HIV Life Cycle (Homo sapiens)

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12, 1532, 51, 888158, 64, 85, 892132, 1024, 32, 83921, 6018, 25, 30, 39, 91...45, 10836, 53321238, 5517, 35, 66, 71, 74...6, 56, 8229, 48, 573, 10, 20, 24, 28...677, 8, 11, 26, 77...14, 19, 44, 47708467, 103675, 12, 38, 54, 55, 865519, 31, 4716, 212922, 51, 95, 104, 10938, 5522, 68, 10964, 8910552, 783232, 51, 10462-64, 895542, 43, 49, 79, 96...259, 61, 79, 113462723, 1069741, 105327638, 55327372, 90, 9813, 672721, 87, 9367Rev multimer-bound HIV-1 mRNA TFIIH XRCC4DNA ligase IV complex CCR5, CXCR4 HIV-1 initiation complex with phosphodiester-PPi intermediate P-TEFb complex TFIIH TFIIF RT RT p6 protein TFIIF gp41 homotrimer with hairpin structure formation TFIIF FACT complex RNA Polymerase II holoenzyme complex CAK Elongin BC complex TatP-TEFbHIV-1 Tat-containing arrested processive elongation complex RNA templatetRNA primer TFIIF RNA Polymerase II holoenzyme complex DSIF complex RT CCR5, CXCR4 RNA Polymerase II holoenzyme complex TFIIH p6 protein RanGTP DSIF complex IN bound to sticky 3' ends of viral DNA Matrix RNA Polymerase II holoenzyme complex TFIIF ubiquitin gp41 homotrimer Matrix cytosolHIV-1 transcription complex containing 4 nucleotide long transcript TFIIF Cap Binding Complex Vps/Vta1 Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELF Elongin BC complex ESCRT-I TFIIE RNA Pol II RNA Polymerase II holoenzyme complex RNA Polymerase II Elongin Complex Elongin BC complex PIC TFIIH P-TEFbEncapsidated viral core HIV-1 Tat-containing processive elongation complex Cap Binding Complex RNA Polymerase II holoenzyme complex gp120 homotrimer CAK Matrix CAK Nucleocapsid RNA Polymerase II holoenzyme complex Elongin Complex CCR5, CXCR4 RT gp120 homotrimer CAK CAK P-TEFb complex p6 protein ESCRT-III RNA Polymerase II holoenzyme complex gp41 homotrimer TFIIH CEPol II CTDSpt5 complex Ran-GDP CD4Env gp120/gp41 fusion peptide complex p6 protein TFIIF HIV-1 elongation complex containing Tat P-TEFbRNA Pol II with phosphorylated CTD CE complex TFIIH CAK linear duplex viral DNA Virion Budding Complex RT TFIIA TFIIF TFIIF CHMP4 HIV-1 paused processive elongation complex p6 protein Virion with fusogenically activated gp41 CAK Cap Binding Complex Vps/Vta1 minus sssDNA primer for minus strand DNA extension RTC with minus sssDNA transferred to 3'-end of viral RNA template RTC with minus sssDNAtRNA primerRNA template NTP HIV-1 RNA homodimer RNA Polymerase II holoenzyme complex HIV-1 Polymerase II TFIID NELF complex IN bound to sticky 3' ends of viral DNA Virion with CD4 bound to gp120 RNA Polymerase II DSIF complex TFIID DSIF complex Tat-containing early elongation complex with hyperphosphorylated Pol II CTD minus sssDNARNA templatetRNA primer HIV-1 RNA homodimer monoubiquitinated N-myristoyl GAG TFIIF RNA Polymerase II holoenzyme complex NTP DSIF complex p6 protein Elongin BC complex CAK CHMP2 NTP Cap Binding Complex TFIIE monoubiquitinated N-myristoyl GAG NELF complex Nucleocapsid RNA Pol II viral PIC proteins TFIID RNA Pol II phospho-DSIF complex RTC with integration competent viral DNA viral DNA with 3' sticky ends RanBP1Ran-GTPCRM1Rev-bound mRNA complex TFIIE NELF complex TFIIF RNA Polymerase II holoenzyme complex TFIIF uncoated viral complex RT RTC with nicked minus sssDNAtRNA primerRNA