated NefProtein(UniProt:P04601)POLR2F(1-127)[nucleoplasm]REV (P04618) protein[cytosol]p-NELFE[nucleoplasm]BANF1 [nucleoplasm]POLR2G [nucleoplasm]XRCC6 [nucleoplasm]MNAT1 [nucleoplasm]POLR2E [nucleoplasm]Assembling HIVvirionHIV-1 transcriptioncomplex containing11 nucleotide longtranscriptPOLR2L [nucleoplasm]UBB(77-152) [plasmamembrane]GTF2A1(1-274)[nucleoplasm]UBC(533-608) [plasmamembrane]POLR2I [nucleoplasm]POLR2A [nucleoplasm]GTF2B [nucleoplasm]REV (P04618) protein[nucleoplasm]GTF2A1(275-376)[nucleoplasm]ESCRT-IHIV-1 RNA template[cytosol]Autointegrated viralDNA as smallercirclesNUP98-5 [nuclearenvelope]VIF (P69723) protein[nucleoplasm]UBC(305-380) [plasmamembrane]Rev-multimerP-TEFb(CyclinT1:Cdk9) complexVPS37B [endosomemembrane]VIF (P69723) protein[extracellularregion]AAAS [nuclearenvelope]TAF13 [nucleoplasm]NUP155 [nuclearenvelope]POLR2I [nucleoplasm]ERCC2 [nucleoplasm]UBC(1-76) [cytosol]POLR2F(1-127)[nucleoplasm]p51 (RT) [cytosol]monoubiquitinatedN-myristoyl GAG(P04591) proteinTAF4B [nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]POLR2E [nucleoplasm]p51 (RT) [cytosol]BANF1TBP [nucleoplasm]GTF2H3 [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]POLR2K [nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]REV (P04618) protein[extracellularregion]NCBP1 [nucleoplasm]Host genomic DNAPOLR2J [nucleoplasm]GTF2H4 [nucleoplasm]PPIA [cytosol]ERCC2 [nucleoplasm]VPU (P05919)POLR2K [nucleoplasm]TAF10 [nucleoplasm]HIV-1 Tat-containingpaused processiveelongation complexTransmembraneprotein gp41(P04578) [cytosol]UTP [nucleoplasm]myristoylated NefProtein(UniProt:P04601)[cytosol]Nup45 [nuclearenvelope]POLR2G [nucleoplasm]GTF2H4 [nucleoplasm]NELFA(2-528)[nucleoplasm]GTF2F2(2-249)[nucleoplasm]HIV-1 earlyelongation complexwithhyperphosphorylatedPol II CTDElongin ComplexGTF2H3 [nucleoplasm]PPIA [cytosol]VPR (P69726) protein[extracellularregion]GTF2H1(2-548)[nucleoplasm]NUP43 [nuclearenvelope]GTF2H4 [nucleoplasm]RTC with duplex DNAcontainingdiscontinuous plusstrand flapIN (Integrase)(P04585) protein[cytosol]Surface proteingp120 [viralenvelope]GTF2F2(2-249)[nucleoplasm]Ku proteins bound toviral DNANUP88 [cytosol]GTF2H4 [nucleoplasm]TPR [nucleoplasm]CTDP1 [nucleoplasm]POLR2G [nucleoplasm]RTC with minusstrand DNA synthesisinitiated from3'-endPOLR2G [nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]GTF2H3 [nucleoplasm]POLR2L [nucleoplasm]POLR2F(1-127)[nucleoplasm]HIV-1 abortedelongation complexafter arrestVPU (P05919) protein[extracellularregion]GTF2F1(2-517)[nucleoplasm]P-TEFb(CyclinT1:Cdk9)-containingelongation complexwith separated anduncleaved transcriptPOLR2I [nucleoplasm]POLR2F(1-127)[nucleoplasm]viral PIC proteinsPOLR2B [nucleoplasm]ERCC3 [nucleoplasm]p51 (RT)[extracellularregion]POLR2J [nucleoplasm]TAF4B [nucleoplasm]MA (P04585) protein[cytosol]VPU (P05919) protein[cytosol]GTF2H1(2-548)[nucleoplasm]GTF2H3 [nucleoplasm]PDCD6IP [cytosol]POLR2B [nucleoplasm]MNAT1 [nucleoplasm]ERCC3 [nucleoplasm]RTC with extendingminus strand DNAMA (P04585) protein[nucleoplasm]ELL [nucleoplasm]NCBP2 [nucleoplasm]CD4 [plasmamembrane]POLR2G [nucleoplasm]PIC (PreIntegrationComplex)POLR2F(1-127)[nucleoplasm]ERCC3 [nucleoplasm]TAF4 [nucleoplasm]p6 (P04585) protein[cytosol]Ran:GTPPPIA [cytosol]REV (P04618) protein[cytosol]CCNH [nucleoplasm]TAF9 [nucleoplasm]MA (P04591) protein[cytosol]p6 (P04591) protein[cytosol]POLR2K [nucleoplasm]GTF2H2 [nucleoplasm]POLR2J [nucleoplasm]POLR2B [nucleoplasm]POLR2K [nucleoplasm]ERCC3 [nucleoplasm]PPIA [extracellularregion]CTDP1 [nucleoplasm]NELFB [nucleoplasm]p6 (P04591) protein[cytosol]TAF12 [nucleoplasm]POLR2E [nucleoplasm]POLR2H [nucleoplasm]POLR2L [nucleoplasm]PPIA [cytosol]GTF2F1(2-517)[nucleoplasm]p-SUPT5H[nucleoplasm]CTDP1 [nucleoplasm]CCNH [nucleoplasm]POLR2G [nucleoplasm]GTF2A1(275-376)[nucleoplasm]NCBP2 [nucleoplasm]MA (P04585) protein[nucleoplasm]TAF11 [nucleoplasm]XRCC5 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]PSIP1 [nucleoplasm]UBC(229-304) [plasmamembrane]NUP214 [cytosol]POLR2G [nucleoplasm]CDK7 [nucleoplasm]POLR2J [nucleoplasm]PPIA [cytosol]VIF (P69723) protein[cytosol]VPR (P69726) protein[extracellularregion]SUPT4H1[nucleoplasm]NUP88 [cytosol]p51 (RT) [cytosol]Transmembraneprotein gp41 [viralenvelope]p-S2,S5-POLR2A[nucleoplasm]POLR2D(2-142)[nucleoplasm]ATP [nucleoplasm]Surface proteingp120 [viralenvelope]POLR2L [nucleoplasm]POLR2I [nucleoplasm]TCEB2 [nucleoplasm]TCEB2 [nucleoplasm]UbCCNH [nucleoplasm]POLR2K [nucleoplasm]RNGTT [nucleoplasm]VIF (P69723) protein[cytosol]RNA Polymerase II(unphosphorylated):TFIIFcomplexPOLR2E [nucleoplasm]CCR5 [plasmamembrane]CDK7 [nucleoplasm]PR (Protease)(P04585) protein[extracellularregion]POLR2H [nucleoplasm]IN (Integrase)(P04585) protein[extracellularregion]CXCR4 [plasmamembrane]NELFCD [nucleoplasm]POLR2F(1-127)[nucleoplasm]IN (Integrase)(P04585) protein[nucleoplasm]NELFCD [nucleoplasm]REV (P04618) protein[cytosol]XPO1 [nucleoplasm]TAF10 [nucleoplasm]NUP214 [cytosol]HMGA1 [nucleoplasm]p6 (P04591) protein[extracellularregion]POLR2F(1-127)[nucleoplasm]POLR2K [nucleoplasm]HIV-1 RNA[extracellularregion]p6 (P04585) protein[cytosol]NELFE [nucleoplasm]NC (P04585) protein[extracellularregion]GTF2A2 [nucleoplasm]p-SUPT5H[nucleoplasm]NELFB [nucleoplasm]POLR2E [nucleoplasm]GTF2H3 [nucleoplasm]POLR2I [nucleoplasm]POLR2L [nucleoplasm]POLR2F(1-127)[nucleoplasm]HIV-1 transcriptioncomplex containing4-9 nucleotide longtranscriptRev multimer-boundHIV-1mRNA:Crm1:Ran:GTP:NPCp-SUPT5H[nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]UTP [nucleoplasm]NELFCD [nucleoplasm]MNAT1 [nucleoplasm]MA (P04585) protein[cytosol]NUP85 [nuclearenvelope]RTC without viralRNA templateSpliced Env mRNASurface proteingp120 [viralenvelope]GTF2F1(2-517)[nucleoplasm]POLR2G [nucleoplasm]NUPL2 [cytosol]CTP [nucleoplasm]POLR2C [nucleoplasm]GTF2F1(2-517)[nucleoplasm]PSIP1 [nucleoplasm]HIV-1 RNA[extracellularregion]POLR2D(2-142)[nucleoplasm]MNAT1 [nucleoplasm]POLR2K [nucleoplasm]TCEB3 [nucleoplasm]NC (P04591) protein[extracellularregion]NUP107 [nuclearenvelope]CCR5 [plasmamembrane]GTF2F2(2-249)[nucleoplasm]REV (P04618) protein[cytosol]TBP [nucleoplasm]TCEA1 [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]MA (P04585) protein[cytosol]POLR2L [nucleoplasm]HMGA1 [nucleoplasm]POLR2D(2-142)[nucleoplasm]REV (P04618) protein[cytosol]viral RNA templateextensively digestedexcept in PPT region[cytosol]POLR2I [nucleoplasm]VPS37C [endosomemembrane]ATP [nucleoplasm]Reversetranscriptase/ribonucleaseH [extracellularregion]p6 (P04591) protein[cytosol]SSRP1 [nucleoplasm]TAF4 [nucleoplasm]GTF2H4 [nucleoplasm]POLR2L [nucleoplasm]POLR2B [nucleoplasm]TAF4B [nucleoplasm]GTF2E2 [nucleoplasm]NELFE [nucleoplasm]POLR2H [nucleoplasm]POLR2G [nucleoplasm]MA (P04591) protein[cytosol]GTF2H3 [nucleoplasm]POLR2L [nucleoplasm]p6 (P04585) protein[cytosol]VPR (P69726) protein[nucleoplasm]REV (P04618) protein[cytosol]GTF2F1(2-517)[nucleoplasm]TAF9 [nucleoplasm]TAF6 [nucleoplasm]POLR2E [nucleoplasm]TCEB1 [nucleoplasm]POLR2K [nucleoplasm]POLR2H [nucleoplasm]TCEA1 [nucleoplasm]Surface proteingp120 (P04578)[cytosol]POLR2H [nucleoplasm]POLR2L [nucleoplasm]Aborted HIV-1 earlyelongation complexTAF10 [nucleoplasm]POLR2H [nucleoplasm]NucleocapsidPOLR2G [nucleoplasm]HIV-1 RNA template[cytosol]GTF2E2 [nucleoplasm]POLR2E [nucleoplasm]CCNT1 [nucleoplasm]NC (P04585) protein[extracellularregion]TCEB3 [nucleoplasm]HIV-1 Tat-containingaborted elongationcomplex after arrestGTF2A2 [nucleoplasm]NC (P04591) protein[extracellularregion]XPO1TCEB1 [nucleoplasm]TAF4B [nucleoplasm]VPR (P69726) protein[cytosol]GTF2A2 [nucleoplasm]POLR2B [nucleoplasm]POLR2I [nucleoplasm]GTP [nucleoplasm]VPR (P69726) protein[cytosol]POLR2H [nucleoplasm]TPR [nucleoplasm]CCNH [nucleoplasm]CCNH [nucleoplasm]POLR2H [nucleoplasm]POLR2J [nucleoplasm]MNAT1 [nucleoplasm]NTPGTF2F1(2-517)[nucleoplasm]GTF2H4 [nucleoplasm]VIF (P69723) protein[cytosol]TCEB2 [nucleoplasm]POLR2A [nucleoplasm]HIV-1 mRNA[nucleoplasm]MA (P04591) protein[cytosol]CTDP1 [nucleoplasm]VIF (P69723) protein[extracellularregion]UTP [nucleoplasm]POLR2H [nucleoplasm]POLR2E [nucleoplasm]NTPERCC2 [nucleoplasm]SUPT4H1[nucleoplasm]p6 (P04591) protein[extracellularregion]REV (P04618) protein[cytosol]POLR2E [nucleoplasm]MA (P04591) protein[cytosol]p51 (RT) [cytosol]VIF (P69723) protein[cytosol]POLR2F(1-127)[nucleoplasm]ERCC2 [nucleoplasm]POLR2D(2-142)[nucleoplasm]NELFCD [nucleoplasm]TAF9 [nucleoplasm]MNAT1 [nucleoplasm]p51 (RT) [cytosol]ERCC3 [nucleoplasm]Reversetranscriptase/ribonucleaseH [extracellularregion]BANF1 [nucleoplasm]TCEB1 [nucleoplasm]ATPTAF9 [nucleoplasm]MNAT1 [nucleoplasm]VPU (P05919) protein[cytosol]GTF2F1(2-517)[nucleoplasm]N-myristoyl GAG[plasma membrane]ATPPOLR2H [nucleoplasm]SUPT16H[nucleoplasm]TCEB3 [nucleoplasm]HIV-1 initiationcomplexVIF (P69723) protein[nucleoplasm]REV (P04618) protein[nucleoplasm]POLR2C [nucleoplasm]MA (P04591) protein[cytosol]UBC(77-152) [plasmamembrane]POLR2D(2-142)[nucleoplasm]GTF2B [nucleoplasm]NCBP2 [nucleoplasm]POLR2H [nucleoplasm]POLR2D(2-142)[nucleoplasm]CCNH [nucleoplasm]XRCC6 [nucleoplasm]VPS37A [endosomemembrane]SUPT4H1[nucleoplasm]POLR2L [nucleoplasm]POLR2G [nucleoplasm]p6 (P04591) protein[extracellularregion]Autointegrated viralDNA as an invertedcirclemonoubiquitinatedN-myristoyl GAG(P04591) proteinIN (Integrase)(P04585) protein[cytosol]RPS27A(1-76) [plasmamembrane]VPU (P05919) protein[cytosol]RTC with integrationcompetent viral DNANELFB [nucleoplasm]SUPT16H[nucleoplasm]HIV-1 mRNA [cytosol]POLR2K [nucleoplasm]GTF2H2 [nucleoplasm]POLR2C [nucleoplasm]HIV-1 RNA[extracellularregion]NELFCD [nucleoplasm]POLR2C [nucleoplasm]RANGAP1VPU (P05919) protein[cytosol]POLR2B [nucleoplasm]PPIA [extracellularregion]CTP [nucleoplasm]UBC(153-228)[cytosol]POLR2D(2-142)[nucleoplasm]p-S2,S5-POLR2A[nucleoplasm]p6 (P04591)[nucleoplasm]HIV-1 elongationcomplexNCBP1 [nucleoplasm]TCEB2 [nucleoplasm]VIF (P69723) protein[cytosol]TAF13 [nucleoplasm]GTF2H1(2-548)[nucleoplasm]POLR2L [nucleoplasm]POLR2I [nucleoplasm]VIF (P69723) protein[cytosol]PR (Protease)(P04585) protein[extracellularregion]POLR2D(2-142)[nucleoplasm]POLR2K [nucleoplasm]TAF11 [nucleoplasm]NEDD4L(2-975)GTF2H1(2-548)[nucleoplasm]POLR2C [nucleoplasm]GTF2F2(2-249)[nucleoplasm]TAF11 [nucleoplasm]GTP [nucleoplasm]HIV-1 transcriptioncomplex containing 4nucleotide longtranscriptVIF (P69723) protein[extracellularregion]p-SUPT5H[nucleoplasm]TCEB2 [nucleoplasm]SUPT4H1[nucleoplasm]POLR2J [nucleoplasm]GTF2F1(2-517)[nucleoplasm]MNAT1 [nucleoplasm]UBC(77-152) [plasmamembrane]GTF2H4 [nucleoplasm]BANF1 [nucleoplasm]p-SUPT5H[nucleoplasm]CD4 [plasmamembrane]GTF2F1(2-517)[nucleoplasm]GTF2H3 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]GTF2H3 [nucleoplasm]POLR2H [nucleoplasm]Reversetranscriptase/ribonucleaseH [extracellularregion]POLR2E [nucleoplasm]GTF2F1(2-517)[nucleoplasm]p-SUPT5H[nucleoplasm]CDK7 [nucleoplasm]POLR2H [nucleoplasm]p6 (P04591) protein[cytosol]POLR2B [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]GTF2F2(2-249)[nucleoplasm]ERCC3 [nucleoplasm]p6 (P04591) protein[cytosol]POLR2F(1-127)[nucleoplasm]CCNT1 [nucleoplasm]POLR2C [nucleoplasm]p6 (P04585) protein[cytosol]POLR2C [nucleoplasm]NELFE [nucleoplasm]p-S5-POLR2A[nucleoplasm]POLR2J [nucleoplasm]PR (Protease)(P04585) proteinNUP35 [nuclearenvelope]TCEB3 [nucleoplasm]POLR2J [nucleoplasm]MA (P04585) protein[cytosol]CCNT2 [nucleoplasm]VPR (P69726) protein[cytosol]CDK7 [nucleoplasm]TAF11 [nucleoplasm]REV (P04618) protein[nucleoplasm]ERCC3 [nucleoplasm]TCEA1 [nucleoplasm]NMT1(1-?)TAF12 [nucleoplasm]GTF2E1 [nucleoplasm]TAF5 [nucleoplasm]GTF2A1(1-274)[nucleoplasm]GTF2H1(2-548)[nucleoplasm]POLR2F(1-127)[nucleoplasm]CXCR4 [plasmamembrane]p51 (RT)[extracellularregion]SUPT4H1[nucleoplasm]p-SUPT5H[nucleoplasm]ERCC2 [nucleoplasm]NELFB [nucleoplasm]GTF2F2(2-249)[nucleoplasm]UBC(153-228) [plasmamembrane]p6 (P04591) protein[cytosol]CDK7 [nucleoplasm]POLR2I [nucleoplasm]GTF2H2 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]ERCC3 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]TAF9 [nucleoplasm]GTF2F2(2-249)[nucleoplasm]HIV-1 RNA template[cytosol]CTDP1 [nucleoplasm]CTDP1 [nucleoplasm]POLR2E [nucleoplasm]ATP [nucleoplasm]CHMP5 [cytosol]POLR2E [nucleoplasm]CCNT1 [nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]POLR2B [nucleoplasm]GTF2F2(2-249)[nucleoplasm]POLR2B [nucleoplasm]VPU (P05919) protein[nucleoplasm]CD4 [plasmamembrane]IN (Integrase)(P04585) protein[cytosol]HIV-1 RNA[extracellularregion]PR (Protease)(P04585) protein[cytosol]POLR2F(1-127)[nucleoplasm]Surface proteingp120 [viralenvelope]p-SUPT5H[nucleoplasm]Reversetranscriptase/ribonucleaseH [extracellularregion]ERCC2 [nucleoplasm]VPR (P69726) protein[cytosol]GTF2A1(275-376)[nucleoplasm]NC (P04585) protein[extracellularregion]HIV-1 RNA[extracellularregion]p6 (P04585) protein[extracellularregion]MA (P04591) protein[nucleoplasm]CCNH [nucleoplasm]GTF2F2(2-249)[nucleoplasm]ELL [nucleoplasm]POLR2L [nucleoplasm]CD4REV (P04618) protein[cytosol]VPR (P69726) protein[nucleoplasm]CHMP2A [cytosol]p6 (P04585)[nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]Trimeric gp120:gp41oligomerTat-containing earlyelongation complexwithhyperphosphorylatedPol II CTDCXCR4 [plasmamembrane]CCNT2 [nucleoplasm]MNAT1 [nucleoplasm]VPU (P05919) protein[cytosol]GTF2F2(2-249)[nucleoplasm]Mature HIV virionCTP [nucleoplasm]POLR2I [nucleoplasm]POLR2C [nucleoplasm]XPO1 [nucleoplasm]TAF9 [nucleoplasm]TAF9 [nucleoplasm]GAG-POL Polyprotein(P04585)POLR2B [nucleoplasm]CTDP1 [nucleoplasm]CD4 [plasmamembrane]POLR2H [nucleoplasm]VPR (P69726) protein[cytosol]VPU (P05919) protein[extracellularregion]SUPT4H1[nucleoplasm]GTF2F2(2-249)[nucleoplasm]ERCC2 [nucleoplasm]GTF2H1(2-548)[nucleoplasm]REV (P04618) protein[cytosol]Transmembraneprotein gp41 [viralenvelope]NTPTCEB2 [nucleoplasm]POLR2I [nucleoplasm]POLR2H [nucleoplasm]CCR5 [plasmamembrane]IN:viral DNA boundto host genomic DNAwith staggered endsIntegrated provirusGTF2F2(2-249)[nucleoplasm]Transmembraneprotein gp41(P04578) [cytosol]VPR (P69726) protein[cytosol]p51 (RT) [cytosol]UTP [nucleoplasm]CDK7 [nucleoplasm]POLR2E [nucleoplasm]POLR2F(1-127)[nucleoplasm]SUPT16H[nucleoplasm]POLR2H [nucleoplasm]POLR2L [nucleoplasm]HIV-1 RNA template[cytosol]GTF2H1(2-548)[nucleoplasm]POLR2J [nucleoplasm]myristoylated NefProtein(UniProt:P04601)NELFA(2-528)[nucleoplasm]viral RNA templatebeing digested byRNase-H (extensive)[cytosol]VPR (P69726) protein[cytosol]TAF13 [nucleoplasm]IN (Integrase)(P04585) protein[cytosol]VPR (P69726) protein[nucleoplasm]p-SUPT5H[nucleoplasm]POLR2C [nucleoplasm]viral PIC proteinsPOLR2D(2-142)[nucleoplasm]POLR2K [nucleoplasm]REV (P04618) protein[nucleoplasm]p6 (P04591) protein[cytosol]TCEB2 [nucleoplasm]NELFE [nucleoplasm]CCNH [nucleoplasm]GTF2H1(2-548)[nucleoplasm]GTF2F1(2-517)[nucleoplasm]HIV-1 transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30REV (P04618) protein[extracellularregion]POLR2L [nucleoplasm]POLR2L [nucleoplasm]TAF6 [nucleoplasm]MA (P04585) protein[nucleoplasm]ERCC2 [nucleoplasm]p51 (RT) [cytosol]p-S2,S5-POLR2A[nucleoplasm]POLR2B [nucleoplasm]GTF2B [nucleoplasm]POLR2G [nucleoplasm]p6 (P04585) protein[extracellularregion]VPU (P05919) protein[cytosol]MA (P04585) protein[cytosol]SSRP1 [nucleoplasm]CCR5, CXCR4CTDP1 [nucleoplasm]GTF2H3 [nucleoplasm]p6 (P04585) protein[cytosol]XRCC6 [nucleoplasm]GTP [nucleoplasm]SUPT16H[nucleoplasm]Virion with gp41exposedGTF2A2 [nucleoplasm]POLR2J [nucleoplasm]LIG4 [nucleoplasm]TCEA1 [nucleoplasm]GTF2H2 [nucleoplasm]SSRP1 [nucleoplasm]MA (P04585) protein[cytosol]VPU (P05919) protein[cytosol]p6 (P04591) protein[extracellularregion]NUP188(2-1749)[nuclear envelope]POLR2G [nucleoplasm]TCEB3 [nucleoplasm]TCEB1 [nucleoplasm]ATP [nucleoplasm]GTF2H1(2-548)[nucleoplasm]ELL [nucleoplasm]PPIA [extracellularregion]POLR2I [nucleoplasm]CTDP1CDK7 [nucleoplasm]CoA-SHMA (P04585) protein[nucleoplasm]VIF (P69723) protein[nucleoplasm]UBC(77-152) [plasmamembrane]POLR2G [nucleoplasm]POLR2G [nucleoplasm]p-NELFE[nucleoplasm]POLR2E [nucleoplasm]POLR2H [nucleoplasm]TCEB3 [nucleoplasm]p6 (P04591) protein[cytosol]GTF2B [nucleoplasm]POLR2G [nucleoplasm]POLR2H [nucleoplasm]CCR5 [plasmamembrane]GTF2F1(2-517)[nucleoplasm]UBC(457-532) [plasmamembrane]GTF2F1(2-517)[nucleoplasm]TCEB2 [nucleoplasm]HMGA1Rev-bound HIV-1 mRNASSRP1 [nucleoplasm]Envelopeglycoprotein gp160TAF4B [nucleoplasm]MA (P04585) protein[cytosol]TAF5 [nucleoplasm]TBP [nucleoplasm]HIV-1 mRNA [cytosol]POLR2I [nucleoplasm]VPR (P69726) protein[extracellularregion]VPR (P69726) proteinMA (P04585) protein[nucleoplasm]POLR2D(2-142)[nucleoplasm]XRCC6 [nucleoplasm]POLR2B [nucleoplasm]TAF4 [nucleoplasm]BANF1 [nucleoplasm]VPU (P05919) protein[nucleoplasm]UBC(533-608)[cytosol]NUP62 [nuclearenvelope]NELFB [nucleoplasm]Tat (P04608)[nucleoplasm]GTF2F1(2-517)[nucleoplasm]POLR2J [nucleoplasm]p6 (P04591) protein[extracellularregion]RNMTERCC3 [nucleoplasm]GTPPOLR2G [nucleoplasm]NCBP1 [nucleoplasm]UBB(153-228)[endosome membrane]SUPT16H[nucleoplasm]REV (P04618) protein[nucleoplasm]PDCD6IPNef Protein(UniProt:P04601)VIF (P69723) protein[cytosol]UTP [nucleoplasm]UBB(1-76) [cytosol]MNAT1 [nucleoplasm]Tat (P04608)[nucleoplasm]NELFE [nucleoplasm]Tat-containingelongation complexprior to separationPOLR2H [nucleoplasm]ERCC2 [nucleoplasm]viral DNA:Kuproteins:XRCC4:DNAligase IV complexTBP [nucleoplasm]GTF2H1(2-548)[nucleoplasm]viral PIC proteinsPOLR2H [nucleoplasm]UTP [nucleoplasm]TAF1 [nucleoplasm]MNAT1 [nucleoplasm]MA (P04591) protein[cytosol]CTP [nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]POLR2A [nucleoplasm]HIV-1 template DNAcontaining promoterwith transcript of 2 or 3 nucleotidesNELFCD [nucleoplasm]NELFA(2-528)[nucleoplasm]POLR2F(1-127)[nucleoplasm]CTDP1 [nucleoplasm]NMT2Reversetranscriptase/ribonucleaseH [extracellularregion]GTF2A2 [nucleoplasm]HIV-1 initiationcomplex withphosphodiester-PPiintermediatePOLR2E [nucleoplasm]NUP54 [nuclearenvelope]MNAT1 [nucleoplasm]RANBP2 [cytosol]GTF2F2(2-249)[nucleoplasm]POLR2D(2-142)[nucleoplasm]POLR2D(2-142)[nucleoplasm]VPU (P05919) protein[cytosol]ELL [nucleoplasm]CCNT1 [nucleoplasm]POLR2F(1-127)[nucleoplasm]GTF2F2(2-249)[nucleoplasm]TAF1 [nucleoplasm]HIV-1 mRNAReversetranscriptase/ribonucleaseH [cytosol]RTC with minussssDNA transferredto 3'-end of viralRNA templatePOLR2D(2-142)[nucleoplasm]UBA52(1-76) [plasmamembrane]CCNT1 [nucleoplasm]POLR2B [nucleoplasm]GTF2A1(275-376)[nucleoplasm]SUPT16H[nucleoplasm]Reversetranscriptase/ribonucleaseH [cytosol]XRCC5 [nucleoplasm]myristoylated NefProtein(UniProt:P04601)[extracellularregion]Trimeric ENVprecursorPOLR2J [nucleoplasm]TAF4 [nucleoplasm]GTF2F1(2-517)[nucleoplasm]UBB(77-152)[endosome membrane]RTERCC2 [nucleoplasm]TAF11 [nucleoplasm]VPR (P69726) protein[cytosol]VPS37D [endosomemembrane]PPIA [cytosol]POLR2G [nucleoplasm]SUPT4H1[nucleoplasm]RNA Polymerase II(unphosphorylated):TFIIFcomplexPOLR2F(1-127)[nucleoplasm]p-SUPT5H[nucleoplasm]MA (P04591) protein[nucleoplasm]POLR2G [nucleoplasm]POLR2C [nucleoplasm]IN (Integrase)(P04585) protein[nucleoplasm]GTF2F1(2-517)[nucleoplasm]UBB(77-152) [plasmamembrane]VIF (P69723) protein[cytosol]POLR2D(2-142)[nucleoplasm]POLR2B [nucleoplasm]MNAT1 [nucleoplasm]TCEB2 [nucleoplasm]VPR (P69726) protein[extracellularregion]NELFE [nucleoplasm]PPiREV (P04618) protein[extracellularregion]POLR2J [nucleoplasm]POLR2D(2-142)[nucleoplasm]GTF2BRANBP1(2-201)[nuclear envelope]Transmembraneprotein gp41(P04578) [cytosol]p-S2,S5-POLR2A[nucleoplasm]MA (P04591) protein[cytosol]NELFB [nucleoplasm]tRNA-Lysine3IN (Integrase)(P04585) protein[extracellularregion]ATP [nucleoplasm]NC (P04585) protein[extracellularregion]NUPL1-2 [nuclearenvelope]CHMP4B [cytosol]POLR2L [nucleoplasm]HIV-1 mRNA[nucleoplasm]REV (P04618) protein[extracellularregion]GTF2F1(2-517)[nucleoplasm]NCBP2 [nucleoplasm]VPR (P69726) protein[cytosol]IN (Integrase)(P04585) protein[cytosol]ERCC2 [nucleoplasm]81, 97, 104364341


