HIV Life Cycle (Homo sapiens)

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12, 5030, 62, 8522, 49, 585334, 112808, 25, 26, 43, 44, 57...585815, 10929, 39, 45, 51821061342, 58, 10159, 63, 10018, 26, 32, 35, 69...2026, 81, 86, 94642319, 27, 34, 50, 97...62, 7334, 11214, 42, 47, 92345854, 58, 10114, 42, 5529, 3911, 56, 67, 70, 71, 74...4, 44, 72, 87, 103...29, 37, 39, 402, 6, 48, 95, 10120, 361, 17, 21, 24, 43...7958, 781028, 33, 3898233, 80, 919362, 7610746582020, 9695, 48, 9565, 7552, 8234, 112206241, 10283, 90Rev multimer-bound HIV-1 mRNACRM1 complex TFIIE linear duplex viral DNA gp120 homotrimer with exposed coreceptor binding sites TFIIE RNA Polymerase II holoenzyme complex phospho-NELF complex RNA Polymerase II holoenzyme complex p6 protein p6 protein RTC RNA Polymerase II holoenzyme complex gp120 homotrimer after second conformation change RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex RNA Polymerase II TFIIH Elongin Complex NTP P-TEFb complex RT RNA Polymerase II holoenzyme complex Tat-containing elongation complex prior to separation RNA Polymerase II holoenzyme complex p6 protein gp41 homotrimer with fusion peptide inserted into membrane HIV-1 aborted elongation complex after arrest TFIIE uncoated viral complex Crm1Ran GTPaseGTP NELF complex INviral DNA bound to host genomic DNA RT TFIIF RNA Polymerase II holoenzyme complex monoubiquitinated N-myristoyl GAG gp120 homotrimer minus sssDNA primer for minus strand DNA extension Vps/Vta1 CAK RNA Polymerase II holoenzyme complex TFIIF CAK Cap Binding Complex Elongin Complex Virion Budding Complex TFIID DSIF complex TFIIF HIV-1 transcription complex containing 9 nucleotide long transcript FACT complex Elongin Complex Matrix TFIIF TatP-TEFbHIV-1 RNA homodimer Cap Binding Complex TFIIF RNA Polymerase II Trimeric gp120gp41 oligomer TFIIH RT TFIIH Virion with gp41 exposed RNA Pol II FACT complex gp41 homotrimer with hairpin structure formation p6 protein Trimeric gp120gp41 oligomer TFIIH TFIIH TFIIF RTC without viral RNA template ESCRT-I RNA Polymerase II Env oligomer with gp120HIV-1 transcription complex with TFIIF P-TEFbCD4Env gp120/gp41 fusion peptide complexCCR5 HIV-1 RNA homodimer RNA Polymerase II holoenzyme complex P-TEFbCAK CAK TFIIF TFIIH viral DNA bound with Integrase ubiquitin p6 protein TFIIF RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex CHMP2 DSIF complex HIV-1 RNA homodimer RT TFIIH FACT complex CHMP4 RT Matrix Matrix P-TEFb complex CCR5, CXCR4 Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELF Cap Binding Complex TFIIA Elongin BC complex INviral DNA bound to host genomic DNA with staggered ends CCR5, CXCR4 TFIIF RNA Pol II TFIIA RNA Pol II Elongin BC complex RT gp120 homotrimer with exposed coreceptor binding sites gp41 homotrimer RNA Polymerase II holoenzyme complex Tat-containing early elongation complex with hyperphosphorylated Pol II CTD DSIF complex NELF complex Encapsidated viral core Elongin Complex TFIIH ESCRT-III DSIF complex TFIIF TFIID ESCRT-I Early elongation complex with separated aborted transcript RT DSIF complex 1-LTR form of circular viral DNA TFIIA NELF complex phospho-NELF complex Matrix IN bound to sticky 3' ends of viral DNA Rev-bound HIV-1 mRNA TFIID Golgi membraneElongin BC complex RNA Polymerase II holoenzyme complex RNA Polymerase II RNA Polymerase II holoenzyme complex Matrix p6 protein Matrix CCR5, CXCR4 NELF complex Autointegrated viral DNA as an inverted circle HIV-1 elongation complex p6 protein TFIIF TFIID Assembling HIV virion viral DNAKu proteinsXRCC4DNA ligase IV complex Elongin BC complex RNA Polymerase II TFIIH RT TFIIF Elongin BC complex CAK DSIF complex Ran GTPaseGDP gp120 homotrimer after second conformation change NELF complex Elongin BC complex Rev-bound HIV-1 mRNA monoubiquitinated N-myristoyl GAG Nup62 Complex TFIIF CD4Env gp120CCR5,CXCR4complex RNA Polymerase II holoenzyme complex Elongin Complex CD4Env gp120 with exposed coreceptor binding site p6 protein TFIID IN bound to sticky 3' ends of viral DNA in PIC Rev-bound HIV-1 mRNA TFIIF HIV-1 RNA homodimer Matrix TFIIF Matrix TFIIF NTP RNA Polymerase II holoenzyme complex ESCRT-III P-TEFbRNA Polymerase II holoenzyme complex TFIIF Trimeric gp120gp41 oligomer RT CAK NTP CAK endoplasmic reticulum membraneMatrix Virion with fusogenically activated gp41 RT TFIIA RTC with integration competent viral DNA p6 protein Rev multimer-bound HIV-1 mRNA Rev multimer-bound HIV-1 mRNACRM1 complex CD4Env gp120 TFIIF RNA Polymerase II holoenzyme complex Nucleocapsid RNA Polymerase II holoenzyme complex P-TEFbElongin Complex Ub P-TEFbviral PIC proteins RNA Polymearse IINTPTFIIF complex TFIIF RT Ku70Ku80 heterodimer p6 protein TFIIF IN bound to sticky 3' ends of viral DNA CAK TFIIF RT RNA Polymerase II holoenzyme complex TFIIA Ku70Ku80 heterodimer DSIF complex FACT complex Cap Binding Complex RanGTP HIV-1 transcription complex containing 3 nucleotide long transcript HIV-1 initiation complex with phosphodiester-PPi intermediate Nucleocapsid RNA Polymerase II holoenzyme complex RNA Pol II Virion with gp41 fusion peptide in insertion complex TatP-TEFbRev-bound HIV-1 mRNA TFIIE NELF complex gp120 homotrimer TFIID Matrix XRCC4DNA ligase IV complex HIV-1 promoterTFIIDTFIIATFIIB complex p6 protein gp120 homotrimer TFIIF TFIIH RTC with minus strand DNA synthesis initiated from 3'-end HIV-1 transcription complex containing 4-9 nucleotide long transcript TFIIF RNA Polymerase II holoenzyme complex HIV-1 Polymerase II P-TEFb complex TFIIF TFIIH NELF complex Ku70Ku80 heterodimer P-TEFb complex RNA templatetRNA primer TFIIF p6 protein HIV-1 RNA homodimer p6 protein viral DNA with 3' sticky ends Virion with exposed coreceptor binding sites RNA Polymerase II Ku proteins bound to viral DNA DSIFNELFearly elongation complex RT TFIIH Matrix HIV-1 transcription complex containing transcript to +30 TatP-TEFbRNA polymerase II Rev-bound HIV-1 mRNA RNA Polymerase II holoenzyme complex HIV-1 Tat-containing arrested processive elongation complex viral DNA with 3' sticky ends gp41 homotrimer Elongin BC complex TFIIH HIV-1 RNA homodimer Elongin Complex TFIIE DSIF complex RT Nucleocapsid minus sssDNA primer for minus strand DNA extension FACT complex gp120 homotrimer after second conformation change CAK NELF complex CHMP2 Elongin Complex Matrix FACT complex Rev multimer-bound HIV-1 mRNACrm1RanGTPNPC p6 protein CD4Env gp120/gp41 hairpin complex TFIID NTP linear duplex viral DNA Nucleocapsid P-TEFbviral DNA with 3' sticky ends DSIF complex Elongin Complex RNA Polymerase II holoenzyme complex P-TEFb complex CAK Viral core surrounded by Matrix layer RTC with tRNA primerRNA template TatP-TEFbRNA Polymerase II TFIIH RNA Polymerase II holoenzyme complex RNA Pol II with phosphorylated CTD CE complex CAK DSIF complex Ran-GDP Elongin BC complex RT gp41 homotrimer DSIF complex Autointegrated viral DNA as smaller circles minus sssDNA primer transferred to 3'- end of viral RNA template linear duplex viral DNA TFIIF RT p6 protein Virion with CD4gp120 bound to CCR5/CXCR4 P-TEFbminus sssDNAtRNA primer generated by RNAse-H TFIIF DSIF complex p6 protein minus sssDNA primer transferred to 3'- end of viral RNA template FACT complex NTP RNA Polymerase II holoenzyme complex TFIIF TFIIA TFIIF Matrix Matrix FACT complex Cap Binding Complex CAK gp41 homotrimer p6 protein TFIIA gp120 homotrimer after second conformation change TFIIF RNA Polymerase II holoenzyme complex HIV-1 RNA homodimer RNA Polymerase II RNA Polymerase II Env oligomer with gp41cytosolNup107 Complex RTC with degraded RNA template and minus sssDNA CD4Env gp120/gp41 insertion complex HIV-1 Tat-containing processive elongation complex RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex RNA Polymerase II Env oligomer with gp41gp120 homotrimer Matrix Rev multimer-bound HIV-1 mRNA CAK RT p6 protein p6 protein Rev multimer-bound HIV-1 mRNACrm1RanGTP ubiquitin TatP-TEFbHIV-1 RNA homodimer RNA Polymerase II RTC with nicked minus sssDNAtRNA primerRNA template viral DNA bound with Integrase in PIC TFIIH RNA Polymerase II holoenzyme complex Rev multimer-bound HIV-1 mRNA Matrix TFIIF Nup62 Complex Elongin Complex CD4Env gp120/gp41 hairpin complexCCR5/CXCR4 RNA Polymerase II holoenzyme complex Elongin BC complex DSIF complex RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex Env oligomer with gp41 hairpin structure formation RNA polymerase II minus sssDNA primer for minus strand DNA extension RNA Polymerase II holoenzyme complex FACT complex NELF complex p6 protein RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex CD4Env gp120/gp41insertion complexCCR5/CXCR4 Tat-containing early elongation complex with