template HIV-1 RNA homodimer DSIF complex HIV-1 closed pre-initiation complex FACT complex RT Cap Binding Complex TFIIE Trimeric gp120gp41 oligomer XRCC4DNA ligase IV complex NELF complex RNA Polymerase II holoenzyme complex CAK Virion with exposed coreceptor binding sites TFIID NELF complex HIV-1 transcription complex containing 3 nucleotide long transcript HIV-1 elongation complex Ran-GTP CCR5, CXCR4 DSIF complex NELF complex Ran-GTP Ub Rev multimer-bound HIV-1 mRNACrm1RanGTP TFIIA CD4Env gp120 with exposed coreceptor binding site FACT complex Elongin BC complex Env oligomer with gp120RT TFIIE Matrix Rev multimer-bound HIV-1 mRNA RNA Polymerase II holoenzyme complex p6 protein RT RNA Polymerase II holoenzyme complex nicked minus sssDNARNA templatetRNA primer TFIIA Rev multimer-bound HIV-1 mRNACrm1RanGTP TFIIF CHMP2 HIV-1 Tat-containing paused processive elongation complex FACT complex RNA Polymerase II holoenzyme complex gp120 homotrimer Virion with CD4gp120 bound to CCR5/CXCR4 HIV-1 initiation complex TatP-TEFbHIV-1 transcription complex containing transcript to +30 Golgi membranep6 protein Nucleocapsid Viral core surrounded by Matrix layer TFIID p6 protein RT Rev-bound HIV-1 mRNA Rev multimer-bound HIV-1 mRNA Env oligomer with gp120TFIIH TFIIF HIV-1 RNA homodimer TFIIF Elongin Complex Elongin BC complex Immature HIV virion Tat-containing early elongation complex with hyperphosphorylated Pol II CTD Matrix NTP HIV-1 transcription complex containing 9 nucleotide long transcript minus sssDNA primer transferred to 3'- end of viral RNA template linear duplex viral DNA RT TFIIH viral DNA with 3' sticky ends RNA polymerase II Cap Binding Complex minus sssDNAtRNA primer generated by RNAse-H TFIIF TFIID linear duplex viral DNA TFIIF Elongin Complex HIV-1 capped pre-mRNACBCRNA Pol II Rev multimer-bound HIV-1 mRNA RNA Polymerase II TFIIA Virion with gp41 exposed TFIIF RNA Polymerase II holoenzyme complex Nucleocapsid P-TEFbNuclear Pore Complex TFIIH DSIF complex gp41 homotrimer TFIIE p6 protein 2-LTR form of circular viral DNA TFIIA RT gp41 homotrimer HIV-1 promoterTFIIDTFIIATFIIB complex CAK p6 protein RNA Polymerase II RNA Polymerase II holoenzyme complex TFIIF RNA polymerase II Aborted HIV-1 early elongation complex RNA Polymerase II holoenzyme complex CAK DSIF complex Ku proteins bound to viral DNA NELF complex Matrix TFIIE RT Nucleocapsid IN bound to sticky 3' ends of viral DNA in PIC IN bound to sticky 3' ends of viral DNA in PIC Nucleocapsid RNA Polymerase II holoenzyme complex Ku70Ku80 heterodimer NELF complex Nucleocapsid CAK RTC with extending minus strand DNA RNA Polymerase II P-TEFbRNA Polymerase II holoenzyme complex Rev multimer-bound HIV-1 mRNACrm1RanGTPNPC FACT complex RNA Polymerase II holoenzyme complex viral DNAKu proteinsXRCC4DNA ligase IV complex gp120 homotrimer with exposed coreceptor binding sites NELF complex CAK p6 protein Elongin BC complex TFIIH NTP minus sssDNA primer for minus strand DNA extension HIV-1 RNA homodimer Matrix Elongin Complex gp41 homotrimer with exposed fusion peptide RNA Polymerase II DSIF complex CHMP4 Elongin BC complex p6 protein Elongin Complex Rev multimer-bound HIV-1 mRNACrm1RanGTP RT Env oligomer with gp41 hairpin structure formation Integrated provirus TatP-TEFbMatrix CCR5/CXCR4CD4Env gp120 RNA Polymerase II