Description

The life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surface (a), viral and host cell membranes fuse and the viral particle is uncoated (b), the viral genome is reverse transcribed and the viral preintegration complex (PIC) forms (c), the PIC is transported through the nuclear pore into the nucleoplasm (d), and the viral reverse transcript is integrated into a host cell chromosome (e). In the late phase, viral RNAs are transcribed from the integrated viral genome and processed to generate viral mRNAs and full-length viral genomic RNAs (f), the viral RNAs are exported through the nuclear pore into the cytosol (g), viral mRNAs are translated and the resulting viral proteins are post-translationally processed (h), core particles containing viral genomic RNA and proteins assemble at the host cell membrane and immature viral particles are released by budding. The released particles mature to become infectious (j), completing the cycle (Frankel and Young 1998; Miller and Bushman 1997).
Most of the crucial concepts used to describe these processes were originally elucidated in studies of retroviruses associated with tumors in chickens, birds, and other animal model systems, and the rapid elucidation of the basic features of the HIV-1 life cycle was critically dependent on the intellectual framework provided by these earlier studies. This earlier work has been very well summarized (e.g., Weiss et al. 1984; Coffin et al. 1997); here for brevity and clarity we focus on experimental studies specific to the HIV-1 life cycle.Original Pathway at Reactome: http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=162587