hyperphosphorylated Pol II CTD HIV-1 RNA homodimer TatP-TEFbminus sssDNA primer for minus strand DNA extension NELF complex TFIIH RTC with duplex DNA containing discontinuous plus strand flap monoubiquitinated N-myristoyl GAG RNA Polymerase II NELF complex RT NTP TFIIH TFIID RNA Pol II CAK HIV-1 promoterTFIIDTFIIATFIIBPol IITFIIF complex* Rev multimer-bound HIV-1 mRNACrm1RanGTP HIV-1 transcription complex containing 11 nucleotide long transcript RNA Polymerase II P-TEFbCrm1Ran GTPaseGTP Matrix CCR5, CXCR4 HIV-1 early elongation complex with hyperphosphorylated Pol II CTD RT Nucleocapsid Env oligomer with gp41 hairpin structure formation Nucleocapsid TFIIF Rev-bound HIV-1 mRNA Cap Binding Complex RNA Polymerase II holoenzyme complex TFIIF CAK DSIF complex HIV-1 early elongation complex with hyperphosphorylated Pol II CTD TFIIA TFIIF CAK P-TEFb complex Tat-containing early elongation complex with hyperphosphorylated Pol II CTD CAK Matrix HIV-1 RNA homodimer TFIIH RTC with extending second-strand DNA Rev multimer-bound HIV-1 mRNA RTC with extending minus strand DNA p6 protein TatP-TEFbNuclear Pore Complex p6 protein TFIIH RT HIV-1 RNA homodimer CAK TFIIE NELF complex Ran-GTP NELF complex TFIIF early endosome membraneNTP Nucleocapsid DSIF complex gp41 homotrimer phospho-DSIF complex RT CCR5, CXCR4 RNA Polymerase II holoenzyme complex XRCC4DNA ligase IV complex CEPol II CTDSpt5 complex p6 protein Integrated provirus Rev-bound HIV-1 mRNA RT CD4Env gp120/gp41 fusion peptide complex NTP HIV-1 transcription complex containing 4 nucleotide long transcript p6 protein 2-LTR form of circular viral DNA RNA Pol II Matrix Rev multimer-bound HIV-1 mRNA Nucleocapsid viral PIC proteins RNA Polymerase II p6 protein Matrix gp41 homotrimer TFIIF P-TEFb complex minus sssDNARNA templatetRNA primer P-TEFbRT Matrix NTP Nucleocapsid RNA Polymerase II holoenzyme complex P-TEFbHIV-1 elongation complex containing Tat CHMP4 HIV-1 capped pre-mRNACBCRNA Pol II Elongin Complex ubiquitin RNA Polymerase II holoenzyme complex Trimeric ENV precursor TFIIH RNA Polymerase II holoenzyme complex linear duplex viral DNA Matrix Immature HIV virion Nuclear Pore Complex TFIIF HIV-1 transcription complex linear duplex viral DNA monoubiquitinated N-myristoyl GAG viral DNA with 3' sticky ends gp120 homotrimer RNA Polymerase II holoenzyme complex gp41 homotrimer IN bound to sticky 3' ends of viral DNA Virion with CD4 bound to gp120 RNA Polymerase II gp41 homotrimer with exposed fusion peptide Ku proteins bound to viral DNA RT HIV-1 arrested processive elongation complex Elongin BC complex TatP-TEFbCD4Env gp120 with exposed coreceptor binding site IN bound to sticky 3' ends of viral DNA Virion with gp41 forming hairpin structure CD4Env gp120/gp41 hairpin complexCCR5/CXCR4 RTC with minus sssDNAtRNA primerRNA template Ran-GTP nicked minus sssDNARNA templatetRNA primer HIV-1 initiation complex TFIIH P-TEFbHIV-1 Tat-containing paused processive elongation complex Env oligomer with gp120PIC linear duplex viral DNA ubiquitin CAK Nup107 Complex monoubiquitinated N-myristoyl GAG CAK TFIIE TFIIF RNA Polymerase II DSIF complex P-TEFbCCR5, CXCR4 CD4Env gp120/gp41 hairpin complex linear duplex viral DNA Ku proteins bound to viral DNA Env oligomer with gp120Trimeric gp120gp41 oligomer RNA Polymerase II holoenzyme complex TFIIF CAK RNA Polymerase II RNA Pol II with phosphorylated CTD CE complex with activated GT Nucleocapsid TFIIE RNA Polymerase II holoenzyme complex viral PIC proteins p6 protein TFIIE Rev multimer-bound HIV-1 mRNACrm1RanGTP FACT complex RNA Polymerase II holoenzyme complex viral PIC proteins TFIIF RNA Polymerase II holoenzyme complex Ran-GTP p6 protein HIV-1 closed pre-initiation complex RanGTP TFIIF HIV-1 promoterTFIID complex TFIIF RNA Polymerase II holoenzyme complex RTC with minus sssDNA transferred to 3'-end of viral RNA template RNA Polymerase II holoenzyme complex p6 protein RNA Polymerase II holoenzyme complex FACT complex RNA polymerase II Integration intermediate Ku70Ku80 heterodimer HIV-1 RNA homodimer CAK TFIID linear duplex viral DNA DSIF complex p6 protein RNA Polymerase II CD4gp120gp41 membrane complex RTC with extensive RNase-H digestion RT NELF complex HIV-1 open pre-initiation complex p6 protein RTC with annealed complementary PBS seqments in +sssDNA and -strand DNA Vps/Vta1 p6 protein RNA Polymerase II holoenzyme complex TFIIF RNA Polymerase II holoenzyme complex TFIIE gp41 homotrimer Trimeric gp120gp41 oligomer TFIIH phospho-NELF complex TatP-TEFbElongin BC complex TFIIE NELF complex TFIIH NELF complex RNA Polymerase II holoenzyme complex TFIIH DSIF complex CAK RNA Polymerase II holoenzyme complex RNA Pol II RT TFIIF TFIIA Mature HIV virion Elongin Complex CCR5/CXCR4CD4Env gp120 RNA Polymerase II Matrix RanBP1Ran-GTPCRM1Rev-bound mRNA complex Aborted HIV-1 early elongation complex phospho-DSIF complex Cap Binding Complex HIV-1 transcription complex containing extruded transcript to +30 DSIFNELFearly elongation complex after limited nucleotide addition HIV-1 Tat-containing aborted elongation complex after arrest IN bound to sticky 3' ends of viral DNA in PIC TFIIA TFIIH DSIF complex RNA Polymerase II holoenzyme complex Cap Binding Complex RanGTP CAK RNA Polymerase II holoenzyme complex Elongin Complex Nucleocapsid p6 protein RT Rev multimer-bound HIV-1 mRNACrm1RanGTP Trimeric gp120gp41 oligomer RNA Polymerase II holoenzyme complex HIV-1 paused processive elongation complex nucleoplasmHIV-1 Promoter Escape Complex RNA Polymerase II holoenzyme complex Matrix HIV-1 Polymerase II Cap Binding Complex RNA polymerase II gp120 homotrimer after second conformation change Elongin BC complex Integrated provirus NELF complex P-TEFbTFIID RNA Pol II RNA Polymerase II holoenzyme complex Rev multimer-bound HIV-1 mRNA HIV-1 RNA homodimer Rev multimer-bound HIV-1 mRNACRM1 complex CAK RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex TatP-TEFbFACT complex RNA Pol II RNA polymerase II DSIF complex RNA Pol II Trimeric ENV precursor TFIIF TatP-TEFbTFIIF RNA Pol II TFIIH Elongin BC complex CAK gp41 homotrimer with hairpin structure formation FACT complex HIV-1 processive elongation complex gp41 homotrimer HIV-1 RNA homodimer gp120 homotrimer p6 protein NELF complex RNA polymerase II GTF2H1IN monoubiquitinated N-myristoyl GAG RAE1 UBCTat-containing early elongation complex with hyperphosphorylated Pol II CTDGTF2H3 POLR2FNCBP1 Rev-multimerp6 NELFAp-SUPT5H POLR2J NCBP1 RNGTT IN VPU GTF2E2 POLR2C ERCC3 CTP UBA52POLR2B IN bound to sticky 3' ends of viral DNA in PICCap Binding Complex HIV-1 RNA homodimerCDK7 TAF4 CTDP1 p-SUPT5H POLR2C POLR2K ATP TAF4 ELL GTF2E2 GTF2F2GTF2A2 GTF2F2POLR2E XPO1 VPS28 POLR2E p6 p6 GTF2F2p-SUPT5H ELL POLR2FTAF6 ELL CCNH HIV-1 RNA template DSIFNELFearly elongation complexPOLR2A NUP93 MNAT1 POLR2I POLR2L GTF2H1CTDP1 NCBP2 TAF10 NELFB UBBVIF POLR2I CHMP6HIV-1 open pre-initiation complexCTP myristoylated Nef Protein p6 Rev-bound HIV-1 mRNAHIV-1 template DNA with first transcript dinucleotide, opened to +8 positionGTF2F2p51 viral PIC proteinsReverse transcriptase/ribonuclease H POLR2G POLR2I POLR2H VPR VPU NELFCD GTF2H3 TAF1 Reverse transcriptase/ribonuclease H Surface protein gp120 POLR2FPOLR2H UTP POLR2G POLR2I GTF2H1POLR2B POLR2B RPS27APOLR2G POLR2A UBCp-SUPT5H POLR2DVIF TFIIHPOLR2C TAF4 PR VPU POLR2A ERCC3 GTF2F1Reverse transcriptase/ribonuclease H p6 VIF p51 NUP54 SUPT4H1 MA HIV-1 RNA template POLR2K UBBPOLR2FGTF2H4 POLR2J POLR2I POLR2J POLR2I p6 NELFCD POLR2B CCNH GTP RTC with integration competent viral DNAERCC2 POLR2J TCEB2 POLR2E POLR2H p6 GTF2H2 HIV-1 RNA GTF2F2GTF2F1ERCC2 POLR2E NucleocapsidDSIF complexp6 POLR2B POLR2H TAF9 UBCUBCTat-containing early elongation complex with hyperphosphorylated Pol II CTD NELFE PPIA p6 p-SUPT5H POLR2L GTF2F1GTF2H2 POLR2C NTPNELFE RTC with minus sssDNA transferred to 3'-end of viral RNA templateRCC1VPR p51 REV POLR2H HIV-1 mRNA ESCRT-IPOLR2B VIF POLR2FSurface protein gp120 POLR2A GTF2H1POLR2I POLR2DRANBP1NUP98-5 MA GTF2F1TAF6 TAF4B TFIIDGTF2A2 GTF2H1p51 HIV-1 initiation complex with phosphodiester-PPi intermediateGTF2F2SUPT4H1 GTF2F1HMGA1 p6 POLR2B GTF2F2p6 POLR2I GTF2H4 REV TAF4B POLR2G NCBP2 VPU MNAT1 POLR2A POLR2DReverse transcriptase/ribonuclease H GTF2H2 Surface protein gp120 TAF4 POLR2C POLR2B p-SUPT5H NELFCD CCNH Tat NELFE XPO1 TAF11 dNTPCCNT2 MA POLR2DTCEB2 p6 VPS37D IN TAF5 p-SUPT5H POLR2B NELFE Vps/Vta1p6 uncoated viral complexVPS4AVPU RNA Polymerase II MA CCNH TAF12 GTF2E1 MA CCNT1 GTF2H1POLR2DCTDP1 POLR2FVPR TAF4B POLR2K POLR2H LIG1GTP RPS27ACDK9 NELFB POLR2A NELFCD HIV-1 mRNA GTF2E2 TAF10 p51 CDK7 POLR2E REV ELL POLR2I CTP POLR2FPOLR2L TAF13 POLR2FRev