holoenzyme complex INviral DNA bound to host genomic DNA with staggered ends NELF complex Elongin BC complex FACT complex P-TEFb complex HIV-1 promoterTFIIDTFIIATFIIBPol IITFIIF complex* p6 protein p6 protein P-TEFbRNA Polymerase II holoenzyme complex CAK TatP-TEFbTFIIH HIV-1 transcription complex containing extruded transcript to +30 RNA Pol II HIV-1 Polymerase II TFIIH minus sssDNA primer for minus strand DNA extension gp120 homotrimer with exposed coreceptor binding sites TFIIF Autointegrated viral DNA as an inverted circle Matrix Integration intermediate HIV-1 transcription complex with minus sssDNA primer for minus strand DNA extension TFIIA Nucleocapsid TatP-TEFbMatrix RNA Polymerase II holoenzyme complex P-TEFb complex RT Matrix Elongin Complex DSIFNELFearly elongation complex after limited nucleotide addition TFIIF RNA Polymerase II holoenzyme complex HIV-1 transcription complex RNA Polymerase II holoenzyme complex RTC with annealed complementary PBS seqments in +sssDNA and -strand DNA RTC with minus strand DNA synthesis initiated from 3'-end Elongin Complex NTP RNA polymerase II HIV-1 RNA homodimer IN bound to sticky 3' ends of viral DNA TFIID gp41 homotrimer with fusion peptide inserted into membrane TFIIH TFIIF TFIIH RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex gp120 homotrimer after second conformation change nucleoplasmNup62 Complex p6 protein Env oligomer with gp41RNA Polymerase II holoenzyme complex TFIIF TFIIF RNA Polymerase II holoenzyme complex gp120 homotrimer after second conformation change gp41 homotrimer p6 protein Rev-bound HIV-1 mRNA RNA polymerase II linear duplex viral DNA IN bound to sticky 3' ends of viral DNA RT Rev multimer-bound HIV-1 mRNACRM1 complex monoubiquitinated N-myristoyl GAG P-TEFbp6 protein RNA Polymerase II holoenzyme complex p6 protein Matrix CAK TFIIF Rev-bound HIV-1 mRNA HIV-1 RNA homodimer RNA Polymerase II viral PIC proteins Elongin BC complex CD4Env gp120/gp41 hairpin complex TFIIF TFIIH NTP TFIIF TFIIF gp120 homotrimer after second conformation change RNA Polymerase II holoenzyme complex Matrix TFIIF Elongin Complex DSIF complex RT TFIIF P-TEFb complex CD4Env gp120/gp41 insertion complex RNA Polymerase II holoenzyme complex p6 protein P-TEFbMatrix DSIF complex CAK p6 protein ubiquitin RNA Polymerase II holoenzyme complex DSIF complex CD4Env gp120/gp41 hairpin complexCCR5/CXCR4 RNA Polymerase II CAK TFIIE RNA Polymerase II holoenzyme complex Tat-containing early elongation complex with hyperphosphorylated Pol II CTD RNA Polymerase II Crm1Ran GTPaseGTP RNA Polymerase II RNA Polymerase II holoenzyme complex phospho-NELF complex RanGTP p6 protein HIV-1 RNA homodimer RNA Polymerase II holoenzyme complex Matrix HIV-1 RNA homodimer gp120 homotrimer after second conformation change CD4Env gp120CCR5,CXCR4complex Cap Binding Complex Ran-GTP NTP TFIIF Cap Binding Complex HIV-1 early elongation complex with hyperphosphorylated Pol II CTD TatP-TEFbRNA Polymerase II holoenzyme complex HIV-1 promoterTFIID complex Ku proteins bound to viral DNA HIV-1 transcription complex containing 11 nucleotide long transcript NELF complex RNA Polymerase II holoenzyme complex HIV-1 processive elongation complex RTC with tRNA primerRNA template p6 protein CAK p6 protein Rev-bound HIV-1 mRNA p6 protein RT P-TEFbRTC with duplex DNA