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  86. Tirode F, Busso D, Coin F, Egly JM.; ''Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7.''; PubMed Europe PMC Scholia
  87. Ivanov D, Kwak YT, Guo J, Gaynor RB.; ''Domains in the SPT5 protein that modulate its transcriptional regulatory properties.''; PubMed Europe PMC Scholia
  88. Ryu SE, Kwong PD, Truneh A, Porter TG, Arthos J, Rosenberg M, Dai XP, Xuong NH, Axel R, Sweet RW.; ''Crystal structure of an HIV-binding recombinant fragment of human CD4.''; PubMed Europe PMC Scholia
  89. Lasky LA, Nakamura G, Smith DH, Fennie C, Shimasaki C, Patzer E, Berman P, Gregory T, Capon DJ.; ''Delineation of a region of the human immunodeficiency virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor.''; PubMed Europe PMC Scholia
  90. Chen CH, Matthews TJ, McDanal CB, Bolognesi DP, Greenberg ML.; ''A molecular clasp in the human immunodeficiency virus (HIV) type 1 TM protein determines the anti-HIV activity of gp41 derivatives: implication for viral fusion.''; PubMed Europe PMC Scholia
  91. Delwart EL, Mosialos G, Gilmore T.; ''Retroviral envelope glycoproteins contain a "leucine zipper"-like repeat.''; PubMed Europe PMC Scholia
  92. Meyer BE, Malim MH.; ''The HIV-1 Rev trans-activator shuttles between the nucleus and the cytoplasm.''; PubMed Europe PMC Scholia
  93. Giang DK, Cravatt BF.; ''A second mammalian N-myristoyltransferase.''; PubMed Europe PMC Scholia
  94. Fiedler U, Timmers HT.; ''Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.''; PubMed Europe PMC Scholia
  95. Farnet CM, Bushman FD.; ''HIV cDNA integration: molecular biology and inhibitor development.''; PubMed Europe PMC Scholia
  96. de Souza RF, Aravind L.; ''UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes.''; PubMed Europe PMC Scholia
  97. Sullivan N, Sun Y, Sattentau Q, Thali M, Wu D, Denisova G, Gershoni J, Robinson J, Moore J, Sodroski J.; ''CD4-Induced conformational changes in the human immunodeficiency virus type 1 gp120 glycoprotein: consequences for virus entry and neutralization.''; PubMed Europe PMC Scholia
  98. Cao J, Bergeron L, Helseth E, Thali M, Repke H, Sodroski J.; ''Effects of amino acid changes in the extracellular domain of the human immunodeficiency virus type 1 gp41 envelope glycoprotein.''; PubMed Europe PMC Scholia
  99. Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S, Yano K, Hartzog GA, Winston F, Buratowski S, Handa H.; ''DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.''; PubMed Europe PMC Scholia
  100. Sibanda BL, Critchlow SE, Begun J, Pei XY, Jackson SP, Blundell TL, Pellegrini L.; ''Crystal structure of an Xrcc4-DNA ligase IV complex.''; PubMed Europe PMC Scholia
  101. Inlora J, Chukkapalli V, Derse D, Ono A.; ''Gag localization and virus-like particle release mediated by the matrix domain of human T-lymphotropic virus type 1 Gag are less dependent on phosphatidylinositol-(4,5)-bisphosphate than those mediated by the matrix domain of HIV-1 Gag.''; PubMed Europe PMC Scholia
  102. Eastman SW, Martin-Serrano J, Chung W, Zang T, Bieniasz PD.; ''Identification of human VPS37C, a component of endosomal sorting complex required for transport-I important for viral budding.''; PubMed Europe PMC Scholia
  103. Bischoff FR, Ponstingl H.; ''Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1.''; PubMed Europe PMC Scholia
  104. Gallo SA, Puri A, Blumenthal R.; ''HIV-1 gp41 six-helix bundle formation occurs rapidly after the engagement of gp120 by CXCR4 in the HIV-1 Env-mediated fusion process.''; PubMed Europe PMC Scholia
  105. Mahboobi SH, Javanpour AA, Mofrad MR.; ''The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle.''; PubMed Europe PMC Scholia
  106. Huang CC, Tang M, Zhang MY, Majeed S, Montabana E, Stanfield RL, Dimitrov DS, Korber B, Sodroski J, Wilson IA, Wyatt R, Kwong PD.; ''Structure of a V3-containing HIV-1 gp120 core.''; PubMed Europe PMC Scholia
  107. Hoffmann A, Roeder RG.; ''Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation.''; PubMed Europe PMC Scholia
  108. Weissenhorn W, Wharton SA, Calder LJ, Earl PL, Moss B, Aliprandis E, Skehel JJ, Wiley DC.; ''The ectodomain of HIV-1 env subunit gp41 forms a soluble, alpha-helical, rod-like oligomer in the absence of gp120 and the N-terminal fusion peptide.''; PubMed Europe PMC Scholia
  109. Brown PO, Bowerman B, Varmus HE, Bishop JM.; ''Correct integration of retroviral DNA in vitro.''; PubMed Europe PMC Scholia
  110. Lee WR, Syu WJ, Du B, Matsuda M, Tan S, Wolf A, Essex M, Lee TH.; ''Nonrandom distribution of gp120 N-linked glycosylation sites important for infectivity of human immunodeficiency virus type 1.''; PubMed Europe PMC Scholia
  111. Malim MH, Cullen BR.; ''HIV-1 structural gene expression requires the binding of multiple Rev monomers to the viral RRE: implications for HIV-1 latency.''; PubMed Europe PMC Scholia
  112. Freed EO, Myers DJ, Risser R.; ''Characterization of the fusion domain of the human immunodeficiency virus type 1 envelope glycoprotein gp41.''; PubMed Europe PMC Scholia
  113. Jonckheere H, Anné J, De Clercq E.; ''The HIV-1 reverse transcription (RT) process as target for RT inhibitors.''; PubMed Europe PMC Scholia
  114. Bunick D, Zandomeni R, Ackerman S, Weinmann R.; ''Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts.''; PubMed Europe PMC Scholia
  115. Dvir A, Conaway RC, Conaway JW.; ''A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes.''; PubMed Europe PMC Scholia
  116. Klatzmann D, Champagne E, Chamaret S, Gruest J, Guetard D, Hercend T, Gluckman JC, Montagnier L.; ''T-lymphocyte T4 molecule behaves as the receptor for human retrovirus LAV.''; PubMed Europe PMC Scholia
  117. Bieniasz PD.; ''The cell biology of HIV-1 virion genesis.''; PubMed Europe PMC Scholia
  118. Mousson F, Kolkman A, Pijnappel WW, Timmers HT, Heck AJ.; ''Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes.''; PubMed Europe PMC Scholia
  119. Zhou M, Halanski MA, Radonovich MF, Kashanchi F, Peng J, Price DH, Brady JN.; ''Tat modifies the activity of CDK9 to phosphorylate serine 5 of the RNA polymerase II carboxyl-terminal domain during human immunodeficiency virus type 1 transcription.''; PubMed Europe PMC Scholia
  120. Gallaher WR, Ball JM, Garry RF, Griffin MC, Montelaro RC.; ''A general model for the transmembrane proteins of HIV and other retroviruses.''; PubMed Europe PMC Scholia
  121. Jiang M, Mak J, Ladha A, Cohen E, Klein M, Rovinski B, Kleiman L.; ''Identification of tRNAs incorporated into wild-type and mutant human immunodeficiency virus type 1.''; PubMed Europe PMC Scholia
  122. Malim MH, Bieniasz PD.; ''HIV Restriction Factors and Mechanisms of Evasion.''; PubMed Europe PMC Scholia
  123. Zapp ML, Green MR.; ''Sequence-specific RNA binding by the HIV-1 Rev protein.''; PubMed Europe PMC Scholia
  124. Fischer U, Meyer S, Teufel M, Heckel C, Lührmann R, Rautmann G.; ''Evidence that HIV-1 Rev directly promotes the nuclear export of unspliced RNA.''; PubMed Europe PMC Scholia
  125. Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L.; ''TAF9b (formerly TAF9L) is a bona fide TAF that has unique and overlapping roles with TAF9.''; PubMed Europe PMC Scholia
  126. Fritz CC, Green MR.; ''HIV Rev uses a conserved cellular protein export pathway for the nucleocytoplasmic transport of viral RNAs.''; PubMed Europe PMC Scholia
  127. Kao SY, Calman AF, Luciw PA, Peterlin BM.; ''Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product.''; PubMed Europe PMC Scholia
  128. Parvin JD, Sharp PA.; ''DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.''; PubMed Europe PMC Scholia
  129. Bischoff FR, Krebber H, Kempf T, Hermes I, Ponstingl H.; ''Human RanGTPase-activating protein RanGAP1 is a homologue of yeast Rna1p involved in mRNA processing and transport.''; PubMed Europe PMC Scholia
  130. Frankel AD, Young JA.; ''HIV-1: fifteen proteins and an RNA.''; PubMed Europe PMC Scholia
  131. Ori A, Banterle N, Iskar M, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M.; ''Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.''; PubMed Europe PMC Scholia
  132. Dvir A, Tan S, Conaway JW, Conaway RC.; ''Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.''; PubMed Europe PMC Scholia
  133. Yi R, Bogerd HP, Cullen BR.; ''Recruitment of the Crm1 nuclear export factor is sufficient to induce cytoplasmic expression of incompletely spliced human immunodeficiency virus mRNAs.''; PubMed Europe PMC Scholia
  134. Wild C, Oas T, McDanal C, Bolognesi D, Matthews T.; ''A synthetic peptide inhibitor of human immunodeficiency virus replication: correlation between solution structure and viral inhibition.''; PubMed Europe PMC Scholia
  135. Conaway RC, Conaway JW.; ''ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.''; PubMed Europe PMC Scholia
  136. Farazi TA, Waksman G, Gordon JI.; ''The biology and enzymology of protein N-myristoylation.''; PubMed Europe PMC Scholia
  137. Charneau P, Alizon M, Clavel F.; ''A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication.''; PubMed Europe PMC Scholia
  138. Ehrlich LS, Liu T, Scarlata S, Chu B, Carter CA.; ''HIV-1 capsid protein forms spherical (immature-like) and tubular (mature-like) particles in vitro: structure switching by pH-induced conformational changes.''; PubMed Europe PMC Scholia
  139. Rabut G, Doye V, Ellenberg J.; ''Mapping the dynamic organization of the nuclear pore complex inside single living cells.''; PubMed Europe PMC Scholia
  140. Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JA, Glavy JS, Hurt E, Beck M.; ''Molecular architecture of the inner ring scaffold of the human nuclear pore complex.''; PubMed Europe PMC Scholia
  141. Pal M, Luse DS.; ''Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA.''; PubMed Europe PMC Scholia
  142. Dubay JW, Roberts SJ, Brody B, Hunter E.; ''Mutations in the leucine zipper of the human immunodeficiency virus type 1 transmembrane glycoprotein affect fusion and infectivity.''; PubMed Europe PMC Scholia
  143. McDougal JS, Nicholson JK, Cross GD, Cort SP, Kennedy MS, Mawle AC.; ''Binding of the human retrovirus HTLV-III/LAV/ARV/HIV to the CD4 (T4) molecule: conformation dependence, epitope mapping, antibody inhibition, and potential for idiotypic mimicry.''; PubMed Europe PMC Scholia
  144. Kilby JM, Eron JJ.; ''Novel therapies based on mechanisms of HIV-1 cell entry.''; PubMed Europe PMC Scholia
  145. Rizzuto CD, Wyatt R, Hernández-Ramos N, Sun Y, Kwong PD, Hendrickson WA, Sodroski J.; ''A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding.''; PubMed Europe PMC Scholia
  146. Fiedler U, Marc Timmers HT.; ''Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.''; PubMed Europe PMC Scholia
  147. Goodrich JA, Tjian R.; ''Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.''; PubMed Europe PMC Scholia
  148. Melikyan GB, Markosyan RM, Hemmati H, Delmedico MK, Lambert DM, Cohen FS.; ''Evidence that the transition of HIV-1 gp41 into a six-helix bundle, not the bundle configuration, induces membrane fusion.''; PubMed Europe PMC Scholia
  149. Zhang W, Canziani G, Plugariu C, Wyatt R, Sodroski J, Sweet R, Kwong P, Hendrickson W, Chaiken I.; ''Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic.''; PubMed Europe PMC Scholia
  150. Brown PO, Bowerman B, Varmus HE, Bishop JM.; ''Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein.''; PubMed Europe PMC Scholia
  151. Miller MD, Farnet CM, Bushman FD.; ''Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition.''; PubMed Europe PMC Scholia
  152. Meng B, Lever AM.; ''Wrapping up the bad news: HIV assembly and release.''; PubMed Europe PMC Scholia
  153. Cramer P, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.''; PubMed Europe PMC Scholia
  154. Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H.; ''NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  155. Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR.; ''Identification of a major co-receptor for primary isolates of HIV-1.''; PubMed Europe PMC Scholia
  156. Chen H, Engelman A.; ''The barrier-to-autointegration protein is a host factor for HIV type 1 integration.''; PubMed Europe PMC Scholia
  157. Julias JG, McWilliams MJ, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.; ''Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage.''; PubMed Europe PMC Scholia
  158. Kati WM, Johnson KA, Jerva LF, Anderson KS.; ''Mechanism and fidelity of HIV reverse transcriptase.''; PubMed Europe PMC Scholia
  159. Sackett K, Shai Y.; ''The HIV-1 gp41 N-terminal heptad repeat plays an essential role in membrane fusion.''; PubMed Europe PMC Scholia
  160. Gonatopoulos-Pournatzis T, Cowling VH.; ''Cap-binding complex (CBC).''; PubMed Europe PMC Scholia
  161. Hill BT, Skowronski J.; ''Human N-myristoyltransferases form stable complexes with lentiviral nef and other viral and cellular substrate proteins.''; PubMed Europe PMC Scholia
  162. Rausch JW, Le Grice SF.; '''Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus.''; PubMed Europe PMC Scholia
  163. Dalgleish AG, Beverley PC, Clapham PR, Crawford DH, Greaves MF, Weiss RA.; ''The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus.''; PubMed Europe PMC Scholia
  164. Martin-Serrano J, Zang T, Bieniasz PD.; ''Role of ESCRT-I in retroviral budding.''; PubMed Europe PMC Scholia
  165. Iordanskiy S, Berro R, Altieri M, Kashanchi F, Bukrinsky M.; ''Intracytoplasmic maturation of the human immunodeficiency virus type 1 reverse transcription complexes determines their capacity to integrate into chromatin.''; PubMed Europe PMC Scholia
  166. Zhang H, Dornadula G, Orenstein J, Pomerantz RJ.; ''Morphologic changes in human immunodeficiency virus type 1 virions secondary to intravirion reverse transcription: evidence indicating that reverse transcription may not take place within the intact viral core.''; PubMed Europe PMC Scholia
  167. Bushman FD, Fujiwara T, Craigie R.; ''Retroviral DNA integration directed by HIV integration protein in vitro.''; PubMed Europe PMC Scholia
  168. Pullen KA, Ishimoto LK, Champoux JJ.; ''Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase.''; PubMed Europe PMC Scholia
  169. Holstege FC, Fiedler U, Timmers HT.; ''Three transitions in the RNA polymerase II transcription complex during initiation.''; PubMed Europe PMC Scholia
  170. Carr CM, Kim PS.; ''A spring-loaded mechanism for the conformational change of influenza hemagglutinin.''; PubMed Europe PMC Scholia
  171. Jacob GA, Luse SW, Luse DS.; ''Abortive initiation is increased only for the weakest members of a set of down mutants of the adenovirus 2 major late promoter.''; PubMed Europe PMC Scholia
  172. Mak J, Jiang M, Wainberg MA, Hammarskjöld ML, Rekosh D, Kleiman L.; ''Role of Pr160gag-pol in mediating the selective incorporation of tRNA(Lys) into human immunodeficiency virus type 1 particles.''; PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
112577view15:54, 9 October 2020ReactomeTeamReactome version 73
101491view11:36, 1 November 2018ReactomeTeamreactome version 66
101028view21:16, 31 October 2018ReactomeTeamreactome version 65
100562view19:50, 31 October 2018ReactomeTeamreactome version 64
100110view16:35, 31 October 2018ReactomeTeamreactome version 63
99660view15:06, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99260view12:45, 31 October 2018ReactomeTeamreactome version 62
93960view13:48, 16 August 2017ReactomeTeamreactome version 61
93556view11:27, 9 August 2017ReactomeTeamreactome version 61
87467view14:14, 22 July 2016MkutmonOntology Term : 'infectious disease pathway' added !
86659view09:23, 11 July 2016ReactomeTeamreactome version 56
83257view10:34, 18 November 2015ReactomeTeamVersion54
81368view12:53, 21 August 2015ReactomeTeamVersion53
76836view08:06, 17 July 2014ReactomeTeamFixed remaining interactions
76540view11:52, 16 July 2014ReactomeTeamFixed remaining interactions
75873view09:52, 11 June 2014ReactomeTeamRe-fixing comment source
75573view10:39, 10 June 2014ReactomeTeamReactome 48 Update
74928view13:45, 8 May 2014AnweshaFixing comment source for displaying WikiPathways description
74572view08:37, 30 April 2014ReactomeTeamNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1-LTR form of circular viral DNAComplexREACT_9361 (Reactome)
2-LTR form of circular viral DNAComplexREACT_9104 (Reactome)
AAAS [nuclear envelope]ProteinQ9NRG9 (Uniprot-TrEMBL)
ADPMetaboliteCHEBI:16761 (ChEBI)
ATP [nucleoplasm]MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted HIV-1 early elongation complexComplexREACT_6695 (Reactome)
Assembling HIV virionComplexREACT_164418 (Reactome)
Autointegrated viral

DNA as smaller

circles
ComplexREACT_7557 (Reactome)
Autointegrated viral

DNA as an inverted

circle
ComplexREACT_7515 (Reactome)
BANF1 [cytosol]ProteinO75531 (Uniprot-TrEMBL)
BANF1 [nucleoplasm]ProteinO75531 (Uniprot-TrEMBL)
BANF1ProteinO75531 (Uniprot-TrEMBL)
CCNH [nucleoplasm]ProteinP51946 (Uniprot-TrEMBL)
CCNT1 [nucleoplasm]ProteinO60563 (Uniprot-TrEMBL)
CCNT2 [nucleoplasm]ProteinO60583 (Uniprot-TrEMBL)
CCR5 [plasma membrane]ProteinP51681 (Uniprot-TrEMBL)
CCR5, CXCR4ProteinREACT_8732 (Reactome)
CD4 [plasma membrane]ProteinP01730 (Uniprot-TrEMBL)
CD4:Env gp120/gp41

hairpin

complex:CCR5/CXCR4
ComplexREACT_8249 (Reactome)
CD4ProteinP01730 (Uniprot-TrEMBL)
CDK7 [nucleoplasm]ProteinP50613 (Uniprot-TrEMBL)
CDK9 [nucleoplasm]ProteinP50750 (Uniprot-TrEMBL)
CE:Pol II CTD:Spt5 complexComplexREACT_6491 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CHMP2A [cytosol]ProteinO43633 (Uniprot-TrEMBL)
CHMP2B [cytosol]ProteinQ9UQN3 (Uniprot-TrEMBL)
CHMP3(2-222) [cytosol]ProteinQ9Y3E7 (Uniprot-TrEMBL)
CHMP4A [cytosol]ProteinQ9BY43 (Uniprot-TrEMBL)
CHMP4B [cytosol]ProteinQ9H444 (Uniprot-TrEMBL)
CHMP4C [cytosol]ProteinQ96CF2 (Uniprot-TrEMBL)
CHMP5 [cytosol]ProteinQ9NZZ3 (Uniprot-TrEMBL)
CHMP6(2-201) [cytosol]ProteinQ96FZ7 (Uniprot-TrEMBL)
CHMP7 [cytosol]ProteinQ8WUX9 (Uniprot-TrEMBL)
CTDP1 [nucleoplasm]ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP [nucleoplasm]MetaboliteCHEBI:17677 (ChEBI)
CXCR4 [plasma membrane]ProteinP61073 (Uniprot-TrEMBL)
Cap Binding Complex (CBC)ComplexREACT_3884 (Reactome)
CoA-SHMetaboliteCHEBI:15346 (ChEBI)
DSIF complexComplexREACT_2797 (Reactome)
DSIF:NELF:early

elongation complex after limited

nucleotide addition
ComplexREACT_6432 (Reactome)
DSIF:NELF:early elongation complexComplexREACT_6594 (Reactome)
ELL [nucleoplasm]ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 [nucleoplasm]ProteinP18074 (Uniprot-TrEMBL)
ERCC3 [nucleoplasm]ProteinP19447 (Uniprot-TrEMBL)
ESCRT-IIIComplexREACT_27898 (Reactome)
ESCRT-IComplexREACT_27580 (Reactome)
Early elongation

complex with separated aborted

transcript
ComplexREACT_6590 (Reactome)
Elongin ComplexComplexREACT_5616 (Reactome)
Encapsidated viral coreComplexREACT_9259 (Reactome)
Envelope

glycoprotein gp160 [endoplasmic

reticulum membrane]
ProteinP04578 (Uniprot-TrEMBL)
Envelope glycoprotein gp160ProteinP04578 (Uniprot-TrEMBL)
FACT complexComplexREACT_4314 (Reactome)
FEN1ProteinP39748 (Uniprot-TrEMBL)
FURINProteinP09958 (Uniprot-TrEMBL)
GAG Polyprotein (P04591)ProteinP04591 (Uniprot-TrEMBL)
GAG-POL Polyprotein

(P04585) [extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
GAG-POL Polyprotein

(P04585) [plasma

membrane]
ProteinP04585 (Uniprot-TrEMBL)
GAG-POL Polyprotein (P04585)ProteinP04585 (Uniprot-TrEMBL)
GDP [cytosol]MetaboliteCHEBI:17552 (ChEBI)
GDP [nucleoplasm]MetaboliteCHEBI:17552 (ChEBI)
GDPMetaboliteCHEBI:17552 (ChEBI)
GTF2A1(1-274) [nucleoplasm]ProteinP52655 (Uniprot-TrEMBL)
GTF2A1(275-376) [nucleoplasm]ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 [nucleoplasm]ProteinP52657 (Uniprot-TrEMBL)
GTF2B [nucleoplasm]ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 [nucleoplasm]ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 [nucleoplasm]ProteinP29084 (Uniprot-TrEMBL)
GTF2F1(2-517) [nucleoplasm]ProteinP35269 (Uniprot-TrEMBL)
GTF2F2(2-249) [nucleoplasm]ProteinP13984 (Uniprot-TrEMBL)
GTF2H1(2-548) [nucleoplasm]ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 [nucleoplasm]ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 [nucleoplasm]ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 [nucleoplasm]ProteinQ92759 (Uniprot-TrEMBL)
GTP [cytosol]MetaboliteCHEBI:15996 (ChEBI)
GTP [nucleoplasm]MetaboliteCHEBI:15996 (ChEBI)
GTPMetaboliteCHEBI:15996 (ChEBI)
Glycosylated

Envelope glycoprotein gp160

[Golgi membrane]
ProteinP04578 (Uniprot-TrEMBL)
HIV-1 Polymerase II

(phosphorylated):TFIIF:capped

pre-mRNA
ComplexREACT_6503 (Reactome)
HIV-1 Promoter Escape ComplexComplexREACT_6417 (Reactome)
HIV-1 RNA

[extracellular

region]
ProteinAF033819 (EMBL)
HIV-1 RNA homodimerComplexREACT_8245 (Reactome)
HIV-1 RNA template [cytosol]ProteinAF033819 (EMBL)
HIV-1 Tat-containing

aborted elongation

complex after arrest
ComplexREACT_6602 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
ComplexREACT_6532 (Reactome)
HIV-1 Tat-containing

paused processive

elongation complex
ComplexREACT_6389 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ComplexREACT_6452 (Reactome)
HIV-1 aborted

elongation complex

after arrest
ComplexREACT_6471 (Reactome)
HIV-1 arrested

processive

elongation complex
ComplexREACT_6609 (Reactome)
HIV-1 capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex
ComplexREACT_6374 (Reactome)
HIV-1 closed

pre-initiation

complex
ComplexREACT_6553 (Reactome)
HIV-1 early

elongation complex with hyperphosphorylated

Pol II CTD
ComplexREACT_6467 (Reactome)
HIV-1 elongation

complex containing

Tat
ComplexREACT_6611 (Reactome)
HIV-1 elongation complexComplexREACT_6501 (Reactome)
HIV-1 initiation

complex with phosphodiester-PPi

intermediate
ComplexREACT_6680 (Reactome)
HIV-1 initiation complexComplexREACT_6518 (Reactome)
HIV-1 mRNA [nucleoplasm]ProteinAF033819 (EMBL)
HIV-1 mRNA [cytosol]ProteinAF033819 (EMBL)
HIV-1 mRNARnaAF033819 (EMBL)
HIV-1 open

pre-initiation

complex
ComplexREACT_6605 (Reactome)
HIV-1 paused

processive

elongation complex
ComplexREACT_6459 (Reactome)
HIV-1 processive elongation complexComplexREACT_6579 (Reactome)
HIV-1 template