multimer-bound HIV-1 mRNACrm1RanGTPNPCPOLR2J HIV-1 RNA template POLR2K PPIA GTF2F2RANBP1NC GTF2A1p-S5-POLR2A p6 Assembling HIV virionp6 Transmembrane protein gp41 GTF2A1N-myristoyl GAG p-NELFE NELFB p6 POLR2C MA Integrated provirusRNA Pol II with phosphorylated CTD CE complexGTF2H1p6 POLR2K MA PPiTrimeric ENV precursorTCEB3 TAF4B VIF SUPT4H1 GTP CTP POLR2DCD4 CTDP1 p6 MA N-myristoyl GAG tRNA-Lysine3IN POLR2FERCC3 TCEB3 PPIA MA TAF6 RTC with duplex DNA containing discontinuous plus strand flapCD4 GTF2F2MA XRCC5 GTF2H1ERCC2 UBBNUP107 CDK9 POLR2H POLR2C Viral core surrounded by Matrix layerPOLR2G TCEA1 VIF POLR2C p6 POLR2L GTP CCNH POLR2C GTF2F1POLR2E p6 MNAT1 AAAS POLR2J POLR2B POLR2DUTP POLR2I TAF10 POLR2G GTF2H4 p51 POLR2FPOLR2FMA p-SUPT5H ERCC3 SUPT4H1 UBCATPVirion Budding ComplexVPU ERCC2 Tat NELFB SSRP1 POLR2K GDP GTF2H2 GTF2H3 SSRP1 Tat POLR2C POLR2I PPIAHIV-1 closed pre-initiation complexPOLR2A CTDP1 Reverse transcriptase/ribonuclease H NUP210 POLR2I IN GTF2A1CTP CTDP1 SUPT16H HIV-1 mRNA NC Reverse transcriptase/ribonuclease H RTC with tRNA primerRNA templatePOLR2A REV MA POLR2G NUPL1-2 CCNT1 TAF11 TAF11 ERCC2 TAF9 POLR2H NELFCD RAN UBCGTF2B GTF2H2 NUP35 VPR POLR2I IN POLR2K XPO1 POLR2K CTDP1 HIV-1 RNA RanBP1Ran-GTPCRM1Rev-bound mRNA complexGTF2A1RPS27APOLR2FPOLR2E POLR2K Tat ATPUBBSUPT4H1 TAF4B VPR p6 POLR2K REV TAF5 POLR2E NC CXCR4 p6 TAF12 p51 NELFAREV POLR2G HMGA1 GTF2E2 NELFE GTF2F1GTF2H4 HIV-1 paused processive elongation complexPOLR2FPOLR2G POLR2J p51 UBCSUPT4H1 REV CTDP1 CCR5 VPR p-S2,S5-POLR2A TCEB1 REV GTF2H2 POLR2C TAF13 VPU CDK7 Tat PR GTF2F2RNA Polymerase II NELFB TCEB3 VIF POLR2C NELFCD VTA1 VPS28 p-S5-POLR2A LIG4 GTPERCC3 POLR2A viral PIC proteinsCCNT1 NELFAELL NELFAMA Surface protein gp120 POLR2K SSRP1 myristoylated Nef Protein ELL NELFCD VPR RTC with annealed complementary PBS seqments in +sssDNA and -strand DNACTDP1p-S5-POLR2A ERCC3 UBCPiIN VIF NC POLR2H NCBP1 Reverse transcriptase/ribonuclease H UBCBANF1 CCNT1 ERCC2 TAF4B p6 MNAT1 VPU VIF UBA52RAN NELFAATP Transmembrane protein gp41 ERCC2 p6 MA POLR2G HIV-1 transcription complex containing 11 nucleotide long transcriptPOLR2G p-SUPT5H UBCCCNH POLR2G POLR2G RNA Pol II with phosphorylated CTD CE complex with activated GTGTF2E1 POLR2FGTP NELFE NELFAp51 Reverse transcriptase/ribonuclease H GTF2H3 POLR2B SSRP1 Surface protein gp120 MA GTF2H1VPU GTF2A1p6 NELFAGTF2H2 GTF2B CXCR4 NUP93 POLR2J INviral DNA bound to host genomic DNA with staggered endsTFIIHGTF2E1 POLR2FMNAT1 GTF2H4 REV GTF2A1UBCPOLR2E GTF2A2 POLR2G TCEB1 REV NELFAPOLR2C ERCC3 GTF2BMNAT1 RNGTTRANGAP1REV GTF2H1VPR ATP POLR2DMA PPIA VPR GTF2H4 HIV-1 RNA NELFCD VPU POLR2H XRCC6 POLR2E GTF2E2 GTF2F1GTF2H3 POLR2Dp6 HIV-1 capped pre-mRNACBCRNA Pol II TCEB1 POLR2J POLR2E PR VPU PPIA POLR2FSSRP1 SUPT16H POLR2I PPIA p6 VPS37B POLR2L POLR2G POLR2DSUPT4H1 TAF13 HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotidesGTF2H4 IN TAF12 ADPVIF SUPT4H1 POLR2C TAF12 Reverse transcriptase/ribonuclease H SUPT4H1 PPIA ERCC2 POLR2A NUP62 POLR2G UBBTransmembrane protein gp41 POLR2E POLR2FPOLR2H myristoylated Nef Protein TAF9 XRCC4 POLR2FNTPPOLR2K Reverse transcriptase/ribonuclease H POLR2FCDK7 viral PIC proteinsGTF2F2TPR NC RNA Polymerase II POLR2K NELFE POLR2B GTF2A2 REV UTP REV NCBP2 CD4 PPIA p-NELFE ERCC2 p-SUPT5H p-SUPT5H SUPT16H NELFE POLR2J NC RAN TBP VPR GTF2F2p6 myristoylated Nef Protein POLR2G CCNH Ran-GTPPOLR2I SUPT16H VPU ERCC2 ADPCCNT1 NELFAPOLR2J NELFB VPU POLR2G UBBPOLR2L POLR2DVIF HIV-1 mRNA IN NCBP2 POLR2A NUP210 CDK7 HIV-1 mRNA NELFB NUP37 REV POLR2J TPR VPS37A POLR2H POLR2L GTP PR FACT complexPOLR2L TCEB3 GTF2H4 NUP88 TCEB3 GTF2F2POLR2K Early elongation complex with separated aborted transcriptp6 CCNT1 VPU VPU HIV-1 mRNAp6 NELFE GTF2H3 NELFE POLR2B NEDD4LReverse transcriptase/ribonuclease H POLR2C TCEB1 CHMP4B VIF VPU NUP133 GTF2H2 GTF2H1ADPMNAT1 NELFB NC GTF2H4 POLR2L VPR CCR5 GTF2F2TAF12 TCEB2 CCNH HIV-1 RNA CCNT1 TCEB1 NCBP2 TAF5 TAF1 MA POLR2J GTF2H3 NCBP2 POLR2G GTF2H4 REV p51 POLR2I CHMP5 VPU CCR5 TCEB3 GTF2B GTF2A1POLR2H POLR2L HIV-1 Tat-containing aborted elongation complex after arrestPOLR2I HIV-1 processive elongation complexp6 CDK9 PDCD6IPTBP TAF11 HIV-1 RNA template Reverse transcriptase/ribonuclease H POLR2L TAF12 MA POLR2FMA PPiGTP GTF2H4 SUPT4H1 p51 VPS37A BANF1 Envelope glycoprotein gp160POLR2K RNA Pol II POLR2FIN GTP POLR2E POLR2J HIV-1 aborted elongation complex after arrestNC POLR2Dp-S5-POLR2A POLR2DTAF6 POLR2L myristoylated Nef Protein POLR2K p51 VPU ELL IN TCEB3 POLR2Fp6 XRCC5 NUP62 POLR2G REV UBCUBCPOLR2K TSG101GTF2H3 POLR2I VPR RTGAG-POL Polyprotein NELFB GTF2F1POLR2FTCEB2 Tat-containing elongation complex prior to separationTCEA1 POLR2FMA GTF2H1POLR2G UBCUBA52NTPGTF2F2POLR2H GTF2E1 Rev multimer-bound HIV-1 mRNACrm1RanGTPPOLR2E GTF2F2NC CCNT1 Trimeric gp120gp41 oligomermyristoylated Nef Protein REV p51 POLR2L POLR2I MA GTF2H3 POLR2DTCEB3 POLR2C UBCTAF5 myristoylated Nef Protein POLR2G RNA Polymerase II RTC with minus strand DNA synthesis initiated from 3'-endHMGA1 NUP50 POLR2K POLR2C UBCNELFE p-SUPT5H POLR2DTAF10 MA MatrixVIF POLR2E CHMP4C GTF2F1RAN POLR2K GTF2E2 NUPL2 NMT2GTF2F1GTF2H2 viral RNA template being digested by RNase-H PSIP1 TFIIHGTF2F1AAAS GTF2F2POLR2B POLR2H Transmembrane protein gp41 TCEB2 GTF2F1UTP POLR2H GTF2H3 POLR2A GTF2H1p6 GTF2F1CHMP4A HIV-1 transcription complex containing 3 nucleotide long transcriptSSRP1 POLR2L MA UBCPPiPOLR2K POLR2Fp6 Nuclear Pore Complex UBCERCC2 UBBPOLR2DIN TCEB2 MNAT1 VPR HIV-1 Tat-containing paused processive elongation complexPOLR2L GTF2A2 Reverse transcriptase/ribonuclease H NUPL1-2 GTF2F2UBBNELFE POLR2C GTF2H4 POLR2C p-SUPT5H GTF2H3 CCR5 POLR2E PSIP1 REV POLR2B HIV-1 transcription complex with CCNH GTF2H3 RTC with nicked minus sssDNAtRNA primerRNA templateCHMP3NUP54 Rev multimer-bound HIV-1 mRNACrm1RanGTPTCEA1 POLR2I NUP37 POLR2H POLR2A POLR2G GTF2A1POLR2DPOLR2I POLR2J POLR2H CTDP1 POLR2FCDK7 POLR2H TAF1 CCNH Ran-GDPCHMP2A PPIA CTDP1 CD4IN Tat Transmembrane protein gp41 PR CTDP1 Host genomic DNAPOLR2A MA GTF2H3 UBBPOLR2L GTF2A2 Virion with CD4 bound to gp120NUP188REV p51 MNAT1 POLR2B ELL TAF13 UBBCDK7 CTDP1 POLR2J TAF4B POLR2I ERCC3 GTF2F1TAF5 ERCC3 CTDP1 viral RNA template extensively digested except in PPT region MNAT1 p6 GTF2F1PSIP1 MA POLR2B POLR2C TCEB1 BANF1 POLR2K POLR2K GDPREV POLR2DPOLR2E POLR2FCHMP7 POLR2K GTF2H2 UTP TCEB1 ELL p6 RTC without viral RNA templateTCEA1 p51 NUP160 MNAT1 POLR2I REV CXCR4 TAF4 IN POLR2H PPiTAF13 VPR CTDP1 GTF2F1POLR2B SUPT4H1 TCEA1 NELFCD SUPT16H GTF2H4 VIF TCEB2 UTP POLR2E POLR2E p-S5-POLR2A POLR2I POLR2L TAF1 p6 NELFB POLR2J POLR2K POLR2L POLR2DTAF9 NELFAELLPOLR2DHIV-1 elongation complexCD4Env gp120/gp41 hairpin complexCCR5/CXCR4POLR2B POLR2E ERCC2 POLR2E p6 POLR2C TAF10 POLR2G GTF2H4 HIV-1 Polymerase II CCNT2 UBCPOLR2DTBP POM121 NEDD4LNUP155 MA XRCC6 POLR2H NELFASUPT4H1 ATPNUP85 PR GTF2A1POLR2DPOLR2L CDK9 LIG4 REV HMGA1 2-LTR form of circular viral DNAGTF2F1GTF2A2 POLR2I POLR2L PSIP1 POLR2E UBA52POLR2G DSIFNELFearly elongation complex after limited nucleotide additionGTF2H2 ATP Nup45 PPIA UBBGTF2F2REV CD4 GTF2F1POLR2L POLR2C GTF2F1p6 GTF2H4 ELL p-S2,S5-POLR2A MA p6 POLR2DTAF1 p-S5-POLR2A SUPT16H GTF2H4 TCEB1 POLR2G CD4 UBBTCEA1 CHMP4C CDK7 POLR2E Reverse transcriptase/ribonuclease H UBCNELFANELFCD GTF2F2GTF2F1SSRP1 CTDP1 CDK7 POLR2J REV PR Multimeric capsid coatNCBP1 POLR2H POLR2C NELFCD CCNH PPiPOLR2J GTF2H4 REV MNAT1 POLR2L CD4 ERCC2 XRCC6 CD4 UBBPOLR2E CCNT2 VPR ERCC3 VPR SUPT4H1 HMGA1 PPIA NELFCD GTF2A2 CDK9 POLR2B ERCC3 SUPT16H UBCp-S5-POLR2A TCEB1 p6 MNAT1 Ran GTPaseGDPMNAT1 CCNH TAF11 CXCR4 GTF2A1POLR2B ERCC3 tRNA-Lysine3PPIACDK7 TAF10 POLR2DReverse transcriptase/ribonuclease H RAE1 NELFCD p6 TAF5 VPR CCNT2 PPiCCNT1 GTF2F2p51 UBCPOLR2H GTP TAF10 POLR2DVPR POLR2H SUPT4H1 NELFB VPU POLR2E P-TEFbHMGA1 Nup45 RNMTp51 ERCC2 p6 POLR2K UBCPOLR2C POLR2DTAF11 MA XRCC4 UBCVPU POLR2J HIV-1 Promoter Escape ComplexMA NELFAVIF SSRP1 POLR2B NELFCD NELFB POLR2FVPR TAF9 MA XRCC6 POLR2L POLR2DCDK7 POLR2L p-S2,S5-POLR2A POLR2K POLR2B ATP PPIA MA POLR2J POLR2B p51 POLR2G GTF2F2p-SUPT5H TAF13 p6 NELFB p51 NUP43 GTF2F1CCNH TCEB2 POLR2G POLR2E p-S5-POLR2A POLR2G CTDP1 TAF13 p6 POLR2L Encapsidated viral corePPIA TAF6 POLR2J Immature HIV virionNELFB GTF2H3 TCEA1 MA VPU Ku proteins bound to viral DNAERCC2 RAN GTF2E2 IN SUPT4H1 MA SUPT4H1 POLR2FPOLR2DREV p-NELFE p6 CHMP2A CDK7 GTF2E1 POLR2J MNAT1 Surface protein gp120 CDK7 GTF2H2 NC Transmembrane protein gp41 POLR2C VPS4APOLR2H POLR2B NELFACXCR4 UBCPOLR2C TCEB1 POLR2H CDK7 GTF2H2 NUP153 POLR2I TCEB1 NCBP2 PIC REV MA SUPT16H GTF2H1Tat GTF2H4 p-S5-POLR2A POLR2G MA POLR2J CCNT1 p-S5-POLR2A GTF2F2CCNT1 p6 ERCC2 p6 NTPHIV-1 