containing discontinuous plus strand flap Nup107 Complex RT CAK minus sssDNA primer transferred to 3'- end of viral RNA template Matrix TFIIA TFIIH RNA Pol II Rev-bound HIV-1 mRNA DSIF complex TFIIH endoplasmic reticulum membraneP-TEFb complex CD4Env gp120 with exposed coreceptor binding site TatP-TEFbTrimeric gp120gp41 oligomer FACT complex Matrix HIV-1 RNA homodimer NELF complex Ku proteins bound to viral DNA RNA polymerase II RT linear duplex viral DNA RanGTP RTC with extensive RNase-H digestion Env oligomer with gp41HIV-1 arrested processive elongation complex RNA Polymerase II viral DNA bound with Integrase Ku70Ku80 heterodimer RNA Polymerase II holoenzyme complex p6 protein Rev-bound HIV-1 mRNA CD4Env gp120/gp41 hairpin complexCCR5/CXCR4 Matrix RNA Polymerase II holoenzyme complex RT RTC with extending second-strand DNA HIV-1 RNA homodimer RNA Polymerase II holoenzyme complex HIV-1 early elongation complex with hyperphosphorylated Pol II CTD Matrix P-TEFbTrimeric gp120gp41 oligomer p6 protein TatP-TEFbCD4Env gp120/gp41insertion complexCCR5/CXCR4 FACT complex Early elongation complex with separated aborted transcript FACT complex monoubiquitinated N-myristoyl GAG Cap Binding Complex Elongin BC complex Trimeric ENV precursor TFIIF Trimeric ENV precursor CAK TFIIF RT RTC HIV-1 RNA homodimer Nup107 Complex TFIIA RNA Polymerase II Integrated provirus ubiquitin 1-LTR form of circular viral DNA gp41 homotrimer TFIIF gp120 homotrimer after second conformation change viral DNA with 3' sticky ends Nucleocapsid RNA Polymerase II holoenzyme complex CCR5, CXCR4 Ku70Ku80 heterodimer Matrix RNA Polymerase II holoenzyme complex NELF complex P-TEFbEnv oligomer with gp120viral DNA with 3' sticky ends Nucleocapsid CD4Env gp120/gp41 hairpin complex p6 protein Nuclear Pore Complex RTC with degraded RNA template and minus sssDNA RNA Polymearse IINTPTFIIF complex CAK phospho-NELF complex RNA Polymerase II holoenzyme complex gp41 homotrimer linear duplex viral DNA HIV-1 open pre-initiation complex HIV-1 RNA homodimer RNA Polymerase II Nup62 Complex ubiquitin RNA Pol II with phosphorylated CTD CE complex with activated GT RNA Polymerase II RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex TatP-TEFbphospho-NELF complex HIV-1 RNA homodimer Env oligomer with gp41 hairpin structure formation Matrix Ku70Ku80 heterodimer gp41 homotrimer gp120 homotrimer TFIIF RNA Polymerase II HIV-1 Tat-containing aborted elongation complex after arrest RNA Polymerase II holoenzyme complex TFIIH CD4gp120gp41 membrane complex TFIIH TFIIF Matrix RT TFIIH Crm1Ran GTPaseGTP Elongin Complex TFIIF Matrix RNA Polymerase II FACT complex Rev multimer-bound HIV-1 mRNACRM1 complex RT TFIIE Rev multimer-bound HIV-1 mRNA RNA Pol II TFIID RNA Polymerase II holoenzyme complex TFIIF p6 protein TFIIF RT TFIIF Elongin Complex RNA Polymerase II holoenzyme complex INviral DNA bound to host genomic DNA linear duplex viral DNA monoubiquitinated N-myristoyl GAG TFIIE TFIIE Autointegrated viral DNA as smaller circles NTP Assembling HIV virion RNA Polymerase II holoenzyme complex Trimeric gp120gp41 oligomer p6 protein Mature HIV virion RNA Pol II TFIIA viral PIC proteins p6 protein ESCRT-III RT FACT complex TFIIH TFIIF TFIIH viral PIC proteins gp120 homotrimer CAK phospho-DSIF complex P-TEFbNELF complex TFIIH RNA Pol