DNA:4-9 nucleotide

transcript hybrid
REACT_6414 (Reactome)
HIV-1 template DNA

containing promoter with transcript of

2 or 3 nucleotides
REACT_6665 (Reactome)
HIV-1 template DNA

with first transcript dinucleotide, opened

to +8 position
REACT_6558 (Reactome)
HIV-1 transcription

complex containing 11 nucleotide long

transcript
ComplexREACT_6664 (Reactome)
HIV-1 transcription

complex containing 4-9 nucleotide long

transcript
ComplexREACT_6563 (Reactome)
HIV-1 transcription

complex containing extruded transcript

to +30
ComplexREACT_6516 (Reactome)
HIV-1 transcription

complex containing

transcript to +30
ComplexREACT_6514 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
ComplexREACT_6450 (Reactome)
HIV-1 transcription

complex containing 4 nucleotide long

transcript
ComplexREACT_6640 (Reactome)
HIV-1 transcription

complex containing 9 nucleotide long

transcript
ComplexREACT_6561 (Reactome)
HIV-1 transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
ComplexREACT_6638 (Reactome)
HIV-1 transcription complexComplexREACT_6433 (Reactome)
HIV-1 unspliced RNARnaAF033819 (EMBL)
HMGA1 [cytosol]ProteinP17096 (Uniprot-TrEMBL)
HMGA1 [nucleoplasm]ProteinP17096 (Uniprot-TrEMBL)
HMGA1ProteinP17096 (Uniprot-TrEMBL)
Host genomic DNAREACT_7748 (Reactome)
IN (Integrase)

(P04585) protein

[cytosol]
ProteinP04585 (Uniprot-TrEMBL)
IN (Integrase)

(P04585) protein [extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
IN (Integrase)

(P04585) protein

[nucleoplasm]
ProteinP04585 (Uniprot-TrEMBL)
IN (Integrase) (P04585) proteinProteinP04585 (Uniprot-TrEMBL)
IN bound to sticky

3' ends of viral DNA

in PIC
ComplexREACT_7635 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
ComplexREACT_8354 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
ComplexREACT_9176 (Reactome)
Immature HIV virionComplexREACT_165539 (Reactome)
Integrated provirusComplexREACT_7455 (Reactome)
Integration intermediateComplexREACT_9115 (Reactome)
Ku proteins bound to viral DNAComplexREACT_7016 (Reactome)
Ku70:Ku80 heterodimerComplexREACT_3482 (Reactome)
LIG1ProteinP18858 (Uniprot-TrEMBL)
LIG4 [nucleoplasm]ProteinP49917 (Uniprot-TrEMBL)
MA (P04585) protein [cytosol]ProteinP04585 (Uniprot-TrEMBL)
MA (P04585) protein [nucleoplasm]ProteinP04585 (Uniprot-TrEMBL)
MA (P04591) protein [cytosol]ProteinP04591 (Uniprot-TrEMBL)
MA (P04591) protein [nucleoplasm]ProteinP04591 (Uniprot-TrEMBL)
MNAT1 [nucleoplasm]ProteinP51948 (Uniprot-TrEMBL)
MYS-CoAMetaboliteCHEBI:15532 (ChEBI)
MatrixProteinREACT_8346 (Reactome)
Mature HIV virionComplexREACT_8805 (Reactome)
Multimeric capsid coatREACT_8190 (Reactome)
N-myristoyl GAG

(P04591) protein

[cytosol]
ProteinP04591 (Uniprot-TrEMBL)
N-myristoyl GAG

(P04591) protein

[endosome membrane]
ProteinP04591 (Uniprot-TrEMBL)
N-myristoyl GAG

(P04591) protein [extracellular

region]
ProteinP04591 (Uniprot-TrEMBL)
N-myristoyl GAG (P04591) proteinProteinP04591 (Uniprot-TrEMBL)
N-myristoyl GAG [plasma membrane]ProteinP04591 (Uniprot-TrEMBL)
NC (P04585) protein [cytosol]ProteinP04585 (Uniprot-TrEMBL)
NC (P04585) protein

[extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
NC (P04591) protein [cytosol]ProteinP04591 (Uniprot-TrEMBL)
NC (P04591) protein

[extracellular

region]
ProteinP04591 (Uniprot-TrEMBL)
NCBP1 [nucleoplasm]ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 [nucleoplasm]ProteinP52298 (Uniprot-TrEMBL)
NEDD4L(2-975) [cytosol]ProteinQ96PU5 (Uniprot-TrEMBL)
NEDD4L(2-975)ProteinQ96PU5 (Uniprot-TrEMBL)
NELF complexComplexREACT_2737 (Reactome)
NELFA(2-528) [nucleoplasm]ProteinQ9H3P2 (Uniprot-TrEMBL)
NELFB [nucleoplasm]ProteinQ8WX92 (Uniprot-TrEMBL)
NELFCD [nucleoplasm]ProteinQ8IXH7 (Uniprot-TrEMBL)
NELFE [nucleoplasm]ProteinP18615 (Uniprot-TrEMBL)
NMT1(1-?)ProteinP30419 (Uniprot-TrEMBL)
NMT2ProteinO60551 (Uniprot-TrEMBL)
NTPMetaboliteREACT_4491 (Reactome)
NUP107 [nuclear envelope]ProteinP57740 (Uniprot-TrEMBL)
NUP133 [nuclear envelope]ProteinQ8WUM0 (Uniprot-TrEMBL)
NUP153 [nucleoplasm]ProteinP49790 (Uniprot-TrEMBL)
NUP155 [nuclear envelope]ProteinO75694 (Uniprot-TrEMBL)
NUP160 [nuclear envelope]ProteinQ12769 (Uniprot-TrEMBL)
NUP188(2-1749) [nuclear envelope]ProteinQ5SRE5 (Uniprot-TrEMBL)
NUP205(2-2012) [nuclear envelope]ProteinQ92621 (Uniprot-TrEMBL)
NUP210 [nuclear envelope]ProteinQ8TEM1 (Uniprot-TrEMBL)
NUP214 [cytosol]ProteinP35658 (Uniprot-TrEMBL)
NUP35 [nuclear envelope]ProteinQ8NFH5 (Uniprot-TrEMBL)
NUP37 [nuclear envelope]ProteinQ8NFH4 (Uniprot-TrEMBL)
NUP43 [nuclear envelope]ProteinQ8NFH3 (Uniprot-TrEMBL)
NUP50 [nucleoplasm]ProteinQ9UKX7 (Uniprot-TrEMBL)
NUP54 [nuclear envelope]ProteinQ7Z3B4 (Uniprot-TrEMBL)
NUP62 [nuclear envelope]ProteinP37198 (Uniprot-TrEMBL)
NUP85 [nuclear envelope]ProteinQ9BW27 (Uniprot-TrEMBL)
NUP88 [cytosol]ProteinQ99567 (Uniprot-TrEMBL)
NUP93 [nuclear envelope]ProteinQ8N1F7 (Uniprot-TrEMBL)
NUP98-5 [nuclear envelope]ProteinP52948-5 (Uniprot-TrEMBL)
NUPL1-2 [nuclear envelope]ProteinQ9BVL2-1 (Uniprot-TrEMBL)
NUPL2 [cytosol]ProteinO15504 (Uniprot-TrEMBL)
Nef Protein (UniProt:P04601)ProteinP04601 (Uniprot-TrEMBL)
Nuclear Pore Complex (NPC)ComplexREACT_5542 (Reactome)
NucleocapsidProteinREACT_8930 (Reactome)
Nup45 [nuclear envelope]ProteinQ9BVL2-2 (Uniprot-TrEMBL)
P-TEFb complexComplexREACT_3433 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complexComplexREACT_6577 (Reactome)
P-TEFb(Cyclin

T1:Cdk9)-containing elongation complex with separated and

uncleaved transcript
ComplexREACT_6686 (Reactome)
PDCD6IP [cytosol]ProteinQ8WUM4 (Uniprot-TrEMBL)
PDCD6IPProteinQ8WUM4 (Uniprot-TrEMBL)
PIC (PreIntegration Complex)ComplexREACT_9179 (Reactome)
POLR2A [nucleoplasm]ProteinP24928 (Uniprot-TrEMBL)
POLR2B [nucleoplasm]ProteinP30876 (Uniprot-TrEMBL)
POLR2C [nucleoplasm]ProteinP19387 (Uniprot-TrEMBL)
POLR2D(2-142) [nucleoplasm]ProteinO15514 (Uniprot-TrEMBL)
POLR2E [nucleoplasm]ProteinP19388 (Uniprot-TrEMBL)
POLR2F(1-127) [nucleoplasm]ProteinP61218 (Uniprot-TrEMBL)
POLR2G [nucleoplasm]ProteinP62487 (Uniprot-TrEMBL)
POLR2H [nucleoplasm]ProteinP52434 (Uniprot-TrEMBL)
POLR2I [nucleoplasm]ProteinP36954 (Uniprot-TrEMBL)
POLR2J [nucleoplasm]ProteinP52435 (Uniprot-TrEMBL)
POLR2K [nucleoplasm]ProteinP53803 (Uniprot-TrEMBL)
POLR2L [nucleoplasm]ProteinP62875 (Uniprot-TrEMBL)
POM121 [nuclear envelope]ProteinQ96HA1 (Uniprot-TrEMBL)
PPIA [cytosol]ProteinP62937 (Uniprot-TrEMBL)
PPIA [extracellular region]ProteinP62937 (Uniprot-TrEMBL)
PPIAProteinP62937 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
PR (Protease)

(P04585) protein

[cytosol]
ProteinP04585 (Uniprot-TrEMBL)
PR (Protease)

(P04585) protein [extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
PR (Protease) (P04585) proteinProteinP04585 (Uniprot-TrEMBL)
PSIP1 [cytosol]ProteinO75475 (Uniprot-TrEMBL)
PSIP1 [nucleoplasm]ProteinO75475 (Uniprot-TrEMBL)
PSIP1ProteinO75475 (Uniprot-TrEMBL)
PiMetaboliteCHEBI:18367 (ChEBI)
RAE1 [nuclear envelope]ProteinP78406 (Uniprot-TrEMBL)
RAN [cytosol]ProteinP62826 (Uniprot-TrEMBL)
RAN [nucleoplasm]ProteinP62826 (Uniprot-TrEMBL)
RANBP1(2-201) [nuclear envelope]ProteinP43487 (Uniprot-TrEMBL)
RANBP1(2-201)ProteinP43487 (Uniprot-TrEMBL)
RANBP2 [cytosol]ProteinP49792 (Uniprot-TrEMBL)
RANGAP1ProteinP46060 (Uniprot-TrEMBL)
RCC1ProteinP18754 (Uniprot-TrEMBL)
REV (P04618) protein [cytosol]ProteinP04618 (Uniprot-TrEMBL)
REV (P04618) protein

[extracellular

region]
ProteinP04618 (Uniprot-TrEMBL)
REV (P04618) protein [nucleoplasm]ProteinP04618 (Uniprot-TrEMBL)
REV (P04618) proteinProteinP04618 (Uniprot-TrEMBL)
RNA Pol II

(hypophosphorylated) complex bound to

DSIF protein
ComplexREACT_6426 (Reactome)
RNA Pol II

(hypophosphorylated):capped

pre-mRNA complex
ComplexREACT_6382 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
ComplexREACT_6659 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
ComplexREACT_6521 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
ComplexREACT_2692 (Reactome)
RNGTT [nucleoplasm]ProteinO60942 (Uniprot-TrEMBL)
RNGTTProteinO60942 (Uniprot-TrEMBL)
RNMT [nucleoplasm]ProteinO43148 (Uniprot-TrEMBL)
RNMTProteinO43148 (Uniprot-TrEMBL)
RPS27A(1-76) [cytosol]ProteinP62979 (Uniprot-TrEMBL)
RPS27A(1-76) [endosome membrane]ProteinP62979 (Uniprot-TrEMBL)
RPS27A(1-76) [plasma membrane]ProteinP62979 (Uniprot-TrEMBL)
RTC (Reverse

Transcription Complex) with RNA

template
ComplexREACT_9085 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
ComplexREACT_9090 (Reactome)
RTC with degraded

RNA template and

minus sssDNA
ComplexREACT_9203 (Reactome)
RTC with duplex DNA

containing discontinuous plus

strand flap
ComplexREACT_9261 (Reactome)
RTC with extending minus strand DNAComplexREACT_9298 (Reactome)
RTC with extending second-strand DNAComplexREACT_9199 (Reactome)
RTC with extensive RNase-H digestionComplexREACT_9290 (Reactome)
RTC with integration competent viral DNAComplexREACT_9124 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
ComplexREACT_9360 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
ComplexREACT_9297 (Reactome)
RTC with minus

strand DNA synthesis initiated from

3'-end
ComplexREACT_9302 (Reactome)
RTC with nicked

minus sssDNA:tRNA

primer:RNA template
ComplexREACT_9226 (Reactome)
RTC with tRNA primer:RNA templateComplexREACT_9371 (Reactome)
RTC without viral RNA templateComplexREACT_9260 (Reactome)
RTComplexREACT_8803 (Reactome)
Ran GTPase:GDPComplexREACT_6416 (Reactome)
Ran-GDPComplexREACT_9732 (Reactome)
Ran-GTPComplexREACT_8980 (Reactome)
Ran:GTPComplexREACT_8632 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexComplexREACT_8366 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP:NPC
ComplexREACT_6537 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ComplexREACT_6428 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ComplexREACT_6601 (Reactome)
Rev multimer-bound

HIV-1 mRNA:CRM1

complex
ComplexREACT_8117 (Reactome)
Rev multimer-bound HIV-1 mRNAComplexREACT_6517 (Reactome)
Rev-bound HIV-1 mRNAComplexREACT_6419 (Reactome)
Rev-multimerREACT_6379 (Reactome)
Rev-multimerREACT_6511 (Reactome)
Reverse

transcriptase/ribonuclease

H [cytosol]
ProteinP04585 (Uniprot-TrEMBL)
Reverse

transcriptase/ribonuclease H [extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
SEH1L-2 [nuclear envelope]ProteinQ96EE3-2 (Uniprot-TrEMBL)
SSRP1 [nucleoplasm]ProteinQ08945 (Uniprot-TrEMBL)
SUPT16H [nucleoplasm]ProteinQ9Y5B9 (Uniprot-TrEMBL) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
SUPT4H1 [nucleoplasm]ProteinP63272 (Uniprot-TrEMBL)
Spliced Env mRNARnaAF033819 (EMBL)
Surface protein

gp120 (P04578)

[cytosol]
ProteinP04578 (Uniprot-TrEMBL)
Surface protein

gp120 [viral

envelope]
ProteinP04578 (Uniprot-TrEMBL)
TAF1 [nucleoplasm]ProteinP21675 (Uniprot-TrEMBL)
TAF10 [nucleoplasm]ProteinQ12962 (Uniprot-TrEMBL)
TAF11 [nucleoplasm]ProteinQ15544 (Uniprot-TrEMBL)
TAF12 [nucleoplasm]ProteinQ16514 (Uniprot-TrEMBL)
TAF13 [nucleoplasm]ProteinQ15543 (Uniprot-TrEMBL)
TAF4 [nucleoplasm]ProteinO00268 (Uniprot-TrEMBL)
TAF4B [nucleoplasm]ProteinQ92750 (Uniprot-TrEMBL)
TAF5 [nucleoplasm]ProteinQ15542 (Uniprot-TrEMBL)
TAF6 [nucleoplasm]ProteinP49848 (Uniprot-TrEMBL)
TAF9 [nucleoplasm]ProteinQ16594 (Uniprot-TrEMBL)
TBP [nucleoplasm]ProteinP20226 (Uniprot-TrEMBL)
TCEA1 [nucleoplasm]ProteinP23193 (Uniprot-TrEMBL)
TCEA1ProteinP23193 (Uniprot-TrEMBL)
TCEB1 [nucleoplasm]ProteinQ15369 (Uniprot-TrEMBL)
TCEB2 [nucleoplasm]ProteinQ15370 (Uniprot-TrEMBL)
TCEB3 [nucleoplasm]ProteinQ14241 (Uniprot-TrEMBL)
TFIIAComplexREACT_5743 (Reactome)
TFIIDComplexREACT_5886 (Reactome)
TFIIEComplexREACT_2368 (Reactome)
TFIIHComplexREACT_3832 (Reactome)
TPR [nucleoplasm]ProteinP12270 (Uniprot-TrEMBL)
TSG101(2-390) [endosome membrane]ProteinQ99816 (Uniprot-TrEMBL)
Tat (P04608) [nucleoplasm]ProteinP04608 (Uniprot-TrEMBL)
Tat (P04608)ProteinP04608 (Uniprot-TrEMBL)
Tat-containing

elongation complex

prior to separation
ComplexREACT_6548 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF phospho

DSIF)
ComplexREACT_6633 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
ComplexREACT_6495 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
ComplexREACT_6536 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexComplexREACT_6496 (Reactome)
Transmembrane

protein gp41

(P04578) [cytosol]
ProteinP04578 (Uniprot-TrEMBL)
Transmembrane

protein gp41 [viral

envelope]
ProteinP04578 (Uniprot-TrEMBL)
Trimeric ENV precursorComplexREACT_164089 (Reactome)
Trimeric ENV precursorComplexREACT_165165 (Reactome)
Trimeric gp120:gp41 oligomerComplexREACT_164721 (Reactome)
Trimeric gp120:gp41 oligomerComplexREACT_165266 (Reactome)
UBA52(1-76) [cytosol]ProteinP62987 (Uniprot-TrEMBL)
UBA52(1-76) [endosome membrane]ProteinP62987 (Uniprot-TrEMBL)
UBA52(1-76) [plasma membrane]ProteinP62987 (Uniprot-TrEMBL)
UBB(1-76) [cytosol]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(1-76) [endosome membrane]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(1-76) [plasma membrane]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(153-228) [cytosol]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(153-228) [endosome membrane]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(153-228) [plasma membrane]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(77-152) [cytosol]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(77-152) [endosome membrane]ProteinP0CG47 (Uniprot-TrEMBL)
UBB(77-152) [plasma membrane]ProteinP0CG47 (Uniprot-TrEMBL)
UBC(1-76) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(1-76) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(1-76) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(153-228) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(153-228) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(153-228) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(229-304) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(229-304) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(229-304) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(305-380) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(305-380) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(305-380) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(381-456) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(381-456) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(381-456) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(457-532) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(457-532) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(457-532) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(533-608) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(533-608) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(533-608) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(609-684) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(609-684) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(609-684) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(77-152) [cytosol]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(77-152) [endosome membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UBC(77-152) [plasma membrane]ProteinP0CG48 (Uniprot-TrEMBL)
UTP [nucleoplasm]MetaboliteCHEBI:15713 (ChEBI)
UbProteinREACT_3316 (Reactome)
VIF (P69723) protein [cytosol]ProteinP69723 (Uniprot-TrEMBL)
VIF (P69723) protein

[extracellular

region]
ProteinP69723 (Uniprot-TrEMBL)
VIF (P69723) protein [nucleoplasm]ProteinP69723 (Uniprot-TrEMBL)
VIF (P69723) proteinProteinP69723 (Uniprot-TrEMBL)
VPR (P69726) protein [cytosol]ProteinP69726 (Uniprot-TrEMBL)
VPR (P69726) protein