unspliced RNAPOLR2E POLR2J GTF2H3 CDK9 POLR2L MYS-CoACTDP1 GTF2F1TAF11 CDK9 POLR2C NELFAGTF2BPOLR2L Surface protein gp120 POLR2H GTF2H2 POLR2I GTF2H3 VPU VPU GTF2F2RTGTF2F2SUPT16H N-myristoyl GAG NELFB UTP NUP43 GTF2A1POLR2H ERCC2 BANF1 GTF2H2 VIF ERCC2 NTPXPO1NELF complexCDK7 POLR2J POLR2FVPR POLR2H CTP VPR POLR2B PR N-myristoyl GAG REV GTF2F1TAF9 POLR2H RTC p-S2,S5-POLR2A p6 GTF2F2TAF12 POLR2E POLR2I GTF2H3 MNAT1 SUPT16H CDK7 viral DNA bound with Integrase in PICCHMP7 p-SUPT5H POLR2B NC POLR2G VPU GTF2H1POLR2C UBCVPU GTF2F1Cap Binding Complex POLR2C SUPT4H1 CCNT1 TCEA1 CTDP1 POLR2H GTF2H3 POLR2G Reverse transcriptase/ribonuclease H CD4 POLR2L POLR2I POLR2C TFIIHERCC2 p6 POLR2K POLR2I GTF2F1myristoylated Nef Protein CTP POLR2C ERCC2 POLR2K HIV-1 RNA POLR2B UBBp6 SSRP1 PR POLR2I NC SEH1L-2 Reverse transcriptase/ribonuclease H myristoylated Nef Protein POLR2H HIV-1 transcription complex containing extruded transcript to +30VPU PPIA p6 REV TCEB3 GTF2B GTF2F2TAF4 FURINVPR NELFB TBP GTF2H2 SEH1L-2 VPS4B TAF6 Trimeric ENV precursorPOLR2E GTF2H4 POLR2K RAN TAF1 Surface protein gp120 POLR2DVPS37B GTF2F2POLR2J NCBP1 POLR2I GTF2F2POLR2B POLR2K N-myristoyl GAG Aborted HIV-1 early elongation complexmonoubiquitinated N-myristoyl GAG POLR2DTAF9 VPU GTF2F1HIV-1 transcription complex containing 4-9 nucleotide long transcriptPOLR2C VIF POLR2DNCBP1 NUP205NUP85 ATP IN HIV-1 RNA TCEA1p6 TAF10 REV TCEA1 RNA Polymerase II NC POLR2J p-S5-POLR2A Transmembrane protein gp41 GTF2F1POLR2DERCC3 POLR2K RAN POLR2H POLR2FGTF2H3 POLR2G GAG Polyprotein POLR2B GTF2F2GTP POLR2I SUPT4H1 viral RNA template degraded by RNase-H CHMP3p6 POLR2DGTF2F1POLR2J POLR2B GTF2F2GTF2H1GTF2F1GTF2F1GTF2E2 TAF12 POLR2C NELFB POLR2E TAF5 TCEB2 GTP POLR2I POLR2J TCEB2 ERCC3 GTF2H2 p6 MNAT1 Transmembrane protein gp41 GTF2H4 SUPT4H1 CTDP1 Elongin ComplexGTF2F2XRCC4DNA ligase IV complexNELFAGTF2H1p51 POLR2I Transmembrane protein gp41 GTF2H3 NELFE ESCRT-IIIviral RNA template degraded by RNase-H POLR2G VIF ATP POLR2B GTF2A1GTF2A1GTF2F1POLR2K POLR2C p6 MA MNAT1 NTPP-TEFb complexPOLR2C POLR2J p51 GTF2F1MNAT1 GAG-POL Polyprotein VPU POLR2H Tat TCEB1 POLR2I POLR2E NC CDK7 VPR GTF2E2 POLR2E p-SUPT5H GTF2F2GTF2H2 HIV-1 Tat-containing arrested processive elongation complexERCC2 p-S2,S5-POLR2A HIV-1 RNA template VIF XRCC5 TAF6 NELFAp-S2,S5-POLR2A NELFB RANBP1VPR HIV-1 RNA UBCCCNT1 TAF12 POLR2FRPS27ACDK7 GTP POLR2C CHMP5 MA GTF2F2POLR2L POLR2B PPIA TFIIANUP107 TCEB2 IN bound to sticky 3' ends of viral DNA in PICTat CDK9 PPIA other viral genomic RNAPOLR2J TBP p-SUPT5H MA PPIA POLR2G GTF2H3 GTF2H2 POLR2L p6 Virion with gp41 forming hairpin structureRev multimer-bound HIV-1 mRNACRM1 complexIN p6 POLR2FCCNH POLR2L POLR2H HIV-1 Tat-containing processive elongation complexGTF2H4 POLR2J ATP POLR2DHIV-1 elongation complex containing TatRNGTT GTF2A2 TAF12 Transmembrane protein gp41 POLR2J CCNT2 POLR2I ERCC3 POLR2I NCBP1 REV TCEB3 UBCReverse transcriptase/ribonuclease H GTF2F2RNA Polymerase II Reverse transcriptase/ribonuclease H ELL VIF VPS37C IN Virion with gp41 exposedPOLR2L GTF2F2Rev-multimerPOLR2K POLR2C GTF2H1NUP35 IN TCEA1 VIF CXCR4 GTF2F1NELFCD POLR2C TAF9 POLR2G POLR2E POLR2B CoA-SHTFIIAGTF2A1HMGA1 UBCGTF2H2 PPIA IN Surface protein gp120 PPIA FEN1Glycosylated Envelope glycoprotein gp160 POLR2DPOLR2DGTF2F1TCEB3 POLR2J TBP Surface protein gp120 NCBP2 p6 CCNT2 GTF2H2 MA NELFB VIF VIF IN POLR2E VIF VIF PSIP1 IN CCNH TAF10 NC UBCTAF1 myristoylated Nef Protein GTF2F1MNAT1 CDK7 TAF6 BANF1 ERCC3 XPO1POLR2E VIF VPR Transmembrane protein gp41 RTC with extending second-strand DNAPOLR2DUBCCTDP1 NELFCD POLR2I POLR2E NUP160 CHMP6POLR2B POLR2B GTF2H1GTF2F1UBCMature HIV virionTBP POLR2H ERCC2 p51 XRCC5 GTF2H4 POLR2J CDK7 p-S5-POLR2A GTF2F2GTF2H4 Reverse transcriptase/ribonuclease H GTF2A2 POLR2J POLR2DREV VPU p-S2,S5-POLR2A Reverse transcriptase/ribonuclease H REV N-myristoyl GAG POLR2J ERCC3 UBA52GTF2E1 HIV-1 initiation complexTrimeric gp120gp41 oligomerPOLR2DGTF2F2VPR TAF10 UBCPOLR2E BANF1 POLR2H p-S2,S5-POLR2A MNAT1 p6 POLR2G TAF4 GDP GTF2H4 POLR2G NUP88 CDK9 p-S2,S5-POLR2A PPIA Transmembrane protein gp41 POLR2K TSG101TAF5 TAF6 Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELFPOLR2G POLR2A TFIIHVIF POLR2K POLR2K Virion with exposed coreceptor binding sitesHIV-1 RNA POLR2G RAN POLR2L UBBPOLR2L POLR2L Reverse transcriptase/ribonuclease H GTF2H1TAF11 POLR2I VPS37C MA VPU TCEB2 POLR2I VPR GTF2F2UBCPOLR2FHIV-1 RNA template RTC with extending minus strand DNAERCC3 POLR2K HIV-1 RNA template Envelope glycoprotein gp160 p51 CCNH RTC with degraded RNA template and minus sssDNAp-SUPT5H Tat TAF4 POLR2K POLR2E RNA Pol II POLR2J CCNT2 CDK7 Reverse transcriptase/ribonuclease H RPS27AGTF2F2NELFAGTF2H1ERCC2 PPIA GTF2F2IN p-SUPT5H POLR2FPOLR2H POLR2C NUP133 GTF2E1 GTF2A1CHMP4B TBP TAF1 GTF2B GTF2H4 SUPT4H1 POLR2E GTF2H2 GTF2H3 POLR2L TAF1 REV Surface protein gp120 POLR2B POLR2E ERCC3 POLR2G POLR2H POLR2H PiHIV-1 transcription complex containing 4 nucleotide long transcriptPOLR2L VPR NUP188POLR2K GTF2H1RTC with minus sssDNAtRNA primerRNA templateGTF2H4 GTF2E2 PPIA NC CDK9 GTF2H3 HIV-1 mRNA POLR2Dp-S2,S5-POLR2A NELFCD CCNH POLR2I TAF11 TFIIDBANF1GTF2H1TAF9 CDK7 viral RNA template extensively digested except in PPT region REV p-SUPT5Hp-SUPT5H POLR2K SUPT16H GTP MA TFIIEVIF POLR2DCCR5, CXCR4POLR2H p6 p6 POLR2E Reverse transcriptase/ribonuclease H POLR2G NELFCD PPIA SUPT16H POLR2FSSRP1 p51 REV POLR2FERCC2 NELFB POLR2C CTDP1 GTF2F1VIF ERCC3 NELFCD CCNH p-SUPT5H Rev multimer-bound HIV-1 mRNAHIV-1 arrested processive elongation complexTat POLR2DVPU CCNT1 NELFCD NCBP2 ERCC3 VIF PPIA TAF9 CDK9 TCEB3 NELFE BANF1 NUP205TAF11 NC IN GTF2F1UTP CDK7 UTP NELFCD POLR2E CCR5 SSRP1 MA GTF2H2 VIF TFIIEPOLR2L TAF4B POLR2L RNMT p51 HIV-1 template DNA4-9 nucleotide transcript hybridPOLR2K NELFE GTP CCNH POLR2C VIF SSRP1 ERCC2 NC GTF2F2p6 POLR2A SSRP1 CCNH TatP-TEFbSUPT4H1 VIF POLR2L GTF2F2GTF2F1POLR2FGTF2F1ELL POLR2H PSIP1 viral DNAKu proteinsXRCC4DNA ligase IV complexGTF2F1GTF2F2POLR2E NUP50 CDK9 POLR2DTAF4B CCNT1 SUPT16H NC NELFE p-S2,S5-POLR2A NUP214 POLR2FPPIA Nef Protein GTF2A1POLR2I GTF2F2POLR2K POLR2B TAF6 CHMP2B TCEA1 RanGTPIN POLR2J 1-LTR form of circular viral DNAREV GTF2E1 VPR POLR2FVirion with CD4gp120 bound to CCR5/CXCR4UBCHMGA1 TFIIHp51 NELFAIN UBCHIV-1 RNA template VPU PPiRTC with extensive RNase-H digestionIN p-S2,S5-POLR2A Virion with fusogenically activated gp41PR POLR2K Spliced Env mRNAPOLR2I POLR2G Ku70Ku80 heterodimerGTP VPR p6 TAF1 VIF POLR2H Autointegrated viral DNA as an inverted circlep-SUPT5H MA TAF5 MNAT1 VPR UBCGAG-POL Polyprotein POLR2K CCNT1 CCNH GTF2H3 RANBP2 VPU VPU POLR2B p6 REV POLR2K POLR2FPSIP1 VPR Integration intermediateCCNT1 UBCPOLR2B POLR2C Autointegrated viral DNA as smaller circlesPOLR2I HIV-1 transcription complex containing 9 nucleotide long transcriptGTF2H1ERCC3 TAF4 UBCMA POLR2B XPO1 NELFE NUP155 POLR2L P-TEFbPOLR2Fp-S2,S5-POLR2A VTA1 PPIA POM121 POLR2L HIV-1 transcription complexPOLR2DSurface protein gp120 TAF13 POLR2L GTF2A1TCEA1 POLR2H POLR2G GTF2F2POLR2G TAF4B NMT1POLR2J VPU GTF2H3 CDK9 GTF2F1NCBP1 NUPL2 UBCGTF2A1POLR2J POLR2E POLR2K POLR2I UBCTAF5 VPU POLR2A TBP NUP153 GTF2A1Reverse transcriptase/ribonuclease H ERCC3 POLR2H POLR2C REV UBCPOLR2L POLR2G VPU HMGA1PR CCNT1 REV GTF2B MA POLR2B GTF2H2 PSIP1 POLR2A TFIIHCCNH NELFACCNH UBCHIV-1 mRNA CDK9 TAF13 GTF2E1 PDCD6IP HIV-1 transcription complex containing transcript to +30IN HIV-1 RNA GTF2E1 CCNH monoubiquitinated N-myristoyl GAG GTF2H1TBP POLR2B Ku proteins bound to viral DNAp51 GAG-POL Polyprotein p-S2,S5-POLR2A Reverse transcriptase/ribonuclease H NC NUP214 p-S2,S5-POLR2A GTF2H2 IN UBCPOLR2DVirion with gp41 fusion peptide in insertion complexNCBP1 MNAT1 Transmembrane protein gp41 IN CCNH POLR2C ERCC3 GTF2A1POLR2B ERCC3 POLR2K CDK9 IN POLR2E POLR2FSurface protein gp120 CDK7 NC IN POLR2FGTF2E2 HIV-1 early elongation complex with hyperphosphorylated Pol II CTDRANBP2 viral PIC proteinsTCEB2 VPU MNAT1 POLR2E myristoylated Nef Protein UBCCDK7 POLR2J ERCC3 POLR2DPOLR2J POLR2B GTF2F1myristoylated Nef Protein REV CDK9 VPR POLR2G HIV-1 RNA template POLR2FMA CDK9 VPS4B POLR2L UbIN GTF2F1MA POLR2J GTF2H1CTP CDK9 VPR ERCC2 MNAT1 XPO1 POLR2B TAF13 myristoylated Nef Protein IN POLR2DPOLR2A POLR2L TCEB3 PPIA TAF4 CCR5 NUP98-5 TCEB1 p-SUPT5H GTF2F2POLR2H POLR2C MNAT1 GTF2H3 ATP CHMP2B SUPT4H1 GTF2E1 GTF2H2 CCNH REV RNGTT NELFE NC POLR2E POLR2B p-S2,S5-POLR2A CDK7 CTP VPS37D POLR2J Tat GTF2F1CEPol II CTDSpt5 complexNELFB CTDP1 VPR IN POLR2C VIF VPR POLR2J VIF POLR2H POLR2I GTF2F1PSIP1POLR2L NELFAIN Reverse transcriptase/ribonuclease H POLR2FMA CCNT1 POLR2FCDK9 BANF1 REV PR CHMP4A REV GTF2B p6 POLR2C 7, 13, 16846831