II CAK DSIF complex TatP-TEFbCAK P-TEFb complex TFIIH TFIIF DSIF complex TFIIH RNA Polymerase II holoenzyme complex TFIID Nucleocapsid Elongin BC complex CD4Env gp120 RNA Polymerase II holoenzyme complex p6 protein Rev multimer-bound HIV-1 mRNACrm1RanGTP NELF complex Tat-containing elongation complex prior to separation DSIF complex RNA Polymerase II NELF complex RNA Polymerase II holoenzyme complex Matrix TFIID CAK RNA Pol II TFIIF ESCRT-I Ran GTPaseGDP TFIIH TFIIF Elongin BC complex CD4Env gp120/gp41 fusion peptide complexCCR5 RT Virion with gp41 fusion peptide in insertion complex Rev multimer-bound HIV-1 mRNACRM1 complex gp120 homotrimer FACT complex RNA Polymerase II holoenzyme complex early endosome membraneRNA Polymerase II TFIIF RTC without viral RNA template RNA polymerase II HIV-1 transcription complex containing 4-9 nucleotide long transcript RNA Polymerase II holoenzyme complex gp41 homotrimer with hairpin structure formation NELF complex linear duplex viral DNA DSIF complex HIV-1 Promoter Escape Complex TFIIA RNA Polymerase II holoenzyme complex FACT complex Rev-bound HIV-1 mRNA Trimeric gp120gp41 oligomer Rev multimer-bound HIV-1 mRNA HIV-1 aborted elongation complex after arrest TFIIF TFIIF P-TEFbElongin Complex DSIF complex RNA Polymerase II holoenzyme complex RNA Pol II DSIF complex Trimeric gp120gp41 oligomer DSIFNELFearly elongation complex P-TEFbTatP-TEFbRNA Polymerase II holoenzyme complex CAK NELF complex RNA Polymerase II CCR5, CXCR4 Elongin Complex RNA Polymerase II holoenzyme complex Virion with gp41 forming hairpin structure p6 protein gp41 homotrimer viral DNA bound with Integrase in PIC RNA Pol II RNA Polymerase II holoenzyme complex GTF2F1REV RPS27ATPR UBCGTF2F1GTF2H2 POLR2I CTDP1 RanGTPp6 NELFB CTDP1 POLR2FCTDP1 RNMTPR VPU CDK7 POLR2H GTF2H3 GTP UBBPOLR2DMA NCBP2 HIV-1 RNA template CCNH TAF13 NELFACTDP1 POLR2L POLR2E CTP TAF13 CTDP1 TFIIHGTF2A1TAF5 POLR2J POLR2FRAN VPS37A POLR2Fp6 p6 GTF2B CTDP1 CTDP1 POLR2L TBP CTDP1 MNAT1 VIF NELFAPOLR2J POM121 ERCC2 POLR2B GTF2F1POLR2A HIV-1 transcription complex containing 4-9 nucleotide long transcriptNCBP1 TAF6 NELFCD UBCVPR POLR2B CHMP7 GTF2A1GTP Virion with gp41 forming hairpin structurep51 HIV-1 mRNA PPiPOLR2J Reverse transcriptase/ribonuclease H MA MA POLR2C POLR2B POLR2K VPU RTC with minus strand DNA synthesis initiated from 3'-endNELFE GTF2H2 TAF11 MA CCR5 POLR2I p-S2,S5-POLR2A HIV-1 arrested processive elongation complexPOLR2E POLR2B p-S5-POLR2A POLR2DPOLR2DUBA52POLR2C POLR2J UBCRNA Pol II with phosphorylated CTD CE complex with activated GTPOLR2G VPR CDK7 POLR2L TAF13 REV myristoylated Nef Protein POLR2J GTF2H3 GTF2F2PPIA p6 VPR Reverse transcriptase/ribonuclease H Nup45 p-SUPT5H PPIA MA POLR2E UBBPOLR2I GTF2H1POLR2I POLR2B POLR2FPOLR2B p6 NELFE POLR2DMNAT1 HIV-1 mRNA p6 ERCC3 POLR2FELL POLR2C p-S5-POLR2A p6 GTF2H4 Surface protein gp120 POLR2J GTF2F2ERCC3 POLR2FRTC with integration competent viral DNASUPT4H1 BANF1 POLR2DPOLR2K GTF2E1 UBCUBCGTF2F1SUPT4H1 IN p6 GTF2F1GTF2F1GTF2F2GTF2H4 POLR2H NTPSUPT4H1 p6 HIV-1 Polymerase II VPU Reverse transcriptase/ribonuclease H VIF POLR2K REV VPS28 POLR2DVPR POLR2I Transmembrane protein gp41 POLR2J p-S5-POLR2A POLR2B POLR2G XPO1NUP37 MA GTF2F2TBP TAF4 TAF5 GTF2B HIV-1 transcription complex containing transcript to +30Reverse transcriptase/ribonuclease