[extracellular

region]
ProteinP69726 (Uniprot-TrEMBL)
VPR (P69726) protein [nucleoplasm]ProteinP69726 (Uniprot-TrEMBL)
VPR (P69726) proteinProteinP69726 (Uniprot-TrEMBL)
VPS28 [endosome membrane]ProteinQ9UK41 (Uniprot-TrEMBL)
VPS37A [endosome membrane]ProteinQ8NEZ2 (Uniprot-TrEMBL)
VPS37B [endosome membrane]ProteinQ9H9H4 (Uniprot-TrEMBL)
VPS37C [endosome membrane]ProteinA5D8V6 (Uniprot-TrEMBL)
VPS37D [endosome membrane]ProteinQ86XT2 (Uniprot-TrEMBL)
VPS4A(1-437) [cytosol]ProteinQ9UN37 (Uniprot-TrEMBL)
VPS4B [cytosol]ProteinO75351 (Uniprot-TrEMBL)
VPU (P05919) protein [cytosol]ProteinP05919 (Uniprot-TrEMBL)
VPU (P05919) protein

[extracellular

region]
ProteinP05919 (Uniprot-TrEMBL)
VPU (P05919) protein [nucleoplasm]ProteinP05919 (Uniprot-TrEMBL)
VPU (P05919)ProteinP05919 (Uniprot-TrEMBL)
VTA1 [cytosol]ProteinQ9NP79 (Uniprot-TrEMBL)
Viral core

surrounded by Matrix

layer
ComplexREACT_8910 (Reactome)
Virion Budding ComplexComplexREACT_164706 (Reactome)
Virion with

CD4:gp120 bound to

CCR5/CXCR4
ComplexREACT_8665 (Reactome)
Virion with

fusogenically

activated gp41
ComplexREACT_8472 (Reactome)
Virion with CD4 bound to gp120ComplexREACT_8731 (Reactome)
Virion with exposed

coreceptor binding

sites
ComplexREACT_8974 (Reactome)
Virion with gp41 exposedComplexREACT_8727 (Reactome)
Virion with gp41

forming hairpin

structure
ComplexREACT_8661 (Reactome)
Virion with gp41

fusion peptide in

insertion complex
ComplexREACT_8875 (Reactome)
Vps/Vta1ComplexREACT_27371 (Reactome)
XPO1 [cytosol]ProteinO14980 (Uniprot-TrEMBL)
XPO1 [nucleoplasm]ProteinO14980 (Uniprot-TrEMBL)
XPO1ProteinO14980 (Uniprot-TrEMBL)
XRCC4 [nucleoplasm]ProteinQ13426 (Uniprot-TrEMBL)
XRCC4:DNA ligase IV complexComplexREACT_3745 (Reactome)
XRCC5 [nucleoplasm]ProteinP13010 (Uniprot-TrEMBL)
XRCC6 [nucleoplasm]ProteinP12956 (Uniprot-TrEMBL)
dNTPMetaboliteREACT_9307 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ComplexREACT_116777 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ComplexREACT_116878 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ComplexREACT_165330 (Reactome)
myristoylated Nef

Protein (UniProt:P04601)

[cytosol]
ProteinP04601 (Uniprot-TrEMBL)
myristoylated Nef

Protein (UniProt:P04601) [extracellular

region]
ProteinP04601 (Uniprot-TrEMBL)
myristoylated Nef

Protein

(UniProt:P04601)
ProteinP04601 (Uniprot-TrEMBL)
other viral genomic RNARnaAF033819 (EMBL)
p-NELFE [nucleoplasm]ProteinP18615 (Uniprot-TrEMBL)
p-S2,S5-POLR2A [nucleoplasm]ProteinP24928 (Uniprot-TrEMBL)
p-S5-POLR2A [nucleoplasm]ProteinP24928 (Uniprot-TrEMBL)
p-SUPT5H [nucleoplasm]ProteinO00267 (Uniprot-TrEMBL)
p-SUPT5HProteinO00267 (Uniprot-TrEMBL)
p51 (RT)

[extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
p51 (RT) [cytosol]ProteinP04585 (Uniprot-TrEMBL)
p6 (P04585) [nucleoplasm]ProteinP04585 (Uniprot-TrEMBL)
p6 (P04585) protein [cytosol]ProteinP04585 (Uniprot-TrEMBL)
p6 (P04585) protein

[extracellular

region]
ProteinP04585 (Uniprot-TrEMBL)
p6 (P04591) [nucleoplasm]ProteinP04591 (Uniprot-TrEMBL)
p6 (P04591) protein [cytosol]ProteinP04591 (Uniprot-TrEMBL)
p6 (P04591) protein

[extracellular

region]
ProteinP04591 (Uniprot-TrEMBL)
tRNA-Lysine3REACT_8477 (Reactome)
uncoated viral complexComplexREACT_9366 (Reactome)
viral DNA bound with Integrase in PICComplexREACT_9078 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
ComplexREACT_9308 (Reactome)
viral PIC proteinsComplexREACT_9170 (Reactome)
viral RNA template

being digested by RNase-H (extensive)

[cytosol]
ProteinAF033819 (EMBL)
viral RNA template

degraded by RNase-H

(initial) [cytosol]
ProteinAF033819 (EMBL)
viral RNA template

extensively digested except in PPT region

[cytosol]
ProteinAF033819 (EMBL)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
1-LTR form of circular viral DNAArrowREACT_9045 (Reactome)
2-LTR form of circular viral DNAArrowREACT_9073 (Reactome)
ADPArrowREACT_6134 (Reactome)
ADPArrowREACT_6311 (Reactome)
ADPArrowREACT_6316 (Reactome)
ATPREACT_6134 (Reactome)
ATPREACT_6311 (Reactome)
ATPREACT_6316 (Reactome)
Aborted HIV-1 early elongation complexArrowREACT_6281 (Reactome)
Assembling HIV virionArrowREACT_163644 (Reactome)
Assembling HIV virionREACT_163803 (Reactome)
Autointegrated viral

DNA as smaller

circles
ArrowREACT_9025 (Reactome)
Autointegrated viral

DNA as an inverted

circle
ArrowREACT_9006 (Reactome)
BANF1REACT_9010 (Reactome)
CCR5, CXCR4REACT_7962 (Reactome)
CD4:Env gp120/gp41

hairpin

complex:CCR5/CXCR4
ArrowREACT_8032 (Reactome)
CD4REACT_8009 (Reactome)
CE:Pol II CTD:Spt5 complexArrowREACT_6295 (Reactome)
CTDP1REACT_6206 (Reactome)
CTDP1mim-catalysisREACT_6206 (Reactome)
Cap Binding Complex (CBC)ArrowREACT_6170 (Reactome)
Cap Binding Complex (CBC)ArrowREACT_6297 (Reactome)
Cap Binding Complex (CBC)REACT_6166 (Reactome)
CoA-SHArrowREACT_115774 (Reactome)
CoA-SHArrowREACT_116143 (Reactome)
DSIF complexREACT_6250 (Reactome)
DSIF:NELF:early

elongation complex after limited

nucleotide addition
ArrowREACT_6192 (Reactome)
DSIF:NELF:early

elongation complex after limited

nucleotide addition
REACT_6159 (Reactome)
DSIF:NELF:early elongation complexArrowREACT_6357 (Reactome)
DSIF:NELF:early elongation complexREACT_6170 (Reactome)
DSIF:NELF:early elongation complexREACT_6192 (Reactome)
DSIF:NELF:early elongation complexREACT_6281 (Reactome)
DSIF:NELF:early elongation complexREACT_6297 (Reactome)
ELLREACT_6275 (Reactome)
ELLREACT_6358 (Reactome)
ESCRT-IIIREACT_163632 (Reactome)
ESCRT-IREACT_163632 (Reactome)
ESCRT-Imim-catalysisREACT_115855 (Reactome)
ESCRT-Imim-catalysisREACT_163872 (Reactome)
Early elongation

complex with separated aborted

transcript
ArrowREACT_6159 (Reactome)
Elongin ComplexREACT_6275 (Reactome)
Elongin ComplexREACT_6358 (Reactome)
Encapsidated viral coreArrowREACT_9044 (Reactome)
Encapsidated viral coreREACT_9038 (Reactome)
Envelope glycoprotein gp160ArrowREACT_163787 (Reactome)
Envelope glycoprotein gp160ArrowREACT_163798 (Reactome)
Envelope glycoprotein gp160REACT_163798 (Reactome)
Envelope glycoprotein gp160REACT_163952 (Reactome)
FACT complexREACT_6275 (Reactome)
FACT complexREACT_6358 (Reactome)
FEN1ArrowREACT_9036 (Reactome)
FURINmim-catalysisREACT_163905 (Reactome)
GAG Polyprotein (P04591)ArrowREACT_115916 (Reactome)
GAG Polyprotein (P04591)REACT_115774 (Reactome)
GAG-POL Polyprotein (P04585)REACT_163644 (Reactome)
GAG-POL Polyprotein (P04585)mim-catalysisREACT_163807 (Reactome)
GDPArrowREACT_9507 (Reactome)
GTF2BArrowREACT_6184 (Reactome)
GTF2BArrowREACT_6203 (Reactome)
GTF2BArrowREACT_6226 (Reactome)
GTPREACT_9507 (Reactome)
HIV-1 Polymerase II

(phosphorylated):TFIIF:capped

pre-mRNA
REACT_6166 (Reactome)
HIV-1 Promoter Escape ComplexREACT_6203 (Reactome)
HIV-1 RNA homodimerREACT_163644 (Reactome)
HIV-1 Tat-containing

aborted elongation

complex after arrest
ArrowREACT_6269 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
ArrowREACT_6174 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
REACT_6269 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
REACT_6330 (Reactome)
HIV-1 Tat-containing

paused processive

elongation complex
ArrowREACT_6347 (Reactome)
HIV-1 Tat-containing

paused processive

elongation complex
REACT_6299 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ArrowREACT_6278 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ArrowREACT_6299 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ArrowREACT_6330 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
REACT_6158 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
REACT_6174 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
REACT_6347 (Reactome)
HIV-1 aborted

elongation complex

after arrest
ArrowREACT_6352 (Reactome)
HIV-1 arrested

processive

elongation complex
ArrowREACT_6254 (Reactome)
HIV-1 arrested

processive

elongation complex
REACT_6252 (Reactome)
HIV-1 arrested

processive

elongation complex
REACT_6352 (Reactome)
HIV-1 capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex
ArrowREACT_6166 (Reactome)
HIV-1 capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex
REACT_6206 (Reactome)
HIV-1 closed

pre-initiation

complex
ArrowREACT_6211 (Reactome)
HIV-1 closed

pre-initiation

complex
REACT_6134 (Reactome)
HIV-1 early

elongation complex with hyperphosphorylated

Pol II CTD
ArrowREACT_6297 (Reactome)
HIV-1 early

elongation complex with hyperphosphorylated

Pol II CTD
REACT_6358 (Reactome)
HIV-1 elongation

complex containing

Tat
ArrowREACT_6275 (Reactome)
HIV-1 elongation

complex containing

Tat
REACT_6278 (Reactome)
HIV-1 elongation complexArrowREACT_6358 (Reactome)
HIV-1 initiation

complex with phosphodiester-PPi

intermediate
ArrowREACT_6285 (Reactome)
HIV-1 initiation

complex with phosphodiester-PPi

intermediate
REACT_6333 (Reactome)
HIV-1 initiation complexArrowREACT_6349 (Reactome)
HIV-1 initiation complexREACT_6285 (Reactome)
HIV-1 mRNAREACT_6161 (Reactome)
HIV-1 open

pre-initiation

complex
ArrowREACT_6134 (Reactome)
HIV-1 open

pre-initiation

complex
REACT_6211 (Reactome)
HIV-1 open

pre-initiation

complex
REACT_6349 (Reactome)
HIV-1 paused

processive

elongation complex
ArrowREACT_6214 (Reactome)
HIV-1 paused

processive

elongation complex
REACT_6155 (Reactome)
HIV-1 processive elongation complexArrowREACT_6155 (Reactome)
HIV-1 processive elongation complexArrowREACT_6252 (Reactome)
HIV-1 processive elongation complexREACT_6214 (Reactome)
HIV-1 processive elongation complexREACT_6254 (Reactome)
HIV-1 template

DNA:4-9 nucleotide

transcript hybrid
ArrowREACT_6265 (Reactome)
HIV-1 template DNA

containing promoter with transcript of

2 or 3 nucleotides
ArrowREACT_6203 (Reactome)
HIV-1 template DNA

with first transcript dinucleotide, opened

to +8 position
ArrowREACT_6226 (Reactome)
HIV-1 transcription

complex containing 11 nucleotide long

transcript
ArrowREACT_6208 (Reactome)
HIV-1 transcription

complex containing 11 nucleotide long

transcript
REACT_6240 (Reactome)
HIV-1 transcription

complex containing 4-9 nucleotide long

transcript
REACT_6265 (Reactome)
HIV-1 transcription

complex containing extruded transcript

to +30
ArrowREACT_6148 (Reactome)
HIV-1 transcription

complex containing extruded transcript

to +30
REACT_6234 (Reactome)
HIV-1 transcription

complex containing

transcript to +30
ArrowREACT_6240 (Reactome)
HIV-1 transcription

complex containing

transcript to +30
REACT_6148 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
ArrowREACT_6325 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
REACT_6184 (Reactome)
HIV-1 transcription

complex containing 4 nucleotide long

transcript
ArrowREACT_6184 (Reactome)
HIV-1 transcription

complex containing 4 nucleotide long

transcript
REACT_6172 (Reactome)
HIV-1 transcription

complex containing 9 nucleotide long

transcript
ArrowREACT_6172 (Reactome)
HIV-1 transcription

complex containing 9 nucleotide long

transcript
REACT_6208 (Reactome)
HIV-1 transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
ArrowREACT_6234 (Reactome)
HIV-1 transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
REACT_6220 (Reactome)
HIV-1 transcription complexArrowREACT_6333 (Reactome)
HIV-1 transcription complexREACT_6226 (Reactome)
HIV-1 transcription complexREACT_6325 (Reactome)
HIV-1 unspliced RNAArrowREACT_6318 (Reactome)
HIV-1 unspliced RNAREACT_115916 (Reactome)
HIV-1 unspliced RNAREACT_163953 (Reactome)
HMGA1REACT_9010 (Reactome)
Host genomic DNAREACT_9054 (Reactome)
IN (Integrase) (P04585) proteinArrowREACT_9001 (Reactome)
IN (Integrase) (P04585) proteinArrowREACT_9006 (Reactome)
IN (Integrase) (P04585) proteinArrowREACT_9025 (Reactome)
IN (Integrase) (P04585) proteinArrowREACT_9045 (Reactome)
IN (Integrase) (P04585) proteinArrowREACT_9073 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
ArrowREACT_9004 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
ArrowREACT_9069 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
REACT_9004 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
REACT_9006 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
REACT_9022 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
REACT_9025 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
REACT_9045 (Reactome)
IN bound to sticky

3' ends of viral DNA

in PIC
REACT_9054 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
ArrowREACT_9054 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
REACT_9048 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
mim-catalysisREACT_9048 (Reactome)
Immature HIV virionArrowREACT_163803 (Reactome)
Immature HIV virionREACT_163807 (Reactome)
Integrated provirusArrowREACT_9001 (Reactome)
Integration intermediateArrowREACT_9048 (Reactome)
Integration intermediateREACT_9001 (Reactome)
Ku proteins bound to viral DNAArrowREACT_9022 (Reactome)
Ku proteins bound to viral DNAREACT_9042 (Reactome)
Ku70:Ku80 heterodimerArrowREACT_9073 (Reactome)
Ku70:Ku80 heterodimerREACT_9022 (Reactome)
LIG1ArrowREACT_9036 (Reactome)
MYS-CoAREACT_115774 (Reactome)
MYS-CoAREACT_116143 (Reactome)
MatrixArrowREACT_9044 (Reactome)
Mature HIV virionArrowREACT_163807 (Reactome)
Mature HIV virionREACT_8009 (Reactome)
Multimeric capsid coatArrowREACT_9038 (Reactome)
N-myristoyl GAG (P04591) proteinArrowREACT_115774 (Reactome)
N-myristoyl GAG (P04591) proteinREACT_115708 (Reactome)
NEDD4L(2-975)REACT_163632 (Reactome)
NELF complexREACT_6357 (Reactome)
NMT1(1-?)mim-catalysisREACT_116143 (Reactome)
NMT2mim-catalysisREACT_115774 (Reactome)
NTPArrowREACT_6158 (Reactome)
NTPArrowREACT_6357 (Reactome)
NTPREACT_6158 (Reactome)
NTPREACT_6172 (Reactome)
NTPREACT_6184 (Reactome)
NTPREACT_6192 (Reactome)
NTPREACT_6208 (Reactome)
NTPREACT_6240 (Reactome)
NTPREACT_6278 (Reactome)
NTPREACT_6325 (Reactome)
NTPREACT_6349 (Reactome)
NTPREACT_6357 (Reactome)
Nef Protein (UniProt:P04601)REACT_116143 (Reactome)
Nuclear Pore Complex (NPC)ArrowREACT_6340 (Reactome)
Nuclear Pore Complex (NPC)REACT_6337 (Reactome)
NucleocapsidArrowREACT_8994 (Reactome)
P-TEFb complexREACT_6297 (Reactome)
P-TEFb complexmim-catalysisREACT_6297 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complexREACT_6356 (Reactome)
P-TEFb(Cyclin