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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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 ProteinQ9NRG9 (Uniprot-TrEMBL)
ADPMetaboliteCHEBI:16761 (ChEBI)
ATP MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted HIV-1 early elongation complexComplexREACT_6695 (Reactome)
Assembling HIV virionComplexREACT_164418 (Reactome)
Autointegrated viral DNA as smaller circlesComplexREACT_7557 (Reactome)
Autointegrated viral DNA as an inverted circleComplexREACT_7515 (Reactome)
BANF1 ProteinO75531 (Uniprot-TrEMBL)
BANF1ProteinO75531 (Uniprot-TrEMBL)
CCNH ProteinP51946 (Uniprot-TrEMBL)
CCNT1 ProteinO60563 (Uniprot-TrEMBL)
CCNT2 ProteinO60583 (Uniprot-TrEMBL)
CCR5 ProteinP51681 (Uniprot-TrEMBL)
CCR5, CXCR4ProteinREACT_8732 (Reactome)
CD4

Env gp120/gp41 hairpin complex

CCR5/CXCR4		ComplexREACT_8249 (Reactome)
CD4 ProteinP01730 (Uniprot-TrEMBL)
CD4ProteinP01730 (Uniprot-TrEMBL)
CDK7 ProteinP50613 (Uniprot-TrEMBL)
CDK9 ProteinP50750 (Uniprot-TrEMBL)
CE