H GTF2A1POLR2J p-SUPT5H GTF2F2REV p51 POLR2DPOLR2J p51 POLR2B GTF2H1PSIP1 TAF4 POLR2C NCBP1 GAG-POL Polyprotein ERCC2 POLR2J POLR2G viral RNA template degraded by RNase-H GTF2H4 Transmembrane protein gp41 TAF13 POLR2H POLR2DCTDP1 NELFE MNAT1 HIV-1 template DNA with first transcript dinucleotide, opened to +8 positionSUPT4H1 Rev-multimerTAF10 RTCDK9 MA POLR2G Tat-containing early elongation complex with hyperphosphorylated Pol II CTDp6 TSG101p-SUPT5HTAF4B CCNT1 POLR2DSUPT4H1 VPS4Ap51 p6 VPS4B uncoated viral complexPOLR2A MA MNAT1 TAF1 GTF2E2 PPIA CDK9 GTF2A1POLR2G CTDP1POLR2L VPU TAF4 POLR2H POLR2K tRNA-Lysine3UTP UBA52P-TEFb complexNELFCD POLR2J NELFE REV CDK7 TAF6 Reverse transcriptase/ribonuclease H CCNH POLR2FVIF CTDP1 POLR2B GTP POLR2I GTF2F1TAF12 POLR2I HIV-1 mRNA POLR2FMA POLR2E IN POLR2J XPO1CD4 GTF2A2 POLR2J p6 VPU p51 Trimeric gp120gp41 oligomerGTF2A2 myristoylated Nef Protein ELLNELFCD p6 POLR2H p6 Integration intermediateCDK7 NEDD4Lp6 POLR2E p6 PPiGlycosylated Envelope glycoprotein gp160 TCEB1 TAF4 VPR p-SUPT5H UTP GTP POLR2G Transmembrane protein gp41 CCNT1 p51 IN monoubiquitinated N-myristoyl GAG Virion with gp41 exposedREV POLR2I GTF2H3 TCEB1 IN MA TBP Surface protein gp120 POLR2J PPIA Ku proteins bound to viral DNAPPiERCC3 UBCNUP98-5 Tat POLR2K POLR2H p6 POLR2E SSRP1 VPR POLR2L p6 GTF2F1Rev-multimerMNAT1 POLR2H GTF2F2POLR2C p6 ERCC2 NUP210 POLR2I POLR2DPOLR2G CCNT1 POLR2B TAF6 POLR2E GTF2H1Reverse transcriptase/ribonuclease H POLR2I POLR2L MA POLR2J GTF2H3 p-SUPT5H UBCRANBP1VPS28 viral PIC proteinsERCC3 HIV-1 Tat-containing paused processive elongation complexNELFCD SUPT16H POLR2E Ran-GTPGTF2H4 GTF2H2 SUPT16H P-TEFbPOLR2L POLR2B TFIIHGTF2E1 POLR2J CCNT1 PPIA NUPL2 POLR2B Autointegrated viral DNA as smaller circlesGTF2A1GTP HIV-1 paused processive elongation complexTCEB3 REV CD4 NC p6 POLR2J VIF MA POLR2E NUP54 CCNT2 TAF10 TAF10 ERCC3 GTF2E1 p-S2,S5-POLR2A NELFE GTP UBCGTF2A1GTF2H4 RANBP2 VPU POLR2B PR POLR2H RAN POLR2E CCNT1 p6 XPO1 GTF2A1UBA52POLR2I POLR2FPOLR2H GAG Polyprotein HIV-1 closed pre-initiation complexUBBp-SUPT5H TAF4 VPU BANF1 POLR2E PSIP1 TAF4B POLR2FNC HIV-1 RNA p51 TAF1 Reverse transcriptase/ribonuclease H NELFB VIF POLR2C REV CDK7 SUPT4H1 GTF2F2GTF2H1GTF2F1POLR2L POLR2E POLR2FReverse transcriptase/ribonuclease H UBCp-SUPT5H Rev multimer-bound HIV-1 mRNACrm1RanGTPNPCNELFACXCR4 VPU CCNT1 TCEB2 VIF GTF2H4 POLR2L TAF12 myristoylated Nef Protein CCNH TCEA1REV POLR2J POLR2A NELFCD TCEB1 VPR POLR2H NELFE PDCD6IP VPS37A GTF2F1XRCC4 Ran-GDPGTF2H3 POLR2J MA CDK9 NELFB CTDP1 NELFB MA Transmembrane protein gp41 POLR2E SUPT16H HIV-1 RNA homodimerCTDP1 p-NELFE VPU p6 HIV-1 Tat-containing processive elongation complexPOLR2J GTF2H3 UBCTFIIEHMGA1 VPR NC p-S2,S5-POLR2A CTDP1 MA UBCHMGA1 CCNT2 ERCC3 TAF4 p6 ERCC2 TFIIAVPR UBBGTP NELFB CTP PPIA ERCC3 p6 p6 POLR2C POLR2A POLR2C POLR2J UBCMNAT1 POLR2C POLR2E CDK7 p6 GTF2E2 POLR2L RTC with duplex DNA containing discontinuous plus strand flapHIV-1 mRNA SUPT4H1 NELFB Reverse transcriptase/ribonuclease H PPIA GTF2H2 POLR2DSUPT16H Transmembrane protein gp41 PPIA HIV-1 template DNA4-9 nucleotide transcript hybridVPU GTF2A1p51 NELFB GTF2H4 TAF5 HIV-1 RNA POM121 POLR2FIN CDK7 GTF2E2 POLR2I ERCC2 GTF2H1VIF GTF2A1UBCPOLR2C HIV-1 transcription complexPOLR2C TCEB2 VIF NELFB POLR2H GTF2H3 TFIIEERCC2 CEPol