T1:Cdk9)-containing elongation complex with separated and

uncleaved transcript
ArrowREACT_6204 (Reactome)
PDCD6IPREACT_163632 (Reactome)
PIC (PreIntegration Complex)ArrowREACT_9010 (Reactome)
PIC (PreIntegration Complex)REACT_9074 (Reactome)
PPIAArrowREACT_9010 (Reactome)
PPIAREACT_163644 (Reactome)
PPiArrowREACT_6172 (Reactome)
PPiArrowREACT_6184 (Reactome)
PPiArrowREACT_6208 (Reactome)
PPiArrowREACT_6240 (Reactome)
PPiArrowREACT_6325 (Reactome)
PPiArrowREACT_6333 (Reactome)
PPiArrowREACT_9039 (Reactome)
PR (Protease) (P04585) proteinArrowREACT_8994 (Reactome)
PSIP1REACT_9010 (Reactome)
PiArrowREACT_6134 (Reactome)
PiArrowREACT_6171 (Reactome)
RANBP1(2-201)ArrowREACT_6171 (Reactome)
RANBP1(2-201)ArrowREACT_6318 (Reactome)
RANBP1(2-201)REACT_9478 (Reactome)
RANGAP1ArrowREACT_6171 (Reactome)
RCC1mim-catalysisREACT_9507 (Reactome)
REACT_115708 (Reactome) Cytosolic N-myristoyl Gag polyprotein is conjugated with a single molecule of ubiquitin. Conjugation is typically to one of two lysine residues in the p6 domain of Gag but can be to lysine residues in the MA, CA, NC, and SP2 domains of the protein. The specific host cell E2 and E3 proteins that mediate Gag ubiquitination have not been identified. The same studies that first identified the p6 ubiquitination sites in Gag also called the biological significance of Gag ubiquitination into question by demonstrating that Gag proteins in which the p6 ubiquitination sites had been removed by mutagenesis could still assemble efficiently into infectious viral particles (Ott et al. 1998, 2000). More recent work, however, has identified additional ubiquitination sites throughout the carboxyterminal region of the Gag polyprotein, and when all of these sites are removed by mutagenesis, both viral assembly involving the mutant Gag polyprotein and infectivity of the resulting viral particles are sharply reduced (Gottwein et al. 2006).
REACT_115774 (Reactome) The amino terminal glycine residue of HIV-1 Gag polyprotein is myristoylated (Henderson et al. 1992). Myristoylation of newly synthesized Gag occurs in the cytosol of the infected host cell, with myristoyl-CoA as the myristate donor and the host cell NMT2 enzyme as the catalyst. Human cells express two isoforms of N-myristoyl transferase (NMT) (Giang and Cravatt 1998). The argumant that the second isoform catalyzes this reaction is indirect, based on the the observations that a stable enzyme:substrate complex forms transiently during the reaction (Farazi et al. 2001), and that Gag polyprotein can be found complexed with NMT2 (but not NMT1) in HIV-1-infected human cells (Hill and Skowronski 2005).
REACT_115855 (Reactome) Monoubiquitinated N-myristoyl Gag polyprotein associates with the ESCRT-1 complex at an endosomal membrane (Eastman et al. 2005; Martin-Serrano et al. 2003; Stuchell et al. 2004).
REACT_115916 (Reactome) Gag is translated from the unspliced viral RNA on free ribosomes in the cytoplasm. The products of the pro and pol genes are also synthesized from the unspliced viral RNA, but never as parts of an independent polyprotein. They are initially contained within the Gag-Pro or Gag-Pro-Pol fusion protein, the product of translational readthrough
REACT_116143 (Reactome) Nef amino terminal myristoylation has been shown to be critical for many of Nef's functions. As expected myristoylated Nef can be identified as co-fractionating with cell membranes and cytoskeletal components.
REACT_163632 (Reactome) The human ESCRT pathway comprises more than 30 different proteins, and this complexity is expanded further by associated regulatory and ubiquitylation machinery. Functional studies have identified a minimal core set of human ESCRT proteins, machinery that is essential for HIV-1 budding. ESCRT-1 recruitment follows an unusal path. The PTAP motif in p6 mimics the ESCRT-1 recruitment motif, bypassing the need for ESCRT-0. The TSG101/ ESCRT-I and ALIX both function by recruiting downstream ESCRT-III and VPS4 complexes, which in turn mediate membrane fission and ESCRT factor recycling.
REACT_163644 (Reactome) Gag assembly leads to formation of the immature lattice. The Gag molecules in the immature virion are extended and oriented radially, with their amino-terminal MA domains bound to the inner membrane leaflet and their carboxy- terminal p6 domains facing the interior of the particle. The GAGPol Pro molecules have arrived at the site of viral assembly in fewer numbers than the Gag protein (20:1). The trimeric gp41:gp120 complex is brought to the plasma membrane by the host vesicular transport system. Only 7-14 trimers per virion. VPU has followed the same ER:Golgi path. Vif, Nef, and Vpr are packaged along with the the HIV genome.
REACT_163666 (Reactome) The VPU protein is produced
REACT_163732 (Reactome) VPU is shuttled through the ER:Golgi protein expression pathway.
REACT_163787 (Reactome) The ENV precursor protein gp160 is synthesized.
REACT_163798 (Reactome) There are numerous N-linked glycosylation sites that are important for infectivity of human immunodeficiency virus type 1. With more than 20 consensus N-linked glycosylation sites in gp120 it is expected that a number are important for virion function.
REACT_163803 (Reactome) The events that lead to the viral component assembly and the recruitment of the ESCRT host machinery are well-characterized. The exact steps that release the immature viral particle are not. Membrane fission is an energy intensive process and an active area of study.
REACT_163807 (Reactome) The proteolytic events that cleave Gag and Gag-Pro-Pol are well characterized, but the event that triggers the protease is not well characterized. The PRGag, that is assembled in the immature virion weakly dimerizes, once PR is cleaved from the proprotein PR dimerizes and becomes an efficient protease. This assembly step may be part of the switch. Once the protease becomes active in the immature virion MA, CA, SP1, NC, SP2, P6, PR, RT, and IN are produced. This event, the production of these fragments would be the switch from immature to mature.
REACT_163857 (Reactome) The cleaved and assembled gp41:gp121 complexes are transport to teh plasma membrane. This complex ultimately arrives via the cellular secretion pathway. Env is an integral membrane protein shuttled through the ER and Golgi where it was glycosylated and cleaved into the gp41 and gp120 subunits. The trimeric complex is brought to the plasma membrane by the host vesicular transport system. Only 7-14 trimers are present per virion.
REACT_163863 (Reactome) Once transported to the plasma membrane the VPU protein will be incorporated into the assembling virus. The Vpu accessory protein is found to be required for efficient virion release from some cell lines but completely dispensible in others.
REACT_163872 (Reactome) Assembling Gag molecules are largely derived from the rapidly diffusing cytoplasmic pool. Gag membrane targeting requires myristoylation and a subset of GAG molecules are shuttled to the plasma membrane in this way.
REACT_163888 (Reactome) The trimeric ENV precursor complex is transported from the ER to the Golgi.
REACT_163905 (Reactome) The trimeric gp160 complexes are cleaved into the gp41 and gp120 subunits by the cellular protease furin.
REACT_163952 (Reactome) The monomeric GP160 ENV precursor protein assembles into a trimer.
REACT_163953 (Reactome) HIV is characterized by the production of multiple-spliced RNA species. The genomic fragmant is processesed creating multiple mRNA fragments.
REACT_6134 (Reactome) After assembly of the complete RNA polymerase II-preinitiation complex, the next step is separation of the two DNA strands. This isomerization step is known as the closed-to-open complex transition and occurs prior to the initiation of mRNA synthesis. In the RNA polymerase II system this step requires the hydrolysis of ATP or dATP into Pi and ADP or dADP (in contrast to the other RNA polymerase systems) and is catalyzed by the XPB subunit of TFIIH. The region of the promoter, which becomes single-stranded , spans from –10 to +2 relative to the transcription start site.

Negative supercoiling in the promoter region probably induces transient opening events and can alleviate requirement of TFIIE, TFIIH and ATP-hydrolysis for open complex formation. ATP is also used in this step by the cdk7-subunit of TFIIH to phosphorylate the heptad repeats of the C-terminal domain of the largest subunit of RNA polymerase II (RPB1) on serine-2

REACT_6140 (Reactome) RanGTP binds to a preformed Rev-CRM1 complex.
REACT_6148 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 transcription complex containing transcript to +30' is present. At the end of this reaction, 1 molecule of 'HIV-1 transcription complex containing extruded transcript to +30' is present.

This reaction takes place in the 'nucleus'.

REACT_6155 (Reactome) Recovery from pausing occurs spontaneously after a variable length of time as the enzyme spontaneously slides forward again. This renders the transcript's 3'-OH terminus realigned with the catalytic Mg2+ site of the enzyme. TFIIS is capable of excising the nascent transcript at 2 or 3 nucleotides upstream of the transcript's 3'-end to reinitiate processive elongation (reviewed by Shilatifard et al., 2003).
REACT_6158 (Reactome) This event was inferred from the corresponding human Poll II transcription elongation event.
REACT_6159 (Reactome) At the beginning of this reaction, 1 molecule of 'DSIF:NELF:early elongation complex after limited nucleotide addition' is present. At the end of this reaction, 1 molecule of 'Early elongation complex with separated aborted transcript' is present.

This reaction takes place in the 'nucleus'.

REACT_6161 (Reactome) Nuclear export of the unspliced and partially spliced HIV-1 transcripts requires the association of the HIV-1 Rev protein with a cis-acting RNA sequence known as the Rev Response Element (RRE) located within the env gene. The RRE forms a stem loop structure that associates with an arginine-rich RNA binding motif (ARM) within Rev.
REACT_6166 (Reactome) The cap binding complex binds to the methylated GMP cap on the nascent mRNA transcript.
REACT_6170 (Reactome) The association between Tat, TAR and P-TEFb is believed to bring the catalytic subunit of P-TEFb(Cyclin T1:Cdk9) in close proximity to Pol II where it hyperphosphorylates the CTD of Pol II (Herrmann et al., 1995; Zhou et al. 2000). In the presence of Tat, P-TEFb(Cyclin T1:CDK9) has been shown to phosphorylate serine 5 in addition to serine 2 suggesting that modification of the substrate specificity of CDK9 may play a role in the ability of Tat to promote transcriptional elongation (Zhou et al. 2000).
REACT_6171 (Reactome) Ran-GAP, a Ran-specific GTPase-activating protein converts Ran-GTP to Ran-GDP, producing a Ran-GTP gradient across the nuclear membrane.
REACT_6172 (Reactome) Formation of the second phosphodiester bond creates a 3-nt product. This transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. At this stage pausing by RNA polymerase II may result in repeated slippage and reextension of the nascent RNA. The transcription complex still requires continued ATP-hydrolysis by TFIIH for efficient promoter escape. Basal transcription factor TFIIE dissociates from the initiation complex before position +10.

Basal transcription factor TFIIF may reassociate and can stimulate transcription elongation at multiple stages. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension, eventually reaching an open region from -9 to +9.

REACT_6174 (Reactome) RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. It is suggested that, arrest leads to extrusion of displaced transcripts 3'-end through the small pore near the Mg2+ ion. Pol II arrest may lead to abortive termination of elongation due to irreversible trapping of the 3'-end of the displaced transcript in the pore (reviewed by Shilatifard et al., 2003).
REACT_6184 (Reactome) Formation of the third phosphodiester bond creates a 4-nt product. This commits the initiation complex to promoter escape. The short 4-nt transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. Inhibition of ATP-hydrolysis by TFIIH does not lead to collapse of the open region any longer. The transcription complex has lost the sensitivity to single-stranded oligo-nucleotide inhibition. However, ATP-hydrolysis and TFIIH are required for efficient promoter escape. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +4.
REACT_6192 (Reactome) In the absence of Tat, transcriptional elongation beyond position +59 does not occur (Kao et al., 1987).
REACT_6203 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 Promoter Escape Complex' is present. At the end of this reaction, 1 molecule of 'TFIIA', 1 molecule of 'TFIIH', 1 molecule of 'HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotides', 1 molecule of 'TFIIE', 1 molecule of 'TFIID', 1 molecule of 'TFIIB', and 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex' are present.

This reaction takes place in the 'nucleus'.

REACT_6204 (Reactome) This event was inferred from the corresponding human Poll II transcription elongation event.
REACT_6206 (Reactome) This HIV-1 event was inferred from the corresponding human RNA Pol II transcription event. FCP1 dephosphorylates RNAP II in ternary elongation complexes as well as in solution and, therefore, is thought to function in the recycling of RNAP II during the transcription cycle. Biochemical experiments suggest that human FCP1 targets CTDs that are phosphorylated at serine 2 (CTD-serine 2) and/or CTD-serine 5. It is also observed to stimulate elongation independent of its catalytic activity. Dephosphorylation of Ser2 - phosphorylated Pol II results in hypophosphorylated form that disengages capping enzymes (CE).
REACT_6208 (Reactome) Formation of phosphodiester bonds nine and ten creates RNA products, which do not dissociate from the RNA pol II initiation complex. The transcription complex has enter the productive elongation phase. TFIIH and ATP-hydrolysis are required for efficient promoter escape. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. The region upstream from the transcription start site (-9 to -3) collapses to the double-stranded state. TFIIH remains associated to the RNA pol II initiation complex.
REACT_6211 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 open pre-initiation complex' is present. At the end of this reaction, 1 molecule of 'HIV-1 closed pre-initiation complex' is present.

This reaction takes place in the 'nucleus'.

REACT_6214 (Reactome) Pol II pausing is believed to result from reversible backtracking of the Pol II enzyme complex by ~2 to 4 nucleotides. This leads to misaligned 3'-OH terminus that is unable to be an acceptor for the incoming NTPs in synthesis of next phosphodiester bond (reviewed by Shilatifard et al., 2003).
REACT_6220 (Reactome) At the beginning of this reaction, 1 molecule of 'mRNA capping enzyme', and 1 molecule of 'HIV-1 transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30' are present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present.

This reaction takes place in the 'nucleus'.

REACT_6226 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 transcription complex' is present. At the end of this reaction, 1 molecule of 'TFIIA', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', 1 molecule of 'TFIID', 1 molecule of 'TFIIB', 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex', and 1 molecule of 'HIV-1 template DNA with first transcript dinucleotide, opened to +8 position' are present.

This reaction takes place in the 'nucleus'.

REACT_6228 (Reactome) In order for Rev to function, multiple molecules must bind sequentiallly to the RRE (Malim and Cullen 1991).
REACT_6234 (Reactome) Phosphorylation of serine 5 residue at the CTD of pol II largest subunit is an important step signaling the end of initiation and escape into processive elongation processes. Cdk7 protein subunit of TFIIH phosphorylates RNA Pol II CTD serine 5 residues on its heptad repeats.
REACT_6240 (Reactome) RNA polymerase II transcription complexes are susceptible to transcriptional stalling and arrest, when extending nascent transcripts to 30-nt. This susceptibility depends on presence on down-stream DNA, the particular DNA-sequence of the template and presence of transcription factors. Transcription factor TFIIH remains associated to the RNA pol II elongation complex until position +30. At this stage transcription elongation factor TFIIS can rescue stalled transcription elongation complexes. The transcription bubble varies between 13- and 22-nt in size.
REACT_6250 (Reactome) This HIV-1 event was inferred from the corresponding human RNA Pol II transcription event. DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160) (Wada et al. 1998). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding. Spt5 subunit of DSIF can be phosphorylated by P-TEFb (Ivanov et al. 2000).
REACT_6252 (Reactome) TFIIS reactivates arrested RNA Pol II directly interacting with the enzyme resulting in endonucleolytic excision of nascent transcript ~7-14 nucleotides upstream of the 3' end. This reaction is catalyzed by the catalytic site and results in the generation of a new 3'-OH terminus that could be used for re-extension from the correctly base paired site (reviewed by Shilatifard et al., 2003).
REACT_6254 (Reactome) RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. It is suggested that, arrest leads to extrusion of displaced transcripts 3'-end through the small pore near the Mg2+ ion. Pol II arrest may lead to abortive termination of elongation due to irreversible trapping of the 3'-end of the displaced transcript in the pore (reviewed by Shilatifard et al., 2003).
REACT_6265 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 transcription complex containing 4-9 nucleotide long transcript' is present. At the end of this reaction, 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', 1 molecule of 'HIV-1 template DNA:4-9 nucleotide transcript hybrid', and 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex' are present.

This reaction takes place in the 'nucleus'.

REACT_6269 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 Tat-containing arrested processive elongation complex' is present. At the end of this reaction, 1 molecule of 'HIV-1 Tat-containing aborted elongation complex after arrest' is present.
This reaction takes place in the 'nucleus'.
REACT_6275 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT complex', 1 molecule of 'Elongin Complex', 1 molecule of 'TFIIH', 1 molecule of 'RNA polymerase II elongation factor ELL', 1 molecule of 'Tat-containing early elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF phospho DSIF)', and 1 molecule of 'TFIIS protein' are present. At the end of this reaction, 1 molecule of 'HIV-1 elongation complex containing Tat' is present.

This reaction takes place in the 'nucleus'.

REACT_6278 (Reactome) This HIV-1 event was inferred from the corresponding human RNA Pol II transcription event. High-resolution structures of free, catalytically active yeast Pol II and of an elongating form reveal that Pol II elongation complex includes features like:
- RNA-DNA hybrid, an unwound template ahead of 3'-OH terminus of growing transcript and an exit groove at the base of the CTD, possibly for dynamic interaction of processing and transcriptional factors.
- a cleft or channel created by Rpb1 and Rpb2 subunits to accommodate DNA template, extending to Mg2+ ion located deep in the enzyme core
-a 50 kDa "clamp" with open confirmation in free polymerase, allowing entry of DNA strands but closed in the processive elongation phase.
The clamp is composed of portions of Rpb1,Rpb2 and Rpb3 , five loops or "switches" that change from unfolded to well-folded structures stabilizing the elongation complex, and a long "bridging helix" that emanates from Rpb1 subunit, crossing near the Mg2+ ion. The bridging helix is thought to "bend" to push on the base pair at the 3'-end of RNA-DNA hybrid like a ratchet, translocating Pol II along the DNA (Cramer et al.,2001; Gnatt et al.,2001).In addition to its dynamic biochemical potential, Pol II possess a repertoire of functions to serve as a critical platform of recruiting and coordinating the actions of a host of additional enzyme and proteins involved in various pathways.

REACT_6281 (Reactome) In the early elongation phase, shorter transcripts typically of ~30 nt in length are generated due to random termination of elongating nascent transcripts. This abortive cessation of elongation has been observed mainly in the presence of DSIF-NELF bound to Pol II complex. (Reviewed in Conaway et al.,2000; Shilatifard et al., 2003 ).
REACT_6285 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 initiation complex' is present. At the end of this reaction, 1 molecule of 'HIV-1 initiation complex with phosphodiester-PPi intermediate' is present.

This reaction takes place in the 'nucleus'.

REACT_6295 (Reactome) The capping enzyme interacts with the Spt5 subunit of transcription elongation factor DSIF. This interaction may couple the capping reaction with promoter escape or elongation, thereby acting as a “checkpoint� to assure that capping has occurred before the polymerase proceeds to make the rest of the transcript.
REACT_6297 (Reactome) The association between Tat, TAR and P-TEFb is believed to bring the catalytic subunit of P-TEFb(Cyclin T1:Cdk9) in close proximity to Pol II where it hyperphosphorylates the CTD of Pol II (Herrmann et al., 1995; Zhou et al. 2000). In the presence of Tat, P-TEFb(Cyclin T1:CDK9) has been shown to phosphorylate serine 5 in addition to serine 2 suggesting that modification of the substrate specificity of CDK9 may play a role in the ability of Tat to promote transcriptional elongation (Zhou et al. 2000).
REACT_6298 (Reactome) At the beginning of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex with activated GT' is present.

This reaction takes place in the 'nucleus'.

REACT_6299 (Reactome) Recovery from pausing occurs spontaneously after a variable length of time as the enzyme spontaneously slides forward again. This renders the transcript's 3'-OH terminus realigned with the catalytic Mg2+ site of the enzyme. TFIIS is capable of excising the nascent transcript at 2 or 3 nucleotides upstream of the transcript's 3'-end to reinitiate processive elongation (reviewed by Shilatifard et al., 2003).
REACT_6311 (Reactome) Phosphorylation of the RD subunit of NEFL by P-TEFb(Cyclin T1:Cdk9) results in the dissociation of NEFL from TAR as well as the conversion of NEFL to an elongation factor (Fujinaga et al., 2004)
REACT_6316 (Reactome) Phosphorylation of the Spt5 subunit of DSIF by P-TEFb(Cyclin T1:Cdk9) results in the conversion of DSIF to an elongation factor (Ivanov al. 2000).
REACT_6318 (Reactome) The association of RanBp1 with RanGTP:CRM1:Rev promotes disassembly of the complex and release of the Rev:RNA cargo.
REACT_6325 (Reactome) Formation of the second phosphodiester bond creates a 3-nt product. This short transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. The transcription complex still requires continued ATP-hydrolysis by TFIIH and remains sensitive to single-stranded oligo-nucleotide inhibition.