Pol II CTD

Spt5 complex		ComplexREACT_6491 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CHMP2A ProteinO43633 (Uniprot-TrEMBL)
CHMP2B ProteinQ9UQN3 (Uniprot-TrEMBL)
CHMP3ProteinQ9Y3E7 (Uniprot-TrEMBL)
CHMP4A ProteinQ9BY43 (Uniprot-TrEMBL)
CHMP4B ProteinQ9H444 (Uniprot-TrEMBL)
CHMP4C ProteinQ96CF2 (Uniprot-TrEMBL)
CHMP5 ProteinQ9NZZ3 (Uniprot-TrEMBL)
CHMP6ProteinQ96FZ7 (Uniprot-TrEMBL)
CHMP7 ProteinQ8WUX9 (Uniprot-TrEMBL)
CTDP1 ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP MetaboliteCHEBI:17677 (ChEBI)
CXCR4 ProteinP61073 (Uniprot-TrEMBL)
Cap Binding Complex ComplexREACT_3884 (Reactome)
CoA-SHMetaboliteCHEBI:15346 (ChEBI)
DSIF

NELF

early elongation complex after limited nucleotide addition		ComplexREACT_6432 (Reactome)
DSIF

NELF

early elongation complex		ComplexREACT_6594 (Reactome)
DSIF complexComplexREACT_2797 (Reactome)
ELL ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 ProteinP18074 (Uniprot-TrEMBL)
ERCC3 ProteinP19447 (Uniprot-TrEMBL)
ESCRT-IIIComplexREACT_27898 (Reactome)
ESCRT-IComplexREACT_27580 (Reactome)
Early elongation complex with separated aborted transcriptComplexREACT_6590 (Reactome)
Elongin ComplexComplexREACT_5616 (Reactome)
Encapsidated viral coreComplexREACT_9259 (Reactome)
Envelope glycoprotein gp160 ProteinP04578 (Uniprot-TrEMBL)
Envelope glycoprotein gp160ProteinP04578 (Uniprot-TrEMBL)
FACT complexComplexREACT_4314 (Reactome)
FEN1ProteinP39748 (Uniprot-TrEMBL)
FURINProteinP09958 (Uniprot-TrEMBL)
GAG Polyprotein ProteinP04591 (Uniprot-TrEMBL)
GAG-POL Polyprotein ProteinP04585 (Uniprot-TrEMBL)
GDP MetaboliteCHEBI:17552 (ChEBI)
GDPMetaboliteCHEBI:17552 (ChEBI)
GTF2A1ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 ProteinP52657 (Uniprot-TrEMBL)
GTF2B ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 ProteinP29084 (Uniprot-TrEMBL)
GTF2F1ProteinP35269 (Uniprot-TrEMBL)
GTF2F2ProteinP13984 (Uniprot-TrEMBL)
GTF2H1ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 ProteinQ92759 (Uniprot-TrEMBL)
GTP MetaboliteCHEBI:15996 (ChEBI)
GTPMetaboliteCHEBI:15996 (ChEBI)
Glycosylated Envelope glycoprotein gp160 ProteinP04578 (Uniprot-TrEMBL)
HIV-1 Polymerase II ComplexREACT_6503 (Reactome)
HIV-1 Promoter Escape ComplexComplexREACT_6417 (Reactome)
HIV-1 RNA ProteinAF033819 (EMBL)
HIV-1 RNA homodimerComplexREACT_8245 (Reactome)
HIV-1 RNA template ProteinAF033819 (EMBL)
HIV-1 Tat-containing aborted elongation complex after arrestComplexREACT_6602 (Reactome)
HIV-1 Tat-containing arrested processive elongation complexComplexREACT_6532 (Reactome)
HIV-1 Tat-containing paused processive elongation complexComplexREACT_6389 (Reactome)
HIV-1 Tat-containing processive elongation complexComplexREACT_6452 (Reactome)
HIV-1 aborted elongation complex after arrestComplexREACT_6471 (Reactome)
HIV-1 arrested processive elongation complexComplexREACT_6609 (Reactome)
HIV-1 capped pre-mRNA

CBC

RNA Pol II 		ComplexREACT_6374 (Reactome)
HIV-1 closed pre-initiation complexComplexREACT_6553 (Reactome)
HIV-1 early elongation complex with hyperphosphorylated Pol II CTDComplexREACT_6467 (Reactome)
HIV-1 elongation complex containing TatComplexREACT_6611 (Reactome)
HIV-1 elongation complexComplexREACT_6501 (Reactome)
HIV-1 initiation complex with phosphodiester-PPi intermediateComplexREACT_6680 (Reactome)
HIV-1 initiation complexComplexREACT_6518 (Reactome)
HIV-1 mRNA ProteinAF033819 (EMBL)
HIV-1 mRNARnaAF033819 (EMBL)
HIV-1 open pre-initiation complexComplexREACT_6605 (Reactome)
HIV-1 paused processive elongation complexComplexREACT_6459 (Reactome)
HIV-1 processive elongation complexComplexREACT_6579 (Reactome)
HIV-1 template DNA 4-9 nucleotide transcript hybridREACT_6414 (Reactome)
HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotidesREACT_6665 (Reactome)
HIV-1 template DNA with first transcript dinucleotide, opened to +8 positionREACT_6558 (Reactome)
HIV-1 transcription complex containing 11 nucleotide long transcriptComplexREACT_6664 (Reactome)
HIV-1 transcription complex containing 3 nucleotide long transcriptComplexREACT_6450 (Reactome)
HIV-1 transcription complex containing 4 nucleotide long transcriptComplexREACT_6640 (Reactome)
HIV-1 transcription complex containing 4-9 nucleotide long transcriptComplexREACT_6563 (Reactome)
HIV-1 transcription complex containing 9 nucleotide long transcriptComplexREACT_6561 (Reactome)
HIV-1 transcription complex containing extruded transcript to +30ComplexREACT_6516 (Reactome)
HIV-1 transcription complex containing transcript to +30ComplexREACT_6514 (Reactome)
HIV-1 transcription complex with ComplexREACT_6638 (Reactome)
HIV-1 transcription complexComplexREACT_6433 (Reactome)
HIV-1 unspliced RNARnaAF033819 (EMBL)
HMGA1 ProteinP17096 (Uniprot-TrEMBL)
HMGA1ProteinP17096 (Uniprot-TrEMBL)
Host genomic DNAREACT_7748 (Reactome)
IN viral DNA bound to host genomic DNA with staggered endsComplexREACT_9176 (Reactome)
IN ProteinP04585 (Uniprot-TrEMBL)
IN bound to sticky 3' ends of viral DNA in PICComplexREACT_7635 (Reactome)
IN bound to sticky 3' ends of viral DNA in PICComplexREACT_8354 (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 ProteinP49917 (Uniprot-TrEMBL)
MA ProteinP04585 (Uniprot-TrEMBL)
MA ProteinP04591 (Uniprot-TrEMBL)
MNAT1 ProteinP51948 (Uniprot-TrEMBL)
MYS-CoAMetaboliteCHEBI:15532 (ChEBI)
MatrixProteinREACT_8346 (Reactome)
Mature HIV virionComplexREACT_8805 (Reactome)
Multimeric capsid coatREACT_8190 (Reactome)
N-myristoyl GAG ProteinP04591 (Uniprot-TrEMBL)
NC ProteinP04585 (Uniprot-TrEMBL)
NC ProteinP04591 (Uniprot-TrEMBL)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NEDD4LProteinQ96PU5 (Uniprot-TrEMBL)
NELF complexComplexREACT_2737 (Reactome)
NELFAProteinQ9H3P2 (Uniprot-TrEMBL)
NELFB ProteinQ8WX92 (Uniprot-TrEMBL)
NELFCD ProteinQ8IXH7 (Uniprot-TrEMBL)
NELFE ProteinP18615 (Uniprot-TrEMBL)
NMT1ProteinP30419 (Uniprot-TrEMBL)
NMT2ProteinO60551 (Uniprot-TrEMBL)
NTPMetaboliteREACT_4491 (Reactome)
NUP107 ProteinP57740 (Uniprot-TrEMBL)
NUP133 ProteinQ8WUM0 (Uniprot-TrEMBL)
NUP153 ProteinP49790 (Uniprot-TrEMBL)
NUP155 ProteinO75694 (Uniprot-TrEMBL)
NUP160 ProteinQ12769 (Uniprot-TrEMBL)
NUP188ProteinQ5SRE5 (Uniprot-TrEMBL)
NUP205ProteinQ92621 (Uniprot-TrEMBL)
NUP210 ProteinQ8TEM1 (Uniprot-TrEMBL)
NUP214 ProteinP35658 (Uniprot-TrEMBL)
NUP35 ProteinQ8NFH5 (Uniprot-TrEMBL)
NUP37 ProteinQ8NFH4 (Uniprot-TrEMBL)
NUP43 ProteinQ8NFH3 (Uniprot-TrEMBL)
NUP50 ProteinQ9UKX7 (Uniprot-TrEMBL)
NUP54 ProteinQ7Z3B4 (Uniprot-TrEMBL)
NUP62 ProteinP37198 (Uniprot-TrEMBL)
NUP85 ProteinQ9BW27 (Uniprot-TrEMBL)
NUP88 ProteinQ99567 (Uniprot-TrEMBL)
NUP93 ProteinQ8N1F7 (Uniprot-TrEMBL)
NUP98-5 ProteinP52948-5 (Uniprot-TrEMBL)
NUPL1-2 ProteinQ9BVL2-1 (Uniprot-TrEMBL)
NUPL2 ProteinO15504 (Uniprot-TrEMBL)
Nef Protein ProteinP04601 (Uniprot-TrEMBL)
Nuclear Pore Complex ComplexREACT_5542 (Reactome)
NucleocapsidProteinREACT_8930 (Reactome)
Nup45 ProteinQ9BVL2-2 (Uniprot-TrEMBL)
P-TEFb complexComplexREACT_3433 (Reactome)
P-TEFbComplexREACT_6577 (Reactome)
P-TEFbComplexREACT_6686 (Reactome)
PDCD6IP ProteinQ8WUM4 (Uniprot-TrEMBL)
PDCD6IPProteinQ8WUM4 (Uniprot-TrEMBL)
PIC ComplexREACT_9179 (Reactome)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2DProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2FProteinP61218 (Uniprot-TrEMBL)
POLR2G ProteinP62487 (Uniprot-TrEMBL)
POLR2H ProteinP52434 (Uniprot-TrEMBL)
POLR2I ProteinP36954 (Uniprot-TrEMBL)
POLR2J ProteinP52435 (Uniprot-TrEMBL)
POLR2K ProteinP53803 (Uniprot-TrEMBL)
POLR2L ProteinP62875 (Uniprot-TrEMBL)
POM121 ProteinQ96HA1 (Uniprot-TrEMBL)
PPIA ProteinP62937 (Uniprot-TrEMBL)
PPIAProteinP62937 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
PR ProteinP04585 (Uniprot-TrEMBL)
PSIP1 ProteinO75475 (Uniprot-TrEMBL)
PSIP1ProteinO75475 (Uniprot-TrEMBL)
PiMetaboliteCHEBI:18367 (ChEBI)
RAE1 ProteinP78406 (Uniprot-TrEMBL)
RAN ProteinP62826 (Uniprot-TrEMBL)
RANBP1ProteinP43487 (Uniprot-TrEMBL)
RANBP2 ProteinP49792 (Uniprot-TrEMBL)
RANGAP1ProteinP46060 (Uniprot-TrEMBL)
RCC1ProteinP18754 (Uniprot-TrEMBL)
REV ProteinP04618 (Uniprot-TrEMBL)
RNA Pol II ComplexREACT_6382 (Reactome)
RNA Pol II ComplexREACT_6426 (Reactome)
RNA Pol II with phosphorylated CTD CE complex with activated GTComplexREACT_6659 (Reactome)
RNA Pol II with phosphorylated CTD CE complexComplexREACT_6521 (Reactome)
RNA Polymerase II ComplexREACT_2692 (Reactome)
RNGTT ProteinO60942 (Uniprot-TrEMBL)
RNGTTProteinO60942 (Uniprot-TrEMBL)
RNMT ProteinO43148 (Uniprot-TrEMBL)
RNMTProteinO43148 (Uniprot-TrEMBL)
RPS27AProteinP62979 (Uniprot-TrEMBL)
RTC ComplexREACT_9085 (Reactome)
RTC with annealed complementary PBS seqments in +sssDNA and -strand DNAComplexREACT_9090 (Reactome)
RTC with degraded RNA template and minus sssDNAComplexREACT_9203 (Reactome)
RTC with duplex DNA containing discontinuous plus strand flapComplexREACT_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