II CTDSpt5 complexRev-bound HIV-1 mRNANMT1TFIIHVIF CTP POLR2G p6 IN VPU GTF2H1p6 NELFE viral PIC proteinsPOLR2K XRCC5 POLR2FCDK7 GTF2F2GTF2H2 POLR2G BANF1 NCBP2 TCEB2 POLR2FPOLR2C REV RTC with extending second-strand DNAIN POLR2L SUPT16H TCEB3 POLR2B IN p6 VPS37C GTF2F1POLR2E POLR2G p-SUPT5H TAF12 HIV-1 aborted elongation complex after arrestGTF2H1REV TAF1 TFIIHVPR p-SUPT5H POLR2L TAF1 PPIA p-SUPT5H IN ERCC3 POLR2J NUPL1-2 POLR2C UBBVPU POLR2C POLR2L POLR2K CD4GTF2E1 2-LTR form of circular viral DNAPOLR2L NTPPOLR2H MA POLR2L CCNH MA NCBP2 SEH1L-2 NC POLR2A POLR2E SUPT4H1 POLR2DGTF2B VIF POLR2A VIF NCBP1 Transmembrane protein gp41 IN SUPT4H1 ERCC3 ATP POLR2J TCEB3 SUPT4H1 POLR2I HIV-1 RNA GTP TAF9 VPU POLR2J p51 Virion with gp41 fusion peptide in insertion complexPOLR2C MNAT1 RAN POLR2B Cap Binding Complex RTC with extending minus strand DNAERCC3 GTPCDK9 NELFB POLR2FNELFCD BANF1POLR2C UBBGTF2F1POLR2G VPR REV PR NCBP1 POLR2J NUPL2 CCNH REV NELFCD NUP62 VIF POLR2I SEH1L-2 VPS37B POLR2K GTF2F1Ran GTPaseGDPREV SSRP1 GTF2F1TCEB1 GTF2H1NUP93 TCEB1 POLR2J POLR2E NELFABANF1 CDK9 myristoylated Nef Protein viral DNA bound with Integrase in PICRev multimer-bound HIV-1 mRNACRM1 complexp51 SUPT4H1 GTF2H2 SUPT4H1 POLR2DFURINMA POLR2H TCEB2 CHMP4C VPR IN NUP107 GTF2H4 p-SUPT5H TFIIHERCC2 NELFCD CD4 GTF2H1POLR2K VPU CXCR4 GTF2A1TAF1 ELL MNAT1 p6 CDK9 TCEB2 NCBP1 TAF4B TAF11 PPIA POLR2FGTF2H2 NCBP1 POLR2E GTF2H1RanBP1Ran-GTPCRM1Rev-bound mRNA complexReverse transcriptase/ribonuclease H POLR2B VTA1 Multimeric capsid coatCXCR4 TCEB1 TAF5 GTF2A2 POLR2K POLR2K POLR2J POLR2B GTF2F1p51 Tat Vps/Vta1TAF9 TAF10 GAG-POL Polyprotein PPiPOLR2K TAF1 MA POLR2I HIV-1 RNA template PPiUTP GTF2H1p-SUPT5H Reverse transcriptase/ribonuclease H VPS37B HMGA1 Trimeric ENV precursorPOLR2E SUPT4H1 POLR2I REV UTP POLR2FPOLR2I POLR2J CD4 POLR2G GTF2F1POLR2G TBP POLR2K CCR5, CXCR4POLR2E Reverse transcriptase/ribonuclease H FEN1CTDP1 XRCC4DNA ligase IV complexTCEB1 POLR2I BANF1 IN NUPL1-2 POLR2C VIF N-myristoyl GAG UBCPOLR2E CHMP2A GTF2H2 POLR2B VPU p51 RPS27ANELFCD GTF2F2POLR2I ELL GTF2F1SSRP1 POLR2I PPIA GTF2F1POLR2C UBCUBBKu proteins bound to viral DNANCBP2 p-S2,S5-POLR2A GTF2E2 XPO1 POLR2C NCBP2 CD4 CCNT2 Surface protein gp120 VIF Reverse transcriptase/ribonuclease H GTF2F1POLR2B MA GTF2H2 POLR2G TCEB1 POLR2H N-myristoyl GAG TAF4B Mature HIV virionPOLR2E POLR2A p6 REV NUP85 POLR2E POLR2L UBCRNA Pol II POLR2J POLR2G TAF6 MA RTC with minus sssDNA transferred to 3'-end of viral RNA templateVPR POLR2C CHMP6GTF2F2GTP POLR2E HIV-1 initiation complex with phosphodiester-PPi intermediateNUP153 CoA-SHGTF2F2GTF2H4 MA VIF CDK7 GTF2F2NUP210 GTF2A1POLR2DPOLR2K Surface protein gp120 ELL GTF2F2CCNT1 p-S2,S5-POLR2A GTF2H2 POLR2J ATPBANF1 GTF2F2CHMP4B POLR2A SUPT16H POLR2K MA UBCNTPPOLR2H POLR2L BANF1 NUP160 UBCERCC3 UBCPOLR2G INviral DNA bound to host genomic DNA with staggered endsELL ERCC2 VPU GTF2F1GTF2F1GTF2B PPIA NUP54 CDK7 UBBSUPT4H1 POLR2L GTF2H1POLR2L CCNT1 GTF2H2 CXCR4 POLR2C VIF XPO1 POLR2DCDK7 MNAT1 GTF2H2 p6 CHMP4A Nup45 HIV-1 mRNA SSRP1 POLR2B NUP62 POLR2K POLR2J POLR2E GTF2A1POLR2G POLR2B POLR2I p-S2,S5-POLR2A NELFAPOLR2L CCNH p-S5-POLR2A TAF11 MNAT1 RAN CHMP2B IN NELFAVirion with fusogenically activated gp41HMGA1 HIV-1 elongation complex containing TatREV REV NELFAIntegrated provirusPOLR2J PPIA GTF2H2 