The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +3.

REACT_6330 (Reactome) TFIIS reactivates arrested RNA Pol II directly interacting with the enzyme resulting in endonucleolytic excision of nascent transcript ~7-14 nucleotides upstream of the 3' end. This reaction is catalyzed by the catalytic site and results in the generation of a new 3'-OH terminus that could be used for re-extension from the correctly base paired site (reviewed by Shilatifard et al., 2003).
REACT_6333 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 initiation complex with phosphodiester-PPi intermediate' is present. At the end of this reaction, 1 molecule of 'HIV-1 transcription complex', and 1 molecule of 'pyrophosphate' are present.

This reaction takes place in the 'nucleus'.

REACT_6337 (Reactome) The Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP complex associates with the NPC.
REACT_6340 (Reactome) Crm1 is a nucleocytoplasmic transport factor that is believed to interact with nucleoporins facilitating docking of the RRE-Rev-CRM1-RanGTP complex to the nuclear pore and the translocation of the complex across the nuclear pore complex (see Cullen 1998) Crm1 has been found in complex with two such nucleoporins, CAN/Nup214 and Nup88 which have been shown to be components of the human nuclear pore complex (Fornerod et al., 1997).
REACT_6347 (Reactome) Pol II pausing is believed to result from reversible backtracking of the Pol II enzyme complex by ~2 to 4 nucleotides. This leads to misaligned 3'-OH terminus that is unable to be an acceptor for the incoming NTPs in synthesis of next phosphodiester bond (reviewed by Shilatifard et al., 2003).
REACT_6349 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 open pre-initiation complex', and 2 molecules of 'NTP' are present. At the end of this reaction, 1 molecule of 'HIV-1 initiation complex' is present.

This reaction takes place in the 'nucleus'.

REACT_6352 (Reactome) At the beginning of this reaction, 1 molecule of 'HIV-1 arrested processive elongation complex' is present. At the end of this reaction, 1 molecule of 'HIV-1 aborted elongation complex after arrest' is present.

This reaction takes place in the 'nucleus'.

REACT_6356 (Reactome) Tat associates with the Cyclin T1 subunit of P-TEFb (Cyclin T1:Cdk9) through a region of cysteine-rich and core sequences referred to as the ARM domain within Tat (Wei et al., 1998; see also Herrmann 1995). This interaction is believed to involve metal ions stabilized by cysteine residues in both proteins (Bieniasz et al., 1998; Garber et al., 1998).
REACT_6357 (Reactome) This HIV-1 event was inferred from the corresponding human RNA Pol II transcription event. NELF complex is a ~ 300 kDa multiprotein complex composed of 5 peptides (A - E): ~66,61,59,58 and 46 kDa (Yamaguchi et al 1999). All these peptides are required for NELF-mediated inhibition of Pol II elongation. NELF complex has been reported to bind to the pre-formed DSIF:RNA Pol II complex that may act as a scaffold for its binding. NELF-A is suspected to be involved in Wolf-Hirschhorn syndrome. Binding of DSIF:NELF to RNA Pol II CTD results in abortive termination of early elongation steps by the growing transcripts.
REACT_6358 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT complex', 1 molecule of 'HIV-1 early elongation complex with hyperphosphorylated Pol II CTD', 1 molecule of 'Elongin Complex', 1 molecule of 'TFIIH', 1 molecule of 'RNA polymerase II elongation factor ELL', and 1 molecule of 'TFIIS protein' are present. At the end of this reaction, 1 molecule of 'HIV-1 elongation complex' is present.

This reaction takes place in the 'nucleus'.

REACT_7953 (Reactome) HIV-1 infection of target cells depends on the sequential interaction of the gp120 glycoprotein with the cellular CD4 receptor as well as members of the chemokine receptor family, such as CCR5. Upon interaction with the cellular CD4 receptor, gp120 undergoes a conformation change which allows interaction with these chemokine receptors to occur. Studies indicate that upon binding to CD4, this conformational change results in a repositioning of V1 and V2 loops of gp120, and exposes or forms the "bridging sheet domain" epitopes, which are then available for co-receptor (chemokine receptor) binding along with other domains of gp120. These epitopes are recognized by 17b, a member of a class of antibodies that recognize CD4-induced (CD4i) epitopes (Kwong et al., 1998, Rizzuto et al., 1998, Zhang et al., 1999).
REACT_7962 (Reactome) Once the viral gp120 protein has bound to cellular CD4, its bridging sheet region becomes exposed/formed as a result of conformation changes in the V1 and V2 loops as well as a conformational change in the gp120 core domain. Once this region is exposed, it is free to bind the HIV co-receptors CCR5 or CXCR4 (also known as chemokine receptors). Different viruses use different co-receptors (CCR5 or CXCR4) for entry, and many studies investigated the structural determinants of interaction between gp120 and the co-receptor.
Studies of CCR5 binding by gp120 revealed that active regions in the second extracellular loop (ECL2), the N-terminal extracellular domain (specifically the NYYTSE motif) and at the junction between the fifth transmembrane domain and third cytoplasmic loop of the receptor are important for viral attachment and subsequent fusion. The N-terminal region likely interacts with the core of gp120 (bridging sheet and adjacent regions) and the base of V3, while ECL2 may be important for interacting with the tip of V3. The transmembrane 5 / cytoplasmic loop 3 junction of CCR5 has been shown to influence the conformation of the receptor which allows for subsequent binding of gp120 (Wang et al.,1999). Deletion of the V3 loop in gp120 abolished Env interaction with co-receptor without affecting the binding of soluble gp120 to CD4, underscoring the importance of this loop in chemokine receptor, but not CD4, binding. Furthermore, the V3 loop is a major determinant of coreceptor specificity, with amino acid at positions 11 and 25 being partly predictive of CCR5 or CXCR4 use. Single amino acid changes in V3 can alter coreceptor use, however sequences outside of V3 can also contribute to coreceptor specificity.

REACT_8003 (Reactome) The HIV protein known as gp41 is a transmembrane protein which is considered the major mediator of fusion of extracellular virions to the target cells in the host. HIV gp120 and gp41 proteins form non-covalently linked oligomers on the surface of virions. The gp41 subunit of the oligomer is anchored in the viral membrane and contains a non-polar fusion peptide at its N-terminus. Upon CD4 and receptor binding, gp120 undergoes a second conformation change. The conformation change exposes gp41 which continues to mediate fusion of the viral envelope with the host plasma membrane. Electron microscopy and circular dichroism measurements of the gp41 protein suggest a rod-like conformation with a high alpha-helical content. Although some studies suggest that gp41must dissociate from gp120 in order to cause fusion between HIV envelope and the target cell plasma membrane, evidence on this point is not conclusive.
REACT_8009 (Reactome) CD4, located on the host cell membrane, is the main cellular receptor for the HIV protein gp120, which aids in mediating viral entry into target cells. The initial step in this cascade of events is the binding of viral gp120 protein to its host receptor, CD4. The key binding sites in CD4 for interaction with gp120 are located in the amino-terminal part of the CD4 molecule, distal to the transmembrane domain. The gp120 protein forms an oligomer (trimer) on the viral membrane with each gp120 protein containing variable domains (known as loops) and conservative domains. The V3 loop is also often obscured by gp120 glycosylation. Crystallization studies of CD4 suggest that the molecule has two immunoglobulin like domains important for the CD4/gp120 interaction, with one of the domains (D1) playing a more prominent role. Further studies suggest the Phe 43 and Arg 59 residues of CD4 play a major role in complex formation. Crystallization of gp120 shows that the polypeptide chain is folded into two major domains (an "inner" and "outer" domain with respect to the N and C termini), with the distal end of the “outer� domain containing the V3 loop. Studies of CD4 complexed with gp120 show that CD4 is bound to gp120 in a depression which is formed at the interface between the inner and outer domains. The complex itself is held together through van der Waals forces and hydrogen bonding.
REACT_8010 (Reactome) The gp41 glycoprotein contains N- and C-terminal heptad repeats, which form a stable six-helical bundle. This six-helix bundle represents a fusion-active gp41 core, and its conformation is critical for membrane fusion. Among the interactions necessary for the six helix bundle conformation is the formation of a salt bridge between the Asp632 residue in the C-terminal heptad repeat and the Lys574 terminal in the N-terminal coiled-coil. Disruption of this interaction has been found to lead to destabilization of the six helix bundle formation, with a subsequent severe reduction in viral fusion activity. Also, the N-terminal heptad repeat alone was found to be important in viral fusion, as removal or truncation of this repeat reduced the fusion activity of the peptide even when the adjacent, full length N-terminal fusion peptide was in place. The bundle itself is formed during the fusion process, prior to pore formation but after insertion of the gp41 fusion peptide into the target cell membrane. Upon insertion of the fusion peptide, the three N-terminal helices of gp41 adjacent to the target cell membrane and three C-terminal helices adjacent to the viral membrane undergo a conformational change which brings them into close proximity with one another, creating a six-helix bundle and leading to eventual fusion.

REACT_8020 (Reactome) Insertion of the N-terminal fusion peptide of the HIV gp41 protein is the first step in the fusion of viral and target cell membranes. Substitutions of polar amino acids at residues 2, 9, 15 and 26 of the N terminus of this peptide completely eliminated its ability to cause fusion, implicating these residues in gp41’s role in insertion and fusion. Studies have also shown that mutations in a stretch of residues from 36-64(568 to 596 of ENV protein) caused gp41 to become partially or completely defective in mediating membrane fusion, suggesting that conformation of the peptide is important for proper insertion and fusion to occur.
REACT_8023 (Reactome) Fusion of HIV with target cell plasma membranes is mediated largely by the gp41 glycoprotein. This glycoprotein contains a stretch of strongly hydrophobic amino acids flanked by a series of polar amino acids at its N terminus. Subsequent to the second conformation change in gp120, the N-terminal fusion peptide of gp41 adopts a position which brings it into close proximity with the target cell plasma membrane. As gp41 is found in trimers within the viral membrane, the resulting structure of this conformational change is often referred to as a “prong�, in which three N-terminal peptides extend towards the target cell plasma membrane. The process of fusion begins at this time, with the N-terminus of gp41 inserting itself into the membrane of the target cell.
REACT_8032 (Reactome) With the transition of gp41 into the six-helix bundle, fusion of the viral and target cell membranes begins to take place. The specifics of fusion are not completely clear, but it is understood that fusion proceeds after insertion of the gp41 fusion peptide, which results in curvature of viral and target cell membranes. This results in a state of hemi-fusion, where only the outer lipid bilayers of each membrane are fused, whereas membrane leaflets that are distal with respect to the intermembrane gap remain separate at this stage. Hemi-fusion allows the exchange of lipids between the contacting leaflets, whereas the exchange of aqueous content between the virus and the cell remains blocked. The next step in fusion is the merger of the distal leaflets, leading to the formation of a nascent fusion pore, which leads to mixing of viral and cellular contents. Studies of fusion of Influenza virus suggested that multiple hairpin structures may form a narrow fusion pore which subsequently expands to a larger opening. In the case of HIV, this larger opening allows for passage of the Matrix-surrounded viral core out of the virus and into the host cell cytoplasm.
REACT_8992 (Reactome) After the second jump, elongation of the plus and minus strands continues. The elongation process requires strand displacement, which RT can mediate, at least in vitro (Huber et al. 1989; Hottiger et al. 1994; Rausch and Le Grice 2004). The final product is a blunt-ended linear duplex DNA with a discontinuity in its "plus" strand at the site of the cPPT sequence motif.
REACT_8994 (Reactome) Reverse transcription complex is a transitory structure where reverse transcription takes place. Initially, it is likely identical to the RNA-protein complex found inside the virion core. Upon maturation, it may shed some HIV proteins (such as MA or Vpr) and incorporate cellular proteins (such as INI1 or PML).
REACT_8999 (Reactome) RNase H catalyzes the precise cleavage of the bonds linking the primer tRNA attached to the minus-strand DNA, the 3' PPT RNA primer to the plus-strand strong-stop DNA, and the cPPT primer to the stretch of plus-strand DNA whose synthesis it primed. In each case, precise cleavage near the RNA-DNA junction occurs (Pullen et al. 1992). HIV-1 RT is the only reverse transcriptase that cleaves the tRNA:DNA junction so as to leave a ribo A residue from the tRNA at the 5' end of the minus strand.

While a single RT heterodimer could in principle catalyze DNA synthesis and primer RNA:DNA bond cleavage, evidence from several in vitro systems suggests that separate RT heterodimers are likely to catalyze these two reactions (Rausch and Le Grice 2004).

REACT_9001 (Reactome) The mechanism by which the integration reaction is completed has not been fully clarified. Unfolding of the integration intermediate resulting from the IN-catalyzed transesterification produces a branched DNA molecule. Denaturation of the host DNA between the points of joining produces DNA gaps at each host-virus DNA junction. How these gaps are repaired is unclear. Well studied host cell gap repair enzymes can carry out this repair step on model virus-host DNA junctions in vitro, providing candidate enzymes. However, efforts to show importance in vivo are complicated by the fact that the functions are either redundant or lethal when mutated.

Because the strand transfer complex formed at the completion of integration is quite stable, there may be a requirement for a disassembly step to remove integrase and potentially other proteins to allow access of the gap repair machinery.
In order to complete the last stages of integration, the viral proteins must be removed, and the gaps at the host virus DNA junctions repaired. The sequence in which the dissembly of PIC occus is not yet understood.

REACT_9004 (Reactome) HIV can infect non-dividing cells, implying that the PIC must be able to traverse the nuclear membrane. In contrast, simple retroviruses such as MLV can only infect cells once they have passed through mitosis, potentially because they require breakdown of the nucleus to access chromosomal integration sites. The mechanism of nuclear localization is controversial. A variety of proposals have been made for nuclear localization sequences (NLS) in the PIC, but most of those have now been shown to be dispensible for HIV integration. According to a new idea from Yamashita and Emerman, it may be that the PIC is imported into the nucleus by a default pathway, while MLV PICs are retained in the cytoplasm because capsid protein is stably associated with PICs.

REACT_9006 (Reactome) Following the integrase-mediated strand transfer reaction of autointegration, the integration complex must be disassembled and the gapped intermediate repaired, just as in normal integration.
REACT_9010 (Reactome) Concomitant with the completion of reverse transcription, the pre-integration complex is formed by shedding of some viral proteins from the viral core, and binding of cellular proteins, thereby yielding complexes capable of integration. The terminal cleavage reaction takes place in the cytoplasm, where two nucleotides are removed from each viral DNA 3' end. This serves to remove heterogeneous extra bases from the viral DNA ends occasionally added by reverse transcription, thereby yielding a homogeneous substrate for downstream steps, and also serves to stablilize the PIC. The DNA in PICs is considerably compacted relative to its length when fully extended, probably due to binding of proteins in addition to the viral integrase. These proteins are not fully clarified, due to the difficulty of biochemical analysis of small amounts of material, but candidates include the viral NC and MA proteins, and the cellular HMGA, BAF, and PSIP1/LEDGF/p75 proteins. Purified integrase is capable of carrying out the terminal cleavage and initial strand transfer reactions.
REACT_9014 (Reactome) The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis (Kati et al. 1992), so the product of the combined DNA synthesis and RNA degradation events catalyzed by the RT heterodimer mediating minus-strand strong stop DNA (-sssDNA) synthesis is a DNA segment still duplexed with extended viral genomic RNA fragments. In vitro, other RT heterodimers bind the remaining RNA:DNA heteroduplexes and their RNase H domains further degrade the viral genomic RNA (Wisniewski et al. 2000a, b).
REACT_9015 (Reactome) Retroviruses use cellular tRNAs as primers for reverse transcription of the viral genomic RNA (Mak and Kleiman 1997). The primer tRNA is selectively packaged during assembly of retrovirus particles. In the case of HIV-1, lysine tRNAs are preferentially incorporated during retroviral packaging, and lysine tRNA 3, the specific isoacceptor form that serves as a primer for reverse transcription, anneals to the PBS (primer binding site) within the U5 region of the viral genomic RNA. This association appears to be mediated by the viral reverse transcriptase (RT) protein, possibly its "thumb" and "connection" domains (Jiang et al. 1993; Mak et al. 1994; Mishima and Steitz 1995).
REACT_9022 (Reactome) The Ku protein can be found bound to active PICs in the cytoplasm. However, ligation of the viral DNA ends to form 2-LTR circles takes place in the nucleus.
REACT_9025 (Reactome) Following the integrase-mediated strand transfer reaction of autointegration, the integration complex must be disassembled and the gapped intermediate repaired, just as in normal integration.
REACT_9033 (Reactome) The minus strand strong stop DNA (-sssDNA) is transferred to the 3' end of the HIV-1 genomic RNA, where the 3' end of the -sssDNA anneals to the viral genomic R sequence motif (Ghosh et al. 1995; Klaver and Berkhout 1994; Ohi and Clever 2000; Telesnitsky and Goff 1997). Viral NC (nucleocapsid) protein may play a role in this transfer (Driscoll and Hughes 2000).
REACT_9036 (Reactome) The fate of the discontinuous viral DNA duplex synthesized in the cytosol of an infected cell by HIV-1 reverse transcriptase is not entirely clear. Studies of some viral systems suggest that this discontinuous structure is required for passage of the viral duplex DNA into the nucleus while there are evidence contrary to this observation. Studies in vitro indicate that human nuclear flap endonuclease and DNA ligase can remove the flap and seal the plus-strand discontinuity in HIV-1 DNA (Miller et al. 1995; Rausch and Le Grice 2004; Rumbaugh et al. 1998), although role of flap is not yet clear.
REACT_9038 (Reactome) The HIV capsid protein (p24) surrounds the viral genome and associated proteins to make up the viral core. Dissolution of the viral capsid allows for release of the viral RNA and other proteins such as Vpr into the cytoplasm, which will subsequently form the Reverse Transcription Complex. Dissolution of capsid proteins may be caused by interaction with cellular proteins, e.g. TRIM5, or may occur in a similar fashion to that of matrix dissolution; as a reaction to a change in pH. Indeed, studies observing capsid assembly and conformation show that this protein-protein interaction is heavily influenced by even small changes in pH (pH7.0 to 6.8).
REACT_9039 (Reactome) To catalyze DNA synthesis, retroviral reverse transcriptase requires a primer strand to extend and a template strand to copy. For HIV-1, the primer is the 3'-end of a partially unwound lysine(3) tRNA annealed to the PBS (primer binding site) 179 bases from the 5' end of the retroviral genomic RNA (Isel et al. 1995). Reverse transcription of the viral genomic RNA proceeds from the bound tRNA primer to the 5' end of the viral RNA, yielding a minus-strand strong-stop DNA (-sssDNA) complementary to the R and U5 elements of the HIV-1 viral genome, as shown in the figure below (Telesnitsky and Goff 1997; Jonckheere et al. 2000). The reaction takes place in the host cell cytosol, and is catalyzed by the reverse transcriptase activity of the HIV-1 RT heterodimer.