tRNA primer

RNA template		ComplexREACT_9297 (Reactome)
RTC with minus sssDNA transferred to 3'-end of viral RNA templateComplexREACT_9360 (Reactome)
RTC with minus strand DNA synthesis initiated from 3'-endComplexREACT_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 GTPComplexREACT_8632 (Reactome)
Ran GTPase GDPComplexREACT_6416 (Reactome)
Ran-GDPComplexREACT_9732 (Reactome)
Ran-GTPComplexREACT_8980 (Reactome)
RanBP1

Ran-GTP CRM1

Rev-bound mRNA complex		ComplexREACT_8366 (Reactome)
Rev multimer-bound HIV-1 mRNA CRM1 complexComplexREACT_8117 (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 mRNAComplexREACT_6517 (Reactome)
Rev-bound HIV-1 mRNAComplexREACT_6419 (Reactome)
Rev-multimerREACT_6379 (Reactome)
Rev-multimerREACT_6511 (Reactome)
Reverse transcriptase/ribonuclease H ProteinP04585 (Uniprot-TrEMBL)
SEH1L-2 ProteinQ96EE3-2 (Uniprot-TrEMBL)
SSRP1 ProteinQ08945 (Uniprot-TrEMBL)
SUPT16H 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 ProteinP63272 (Uniprot-TrEMBL)
Spliced Env mRNARnaAF033819 (EMBL)
Surface protein gp120 ProteinP04578 (Uniprot-TrEMBL)
TAF1 ProteinP21675 (Uniprot-TrEMBL)
TAF10 ProteinQ12962 (Uniprot-TrEMBL)
TAF11 ProteinQ15544 (Uniprot-TrEMBL)
TAF12 ProteinQ16514 (Uniprot-TrEMBL)
TAF13 ProteinQ15543 (Uniprot-TrEMBL)
TAF4 ProteinO00268 (Uniprot-TrEMBL)
TAF4B ProteinQ92750 (Uniprot-TrEMBL)
TAF5 ProteinQ15542 (Uniprot-TrEMBL)
TAF6 ProteinP49848 (Uniprot-TrEMBL)
TAF9 ProteinQ16594 (Uniprot-TrEMBL)
TBP ProteinP20226 (Uniprot-TrEMBL)
TCEA1 ProteinP23193 (Uniprot-TrEMBL)
TCEA1ProteinP23193 (Uniprot-TrEMBL)
TCEB1 ProteinQ15369 (Uniprot-TrEMBL)
TCEB2 ProteinQ15370 (Uniprot-TrEMBL)
TCEB3 ProteinQ14241 (Uniprot-TrEMBL)
TFIIAComplexREACT_5743 (Reactome)
TFIIDComplexREACT_5886 (Reactome)
TFIIEComplexREACT_2368 (Reactome)
TFIIHComplexREACT_3832 (Reactome)
TPR ProteinP12270 (Uniprot-TrEMBL)
TSG101ProteinQ99816 (Uniprot-TrEMBL)
Tat P-TEFbComplexREACT_6496 (Reactome)
Tat ProteinP04608 (Uniprot-TrEMBL)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD ComplexREACT_6633 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELFComplexREACT_6495 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTDComplexREACT_6536 (Reactome)
Tat-containing elongation complex prior to separationComplexREACT_6548 (Reactome)
Transmembrane protein gp41 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)
UBA52ProteinP62987 (Uniprot-TrEMBL)
UBBProteinP0CG47 (Uniprot-TrEMBL)
UBCProteinP0CG48 (Uniprot-TrEMBL)
UTP MetaboliteCHEBI:15713 (ChEBI)
UbProteinREACT_3316 (Reactome)
VIF ProteinP69723 (Uniprot-TrEMBL)
VPR ProteinP69726 (Uniprot-TrEMBL)
VPS28 ProteinQ9UK41 (Uniprot-TrEMBL)
VPS37A ProteinQ8NEZ2 (Uniprot-TrEMBL)
VPS37B ProteinQ9H9H4 (Uniprot-TrEMBL)
VPS37C ProteinA5D8V6 (Uniprot-TrEMBL)
VPS37D ProteinQ86XT2 (Uniprot-TrEMBL)
VPS4AProteinQ9UN37 (Uniprot-TrEMBL)
VPS4B ProteinO75351 (Uniprot-TrEMBL)
VPU ProteinP05919 (Uniprot-TrEMBL)
VTA1 ProteinQ9NP79 (Uniprot-TrEMBL)
Viral core surrounded by Matrix layerComplexREACT_8910 (Reactome)
Virion Budding ComplexComplexREACT_164706 (Reactome)
Virion with CD4 gp120 bound to CCR5/CXCR4ComplexREACT_8665 (Reactome)
Virion with CD4 bound to gp120ComplexREACT_8731 (Reactome)
Virion with exposed coreceptor binding sitesComplexREACT_8974 (Reactome)
Virion with fusogenically activated gp41ComplexREACT_8472 (Reactome)
Virion with gp41 exposedComplexREACT_8727 (Reactome)
Virion with gp41 forming hairpin structureComplexREACT_8661 (Reactome)
Virion with gp41 fusion peptide in insertion complexComplexREACT_8875 (Reactome)
Vps/Vta1ComplexREACT_27371 (Reactome)
XPO1 ProteinO14980 (Uniprot-TrEMBL)
XPO1ProteinO14980 (Uniprot-TrEMBL)
XRCC4 DNA ligase IV complexComplexREACT_3745 (Reactome)
XRCC4 ProteinQ13426 (Uniprot-TrEMBL)
XRCC5 ProteinP13010 (Uniprot-TrEMBL)
XRCC6 ProteinP12956 (Uniprot-TrEMBL)
dNTPMetaboliteREACT_9307 (Reactome)
monoubiquitinated N-myristoyl GAG ComplexREACT_116777 (Reactome)
monoubiquitinated N-myristoyl GAG ComplexREACT_116878 (Reactome)
monoubiquitinated N-myristoyl GAG ComplexREACT_165330 (Reactome)
myristoylated Nef Protein ProteinP04601 (Uniprot-TrEMBL)
other viral genomic RNARnaAF033819 (EMBL)
p-NELFE ProteinP18615 (Uniprot-TrEMBL)
p-S2,S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-SUPT5H ProteinO00267 (Uniprot-TrEMBL)
p-SUPT5HProteinO00267 (Uniprot-TrEMBL)
p51 ProteinP04585 (Uniprot-TrEMBL)
p6 ProteinP04585 (Uniprot-TrEMBL)
p6 ProteinP04591 (Uniprot-TrEMBL)
tRNA-Lysine3REACT_8477 (Reactome)
uncoated viral complexComplexREACT_9366 (Reactome)
viral DNA

Ku proteins XRCC4

DNA ligase IV complex		ComplexREACT_9308 (Reactome)
viral DNA bound with Integrase in PICComplexREACT_9078 (Reactome)
viral PIC proteinsComplexREACT_9170 (Reactome)
viral RNA template being digested by RNase-H ProteinAF033819 (EMBL)
viral RNA template degraded by RNase-H ProteinAF033819 (EMBL)
viral RNA template extensively digested except in PPT region 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)
Autointegrated viral DNA as smaller circlesArrowREACT_9025 (Reactome)
Autointegrated viral DNA as an inverted circleArrowREACT_9006 (Reactome)
BANF1REACT_9010 (Reactome)
CCR5, CXCR4REACT_7962 (Reactome)
CD4

Env gp120/gp41 hairpin complex

CCR5/CXCR4		ArrowREACT_8032 (Reactome)
CD4REACT_8009 (Reactome)
CTDP1REACT_6206 (Reactome)
Cap Binding Complex ArrowREACT_6170 (Reactome)
Cap Binding Complex ArrowREACT_6297 (Reactome)
Cap Binding Complex REACT_6166 (Reactome)
CoA-SHArrowREACT_115774 (Reactome)
CoA-SHArrowREACT_116143 (Reactome)
DSIF

NELF

early elongation complex		ArrowREACT_6357 (Reactome)
DSIF

NELF

early elongation complex		REACT_6170 (Reactome)
DSIF

NELF

early elongation complex		REACT_6192 (Reactome)
DSIF

NELF

early elongation complex		REACT_6297 (Reactome)
DSIF complexREACT_6250 (Reactome)
ELLREACT_6275 (Reactome)
ELLREACT_6358 (Reactome)
ESCRT-IIIREACT_163632 (Reactome)
ESCRT-IREACT_115855 (Reactome)
ESCRT-IREACT_163632 (Reactome)
ESCRT-IREACT_163872 (Reactome)
Elongin ComplexREACT_6275 (Reactome)
Elongin ComplexREACT_6358 (Reactome)
Encapsidated viral coreArrowREACT_9044 (Reactome)
FACT complexREACT_6275 (Reactome)
FACT complexREACT_6358 (Reactome)
FEN1ArrowREACT_9036 (Reactome)
FURINREACT_163905 (Reactome)
GAG Polyprotein REACT_115774 (Reactome)
GAG-POL Polyprotein REACT_163644 (Reactome)
GAG-POL Polyprotein REACT_163807 (Reactome)
GDPArrowREACT_9507 (Reactome)
GTF2BArrowREACT_6184 (Reactome)
GTF2BArrowREACT_6203 (Reactome)
GTF2BArrowREACT_6226 (Reactome)
GTPREACT_9507 (Reactome)
HIV-1 Polymerase II REACT_6166 (Reactome)
HIV-1 RNA homodimerREACT_163644 (Reactome)
HIV-1 Tat-containing processive elongation complexArrowREACT_6278 (Reactome)
HIV-1 Tat-containing processive elongation complexREACT_6158 (Reactome)
HIV-1 capped pre-mRNA

CBC

RNA Pol II 		REACT_6206 (Reactome)
HIV-1 closed pre-initiation complexREACT_6134 (Reactome)
HIV-1 early elongation complex with hyperphosphorylated Pol II CTDArrowREACT_6297 (Reactome)
HIV-1 early elongation complex with hyperphosphorylated Pol II CTDREACT_6358 (Reactome)
HIV-1 elongation complex containing TatREACT_6278 (Reactome)
HIV-1 mRNAREACT_6161 (Reactome)
HIV-1 open pre-initiation complexArrowREACT_6134 (Reactome)
HIV-1 open pre-initiation complexREACT_6349 (Reactome)
HIV-1 template DNA 4-9 nucleotide transcript hybridArrowREACT_6265 (Reactome)
HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotidesArrowREACT_6203 (Reactome)
HIV-1 template DNA with first transcript dinucleotide, opened to +8 positionArrowREACT_6226 (Reactome)
HIV-1 transcription complex containing 11 nucleotide long transcriptArrowREACT_6208 (Reactome)
HIV-1 transcription complex containing 11 nucleotide long transcriptREACT_6240 (Reactome)
HIV-1 transcription complex containing 3 nucleotide long transcriptArrowREACT_6325 (Reactome)
HIV-1 transcription complex containing 3 nucleotide long transcriptREACT_6184 (Reactome)
HIV-1 transcription complex containing 4 nucleotide long transcriptArrowREACT_6184 (Reactome)
HIV-1 transcription complex containing 4 nucleotide long transcriptREACT_6172 (Reactome)
HIV-1 transcription complex containing 9 nucleotide long transcriptArrowREACT_6172 (Reactome)
HIV-1 transcription complex containing 9 nucleotide long transcriptREACT_6208 (Reactome)
HIV-1 transcription complex containing transcript to +30ArrowREACT_6240 (Reactome)
HIV-1 transcription complex with REACT_6220 (Reactome)
HIV-1 transcription complexArrowREACT_6333 (Reactome)
HIV-1 transcription complexREACT_6325 (Reactome)
HIV-1 unspliced RNAArrowREACT_6318 (Reactome)
HMGA1REACT_9010 (Reactome)
Host genomic DNAREACT_9054 (Reactome)
IN viral DNA bound to host genomic DNA with staggered endsArrowREACT_9054 (Reactome)
IN viral DNA bound to host genomic DNA with staggered endsREACT_9048 (Reactome)
IN ArrowREACT_9001 (Reactome)
IN ArrowREACT_9006 (Reactome)
IN ArrowREACT_9025 (Reactome)
IN ArrowREACT_9045 (Reactome)
IN ArrowREACT_9073 (Reactome)
IN bound to sticky 3' ends of viral DNA in PICREACT_9022 (Reactome)
IN bound to sticky 3' ends of viral DNA in PICREACT_9054 (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 virionREACT_8009 (Reactome)
Multimeric capsid coatArrowREACT_9038 (Reactome)
N-myristoyl GAG ArrowREACT_115774 (Reactome)
N-myristoyl GAG REACT_115708 (Reactome)
NEDD4LREACT_163632 (Reactome)
NELF complexREACT_6357 (Reactome)
NMT1REACT_116143 (Reactome)
NMT2REACT_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 REACT_116143 (Reactome)
Nuclear Pore Complex ArrowREACT_6340 (Reactome)
Nuclear Pore Complex REACT_6337 (Reactome)
NucleocapsidArrowREACT_8994 (Reactome)
P-TEFb complexREACT_6297 (Reactome)
P-TEFbREACT_6356 (Reactome)
PDCD6IPREACT_163632 (Reactome)
PIC ArrowREACT_9010 (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 ArrowREACT_8994 (Reactome)
PSIP1REACT_9010 (Reactome)
PiArrowREACT_6134 (Reactome)
PiArrowREACT_6171 (Reactome)
RANBP1ArrowREACT_6171 (Reactome)
RANBP1ArrowREACT_6318 (Reactome)
RANBP1REACT_9478 (Reactome)
RANGAP1ArrowREACT_6171 (Reactome)
RCC1REACT_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 ArrowREACT_6318 (Reactome)
REV REACT_163644 (Reactome)
REV REACT_6161 (Reactome)
RNA Pol II ArrowREACT_6206 (Reactome)
RNA Pol II REACT_6250 (Reactome)
RNA Pol II REACT_6357 (Reactome)
RNA Pol II with phosphorylated CTD CE complex with activated GTREACT_6295 (Reactome)
RNA Polymerase II ArrowREACT_6203 (Reactome)
RNA Polymerase II ArrowREACT_6226 (Reactome)
RNA Polymerase II ArrowREACT_6265 (Reactome)
RNA Polymerase II REACT_6172 (Reactome)
RNA Polymerase II REACT_6184 (Reactome)
RNA Polymerase II REACT_6208 (Reactome)
RNA Polymerase II REACT_6240 (Reactome)
RNA Polymerase II REACT_6325 (Reactome)
RNGTTREACT_6220 (Reactome)
RNMTREACT_6295 (Reactome)
RTArrowREACT_9010 (Reactome)
RTC ArrowREACT_8994 (Reactome)
RTC REACT_9015 (Reactome)
RTC with annealed complementary PBS seqments in +sssDNA and -strand DNAREACT_8992 (Reactome)
RTC with extending minus strand DNAREACT_9075 (Reactome)
RTC with extending second-strand DNAREACT_8999 (Reactome)
RTC with extensive RNase-H digestionREACT_9066 (Reactome)
RTC with integration competent viral DNAREACT_9010 (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 transferred to 3'-end of viral RNA templateREACT_9049 (Reactome)
RTC with minus strand DNA synthesis initiated from 3'-endREACT_9040 (Reactome)
RTC with tRNA primer RNA templateREACT_9039 (Reactome)
RTREACT_9014 (Reactome)
Ran GTPArrowREACT_6318 (Reactome)
Ran GTPase GDPArrowREACT_6171 (Reactome)
Ran-GDPREACT_9507 (Reactome)
Ran-GTPArrowREACT_9507 (Reactome)
Ran-GTPREACT_6140 (Reactome)
Rev multimer-bound HIV-1 mRNA CRM1 complexREACT_6140 (Reactome)
Rev multimer-bound HIV-1 mRNA

Crm1 Ran

GTP		ArrowREACT_6340 (Reactome)
Rev multimer-bound HIV-1 mRNA

Crm1 Ran

GTP		REACT_6171 (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 mRNAREACT_9530 (Reactome)
Rev-bound HIV-1 mRNAREACT_6228 (Reactome)
Rev-multimerArrowREACT_6318 (Reactome)
Rev-multimerREACT_6228 (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_6134 (Reactome)
TFIIHREACT_6184 (Reactome)
TFIIHREACT_6206 (Reactome)
TFIIHREACT_6234 (Reactome)
TFIIHREACT_6275 (Reactome)
TFIIHREACT_6325 (Reactome)
TFIIHREACT_6358 (Reactome)
Tat P-TEFbREACT_6170 (Reactome)
Tat REACT_6356 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD ArrowREACT_6316 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD REACT_6275 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELFArrowREACT_6311 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELFREACT_6316 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTDArrowREACT_6170 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTDREACT_6311 (Reactome)
Tat-containing elongation complex prior to separationArrowREACT_6158 (Reactome)
Trimeric gp120 gp41 oligomerREACT_163644 (Reactome)
UbREACT_115708 (Reactome)
VIF REACT_163644 (Reactome)
VPR REACT_163644 (Reactome)
VPU REACT_163644 (Reactome)
Viral core surrounded by Matrix layerArrowREACT_8032 (Reactome)
Virion Budding ComplexArrowREACT_163803 (Reactome)
Virion with exposed coreceptor binding sitesREACT_7962 (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 REACT_163644 (Reactome)
myristoylated Nef Protein ArrowREACT_116143 (Reactome)
myristoylated Nef Protein ArrowREACT_9044 (Reactome)
myristoylated Nef Protein 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)
viral DNA

Ku proteins XRCC4

DNA ligase IV complex		REACT_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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