NucleoCapsid (NC) protein prevents self-priming by generating or stabilizing a thermodynamically favored RNA-DNA heteroduplex instead of the kinetically favored TAR hairpin seen in reverse transcription experiments in vitro (Driscoll and Hughes 2000).

REACT_9040 (Reactome) As the reverse transcriptase activity of the HIV-1 RT heterodimer catalyzes the extension of the minus-strand DNA, the RNaseH activity catalyzes the degradation of the complementary viral genomic RNA sequences. Telesnitsky and Goff (1993) observed that two defective forms of reverse transcriptase can complement to restore retroviral infectivity. The RNase H active site is positioned within the HIV-1 RT heterodimer so as to attack the RNA strand of the RNA:DNA duplex at a point 18 bases behind the site of reverse transcription (Furfine and Reardon 1991; Ghosh et al. 1995; Gopalakrishnan et al. 1992; Wohrl and Moelling 1990). The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis and the level of its activity in vivo is unclear, however (Kati et al. 1992). The product of these combined DNA synthesis and RNA degradation events is a DNA strand still duplexed with extended viral genomic RNA fragments.
REACT_9042 (Reactome) XRCC4 and DNA ligase 4 are recruited to the complex containing viral DNA.
REACT_9044 (Reactome) After fusion of the viral membrane with the target cell membrane, the viral core, which is surrounded by a layer of Matrix (p17) proteins, is exposed to the cytoplasm. Disintegration of the Matrix layer allows for the conical-shaped viral core to be fully released, and allow for viral capsid dissociation and eventually reverse transcription. Dissociation of the Matrix layer is not well characterized, but is believed to occur due to disruption of protein-protein interactions as a result of the conditions of the cytoplasm (including pH), which differ from that of the internal viral structure.
REACT_9045 (Reactome) The 1-LTR circle can be formed by either of two pathways. The first involves a failure to complete reverse transcription; the second, annotated here, follows the completion of reverse transcription and is mediated by cellular enzymes. In this pathway, the action of host cell homologous recombination enzymes on the long terminal repeat (LTR) termini of the viral DNA results in formation of a single LTR. This reaction probably takes place after partial or complete disassembly of the PIC to expose the viral DNA. Repair of this intermediate as in the late stages of homologous recombination pathways results in formation of the 1-LTR circle. Mutations in the Mre11/Rad50/NBS pathway influence the formation of 1-LTR circles.
REACT_9046 (Reactome) As the reverse transcriptase activity of the HIV-1 RT heterodimer catalyzes the synthesis of minus-strand strong stop DNA (-sssDNA), the RNaseH activity of the same RT heterodimer catalyzes the degradation of the complementary viral genomic RNA sequences. Degradation of this RNA is required for the efficient transfer of the -sssDNA to the 5' end of the viral genomic RNA. The RNase H active site is positioned within the HIV-1 RT heterodimer so as to attack the RNA strand of the RNA:DNA duplex at a point 18 bases behind the site of reverse transcription (Furfine and Reardon 1991; Ghosh et al. 1995; Gopalakrishnan et al. 1992; Wohrl and Moelling 1990). The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis, however (Kati et al. 1992), and may further depend on RT stalling and structural features of the viral genomic RNA template. The product of these combined DNA synthesis and RNA degradation events is a DNA strand still duplexed with extended viral genomic RNA fragments.
REACT_9048 (Reactome) The first chemical step of integration involves a single step transesterification, in which the recessed 3' hydroxyl of the viral DNA becomes covalently joined to a protruding 5' end in the target DNA. This step at the same time cleaves the target DNA.
REACT_9049 (Reactome) Synthesis of minus-strand DNA proceeds toward the 5' end of the PBS motif of the template HIV genomic RNA.
REACT_9054 (Reactome) How the PIC finds favored sites on target DNA has not been fully clarified. Active genes are favored for integration, and favored sequences at the site of integration also influence the reaction. Studies of cells depeleted in PSIP1/LEDGF/p75 suggest that this protein acts as a tethering factor binding HIV PICs near integration target DNA. Access of PICs to sites on chromosomes may be significant, since centromeric alphoid repeats are disfavored for integration, perhaps due to wrapping in compact centromeric heterochromatin. Nucleosomes bound to the integration template also affect target site selection and integration complex binding.
REACT_9056 (Reactome) With the removal of all viral genomic RNA and tRNA, the PBS sequence at the 3' end of the plus-strand strong-stop DNA (+sssDNA) is free to pair with the complementary PBS sequence at the 3' end of the minus-strand DNA, to generate a circular structure (Telesnitsky and Goff 1997).
REACT_9066 (Reactome) The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis (Kati et al. 1992), so the product of the combined DNA synthesis and RNA degradation events catalyzed by the RT heterodimer mediating minus-strand DNA synthesis is a DNA segment still duplexed with extended viral genomic RNA fragments. Other RT heterodimers bind the remaining RNA:DNA heteroduplexes and their RNase H domains further degrade the viral genomic RNA (Wisniewski et al. 2000a, b). Two PPT (polypurine tract) sequence motifs in the template, one immediately 5' to the U3 sequence and one located within the pol gene in the center of the viral genome, are spared from degradation (Charneau et al. 1992; Julias et al. 2004; Pullen et al. 1993).
REACT_9069 (Reactome) Prior to integration, two nucleotides are removed from each 3' end of the linear viral DNA, thereby exposing recessed 3' hydroxyls. This reaction may serve to remove heterogenous extra bases from the viral DNA end, and to stabilize the IN-DNA complex. The chemistry of cleavage is a simple hydrolysis by single-step transesterification.
REACT_9073 (Reactome) Viral DNA that does not become integrated can undergo another fate, which is to have the two viral DNA ends joined together to form a 2-LTR circle. This reaction requires Ku, XRCC4 and ligase 4.
REACT_9074 (Reactome) Upon completion of reverse transcription, the viral integrase protein (IN) becomes bound to the ends of the viral DNA. This is inferred by the fact that this is the site of integrase action, and several biochemical studies have documented integrase interactions with the terminal DNA.
REACT_9075 (Reactome) HIV-1 genomic RNA contains a centrally located PPT (cPPT) within the pol gene that, like 3'PPT, is spared by RNase H during minus-strand DNA synthesis and persists to prime plus-strand DNA synthesis. This ribonucleotide primes the synthesis of a plus-strand DNA extending through the U3 and R regions of the HIV sequence and terminating in the PBS region (the tRNA primer-binding site). This DNA segment is known as plus-strand strong-stop DNA (+sssDNA) (Telesnitsky and Goff 1997; Pullen et al. 1993; Huber and Richardson 1990). cPPT priming is important for efficient viral replication (Alizon et al. 1992; Rausch and Le Grice 2004). Several features of cPPT priming in vivo remain to be clarified.
REACT_9478 (Reactome) Upon translocation to the cytoplasm, RanBP1 associates with Ran-GTP in the Rev-CRM1-Ran-GTP complex.
REACT_9507 (Reactome) Free, nuclear RanGTP is required for export processes out of the nucleus. RCC1 catalyses the conversion of Ran-GDP to Ran-GTP in the nucleus.
REACT_9530 (Reactome) CRM1 associates directly with Rev through the Rev nuclear export signal (NES) domain and acts as the nuclear export receptor for the Rev-RRE ribonucleoprotein complex.
REV (P04618) proteinArrowREACT_6318 (Reactome)
REV (P04618) proteinREACT_163644 (Reactome)
REV (P04618) proteinREACT_6161 (Reactome)
RNA Pol II

(hypophosphorylated) complex bound to

DSIF protein
ArrowREACT_6250 (Reactome)
RNA Pol II

(hypophosphorylated) complex bound to

DSIF protein
REACT_6357 (Reactome)
RNA Pol II

(hypophosphorylated):capped

pre-mRNA complex
ArrowREACT_6206 (Reactome)
RNA Pol II

(hypophosphorylated):capped

pre-mRNA complex
REACT_6250 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
ArrowREACT_6298 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
REACT_6295 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
ArrowREACT_6220 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
REACT_6298 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
ArrowREACT_6203 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
ArrowREACT_6226 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
ArrowREACT_6265 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
mim-catalysisREACT_6172 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
mim-catalysisREACT_6184 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
mim-catalysisREACT_6208 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
mim-catalysisREACT_6240 (Reactome)
RNA Polymerase II

(unphosphorylated):TFIIF

complex
mim-catalysisREACT_6325 (Reactome)
RNGTTREACT_6220 (Reactome)
RNMTREACT_6295 (Reactome)
RTArrowREACT_9010 (Reactome)
RTC (Reverse

Transcription Complex) with RNA

template
ArrowREACT_8994 (Reactome)
RTC (Reverse

Transcription Complex) with RNA

template
REACT_9015 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
ArrowREACT_9056 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
REACT_8992 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
mim-catalysisREACT_8992 (Reactome)
RTC with degraded

RNA template and

minus sssDNA
ArrowREACT_9014 (Reactome)
RTC with degraded

RNA template and

minus sssDNA
REACT_9033 (Reactome)
RTC with duplex DNA

containing discontinuous plus

strand flap
ArrowREACT_8992 (Reactome)
RTC with duplex DNA

containing discontinuous plus

strand flap
REACT_9036 (Reactome)
RTC with extending minus strand DNAArrowREACT_9066 (Reactome)
RTC with extending minus strand DNAREACT_9075 (Reactome)
RTC with extending minus strand DNAmim-catalysisREACT_9075 (Reactome)
RTC with extending second-strand DNAArrowREACT_9075 (Reactome)
RTC with extending second-strand DNAREACT_8999 (Reactome)
RTC with extending second-strand DNAmim-catalysisREACT_8999 (Reactome)
RTC with extensive RNase-H digestionArrowREACT_9040 (Reactome)
RTC with extensive RNase-H digestionREACT_9066 (Reactome)
RTC with extensive RNase-H digestionmim-catalysisREACT_9066 (Reactome)
RTC with integration competent viral DNAArrowREACT_9036 (Reactome)
RTC with integration competent viral DNAREACT_9010 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
ArrowREACT_9033 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
REACT_9049 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
mim-catalysisREACT_9049 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
ArrowREACT_9039 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
REACT_9046 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
mim-catalysisREACT_9046 (Reactome)
RTC with minus

strand DNA synthesis initiated from

3'-end
ArrowREACT_9049 (Reactome)
RTC with minus

strand DNA synthesis initiated from

3'-end
REACT_9040 (Reactome)
RTC with minus

strand DNA synthesis initiated from

3'-end
mim-catalysisREACT_9040 (Reactome)
RTC with nicked

minus sssDNA:tRNA

primer:RNA template
ArrowREACT_9046 (Reactome)
RTC with nicked

minus sssDNA:tRNA

primer:RNA template
REACT_9014 (Reactome)
RTC with tRNA primer:RNA templateArrowREACT_9015 (Reactome)
RTC with tRNA primer:RNA templateREACT_9039 (Reactome)
RTC with tRNA primer:RNA templatemim-catalysisREACT_9039 (Reactome)
RTC without viral RNA templateArrowREACT_8999 (Reactome)
RTC without viral RNA templateREACT_9056 (Reactome)
RTmim-catalysisREACT_9014 (Reactome)
Ran GTPase:GDPArrowREACT_6171 (Reactome)
Ran-GDPREACT_9507 (Reactome)
Ran-GTPArrowREACT_9507 (Reactome)
Ran-GTPREACT_6140 (Reactome)
Ran:GTPArrowREACT_6318 (Reactome)
Ran:GTPREACT_6171 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexArrowREACT_9478 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexREACT_6318 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP:NPC
ArrowREACT_6337 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP:NPC
REACT_6340 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ArrowREACT_6140 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ArrowREACT_6340 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
REACT_6337 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
REACT_9478 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
mim-catalysisREACT_6171 (Reactome)
Rev multimer-bound

HIV-1 mRNA:CRM1

complex
ArrowREACT_9530 (Reactome)
Rev multimer-bound

HIV-1 mRNA:CRM1

complex
REACT_6140 (Reactome)
Rev multimer-bound HIV-1 mRNAArrowREACT_6228 (Reactome)
Rev multimer-bound HIV-1 mRNAREACT_9530 (Reactome)
Rev-bound HIV-1 mRNAArrowREACT_6161 (Reactome)
Rev-bound HIV-1 mRNAREACT_6228 (Reactome)
Rev-multimerArrowREACT_6318 (Reactome)
Rev-multimerREACT_6228 (Reactome)
Spliced Env mRNAArrowREACT_163953 (Reactome)
Spliced Env mRNAREACT_163666 (Reactome)
Spliced Env mRNAREACT_163787 (Reactome)
TCEA1REACT_6275 (Reactome)
TCEA1REACT_6358 (Reactome)
TFIIAArrowREACT_6172 (Reactome)
TFIIAArrowREACT_6203 (Reactome)
TFIIAArrowREACT_6226 (Reactome)
TFIIDArrowREACT_6172 (Reactome)
TFIIDArrowREACT_6203 (Reactome)
TFIIDArrowREACT_6226 (Reactome)
TFIIEArrowREACT_6172 (Reactome)
TFIIEArrowREACT_6203 (Reactome)
TFIIEArrowREACT_6226 (Reactome)
TFIIEArrowREACT_6265 (Reactome)
TFIIHArrowREACT_6203 (Reactome)
TFIIHArrowREACT_6206 (Reactome)
TFIIHArrowREACT_6226 (Reactome)
TFIIHArrowREACT_6265 (Reactome)
TFIIHArrowREACT_6278 (Reactome)
TFIIHREACT_6206 (Reactome)
TFIIHREACT_6275 (Reactome)
TFIIHREACT_6358 (Reactome)
TFIIHmim-catalysisREACT_6134 (Reactome)
TFIIHmim-catalysisREACT_6184 (Reactome)
TFIIHmim-catalysisREACT_6234 (Reactome)
TFIIHmim-catalysisREACT_6325 (Reactome)
Tat (P04608)REACT_6356 (Reactome)
Tat-containing

elongation complex

prior to separation
ArrowREACT_6158 (Reactome)
Tat-containing

elongation complex

prior to separation
REACT_6204 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF phospho

DSIF)
ArrowREACT_6316 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF phospho

DSIF)
REACT_6275 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
ArrowREACT_6311 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
REACT_6316 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
mim-catalysisREACT_6316 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
ArrowREACT_6170 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
REACT_6311 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
mim-catalysisREACT_6311 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexArrowREACT_6356 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexREACT_6170 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexmim-catalysisREACT_6170 (Reactome)
Trimeric ENV precursorArrowREACT_163888 (Reactome)
Trimeric ENV precursorArrowREACT_163952 (Reactome)
Trimeric ENV precursorREACT_163888 (Reactome)
Trimeric ENV precursorREACT_163905 (Reactome)
Trimeric gp120:gp41 oligomerArrowREACT_163857 (Reactome)
Trimeric gp120:gp41 oligomerArrowREACT_163905 (Reactome)
Trimeric gp120:gp41 oligomerREACT_163644 (Reactome)
Trimeric gp120:gp41 oligomerREACT_163857 (Reactome)
UbREACT_115708 (Reactome)
VIF (P69723) proteinREACT_163644 (Reactome)
VPR (P69726) proteinREACT_163644 (Reactome)
VPU (P05919)ArrowREACT_163666 (Reactome)
VPU (P05919)ArrowREACT_163732 (Reactome)
VPU (P05919)ArrowREACT_163863 (Reactome)
VPU (P05919)REACT_163644 (Reactome)
VPU (P05919)REACT_163732 (Reactome)
VPU (P05919)REACT_163863 (Reactome)
Viral core

surrounded by Matrix

layer
ArrowREACT_8032 (Reactome)
Viral core

surrounded by Matrix

layer
REACT_9044 (Reactome)
Virion Budding ComplexArrowREACT_163632 (Reactome)
Virion Budding ComplexArrowREACT_163803 (Reactome)
Virion with

CD4:gp120 bound to

CCR5/CXCR4
ArrowREACT_7962 (Reactome)
Virion with

CD4:gp120 bound to

CCR5/CXCR4
REACT_8003 (Reactome)
Virion with

fusogenically

activated gp41
ArrowREACT_8023 (Reactome)
Virion with

fusogenically

activated gp41
REACT_8020 (Reactome)
Virion with CD4 bound to gp120ArrowREACT_8009 (Reactome)
Virion with CD4 bound to gp120REACT_7953 (Reactome)
Virion with exposed

coreceptor binding

sites
ArrowREACT_7953 (Reactome)
Virion with exposed

coreceptor binding

sites
REACT_7962 (Reactome)
Virion with gp41 exposedArrowREACT_8003 (Reactome)
Virion with gp41 exposedREACT_8023 (Reactome)
Virion with gp41

forming hairpin

structure
ArrowREACT_8010 (Reactome)
Virion with gp41

forming hairpin

structure
REACT_8032 (Reactome)
Virion with gp41

fusion peptide in

insertion complex
ArrowREACT_8020 (Reactome)
Virion with gp41

fusion peptide in

insertion complex
REACT_8010 (Reactome)
Vps/Vta1REACT_163632 (Reactome)
XPO1ArrowREACT_6318 (Reactome)
XPO1REACT_9530 (Reactome)
XRCC4:DNA ligase IV complexArrowREACT_9073 (Reactome)
XRCC4:DNA ligase IV complexREACT_9042 (Reactome)
dNTPREACT_9039 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ArrowREACT_115708 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ArrowREACT_115855 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ArrowREACT_163872 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
REACT_115855 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
REACT_163644 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
REACT_163872 (Reactome)
myristoylated Nef

Protein

(UniProt:P04601)
ArrowREACT_116143 (Reactome)
myristoylated Nef

Protein

(UniProt:P04601)
ArrowREACT_9044 (Reactome)
myristoylated Nef

Protein

(UniProt:P04601)
REACT_163644 (Reactome)
other viral genomic RNAArrowREACT_8994 (Reactome)
p-SUPT5HREACT_6295 (Reactome)
tRNA-Lysine3REACT_163644 (Reactome)
tRNA-Lysine3REACT_9015 (Reactome)
uncoated viral complexArrowREACT_9038 (Reactome)
uncoated viral complexREACT_8994 (Reactome)
viral DNA bound with Integrase in PICArrowREACT_9074 (Reactome)
viral DNA bound with Integrase in PICREACT_9069 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
ArrowREACT_9042 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
REACT_9073 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
mim-catalysisREACT_9073 (Reactome)
viral PIC proteinsArrowREACT_9001 (Reactome)
viral PIC proteinsArrowREACT_9006 (Reactome)
viral PIC proteinsArrowREACT_9022 (Reactome)
viral PIC proteinsArrowREACT_9025 (Reactome)
viral PIC proteinsArrowREACT_9045 (Reactome)
viral PIC proteinsArrowREACT_9048 (Reactome)
viral PIC proteinsArrowREACT_9054 (Reactome)
viral PIC proteinsREACT_9001 (Reactome)
viral PIC proteinsREACT_9048 (Reactome)
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