UBCPOLR2K GTF2B NC NUP205HIV-1 RNA template Reverse transcriptase/ribonuclease H ERCC2 POLR2DCTDP1 TAF12 UBBCCNH NELFAPOLR2FTAF4 POLR2B GTF2H3 GTF2F2TAF4B GTF2H3 NELFAMA ERCC2 p6 GTF2F2VIF p6 POLR2DPOLR2H TCEB2 HMGA1 POLR2E POLR2E RCC1VIF POLR2G POLR2C POLR2L VPS4APOLR2H GTF2H4 CCNT1 TCEB2 CTDP1 p51 p6 SSRP1 Reverse transcriptase/ribonuclease H NUP133 ERCC2 POLR2B VIF HIV-1 RNA TAF13 REV POLR2K TFIIHTAF12 VPU HIV-1 elongation complexGTF2F2POLR2Dp-SUPT5H SSRP1 NELFE TCEB3 GTF2H1VPR ELL CCNT1 POLR2FPOLR2FGTF2F1POLR2B GTF2F1TAF11 p51 NELFCD POLR2I POLR2H GTF2F1POLR2G GTF2E1 NELFB ADPPOLR2G TCEA1 CD4 POLR2DPOLR2FERCC3 POLR2C p6 POLR2L TAF6 POLR2C GTF2H1p-S5-POLR2A CDK9 UBCPOLR2G TAF9 RAE1 PDCD6IPNUP188PPIA XRCC5 POLR2K NELFB p-SUPT5H P-TEFbNUP88 REV GTF2A1POLR2G POLR2K Tat XRCC4 VIF REV Ku70Ku80 heterodimerGTF2F2GTF2B POLR2B POLR2K VIF POLR2C UBBPOLR2C NELFAGTF2H4 CTP AAAS IN UBBNCBP2 VIF Surface protein gp120 GTF2F2POLR2K POLR2L GTF2F2p51 GTF2H1CTDP1 TCEA1 MA p6 POLR2G TAF11 GTF2F1TCEB3 GTF2H1TCEB2 POLR2C Surface protein gp120 UBBSSRP1 CHMP6CCNH POLR2FHIV-1 RNA template UBCNELFB NELFE POLR2J GTF2F2SUPT16H CCNT1 CCNH POLR2I VIF PSIP1MatrixNMT2p-S2,S5-POLR2A POLR2H NELFE MNAT1 HIV-1 Promoter Escape ComplexPOLR2I GTF2H1VIF ERCC2 POLR2K Surface protein gp120 ERCC3 XRCC5 Transmembrane protein gp41 UBCPOLR2FCDK9 VPU GTF2H3 VPU p-SUPT5H REV MA NELFE TFIIDTat POLR2DGTF2H3 TCEB3 UBCGTF2F1TCEB2 p6 ERCC2 RAN ERCC2 MNAT1 TAF10 Virion with CD4 bound to gp120GTF2A2 POLR2DGTF2H3 PPIAviral PIC proteinsCCNH TAF6 POLR2G PPIA TPR p-NELFE p51 TAF4B VPU CDK9 PPiCCNT2 ADPReverse transcriptase/ribonuclease H N-myristoyl GAG p-S5-POLR2A UTP TAF6 POLR2G VPU p-S5-POLR2A p-SUPT5H NELFCD VPR POLR2C CCNT1 REV AAAS RNGTTReverse transcriptase/ribonuclease H ERCC3 p51 POLR2H Virion Budding ComplexPOLR2H POLR2G TAF10 PPIA XRCC6 UBCmyristoylated Nef Protein POLR2I POLR2A MA NELFB VPR SUPT16H POLR2DNELFE NELFCD POLR2L VPU TFIIAMA XRCC5 GTF2F1POLR2G CCNH POLR2K TCEA1 POLR2H POLR2DCTP IN PPIA POLR2I POLR2DReverse transcriptase/ribonuclease H POLR2E RNGTT ATP TAF12 p6 NELFCD Reverse transcriptase/ribonuclease H NUP50 GTF2F2MNAT1 ELL POLR2E POLR2FPOLR2J POLR2E HIV-1 capped pre-mRNACBCRNA Pol II TAF12 p51 GTF2F1p6 IN TBP POLR2I HIV-1 RNA NELFCD GTF2H2 SSRP1 MA myristoylated Nef Protein XRCC6 ERCC3 GTP CDK7 REV p-SUPT5H p6 p-SUPT5H POLR2L POLR2G XPO1 SUPT4H1 p51 CHMP2B CCNH GTF2E2 POLR2FERCC2 Transmembrane protein gp41 CCNH GTF2H4 PPIA CCR5 POLR2L VPS4B POLR2K POLR2DNELFB HIV-1 RNA UBCPOLR2H TCEB2 p-S2,S5-POLR2A CCNH GTF2H4 NUP155 POLR2B TCEB2 NCBP1 MA VIF PPIA TCEB3 HIV-1 transcription complex containing 3 nucleotide long transcriptEarly elongation complex with separated aborted transcriptGTF2H1POLR2J POLR2E MA POLR2I CDK9 GTF2F1CDK7 CDK9 BANF1 ERCC3 p6 NTPRANBP1POLR2C POLR2FGTF2H2 Tat GTF2F1PR ATP GTF2F2TAF10 NELFAPOLR2H NELFB RNA Polymerase II POLR2K HIV-1 RNA POLR2K GTF2H4 POLR2B GTF2H2 RTC with nicked minus sssDNAtRNA primerRNA templatemyristoylated Nef Protein PPip51 GTF2A1TCEB3 Tat NELFCD DSIFNELFearly elongation complex after limited nucleotide additionNUP50 GTF2A1POLR2K ERCC3 IN GTF2H4 VPR ERCC3 NTPRev multimer-bound HIV-1 mRNANELFACCNH POLR2FPOLR2I VPU POLR2K GTP VPU POLR2DREV monoubiquitinated N-myristoyl GAG PSIP1 GTF2F2GTF2E1 p-S2,S5-POLR2A p6 TCEA1 p6 CDK7 TAF1 POLR2FPOLR2B GTF2H2 ERCC2 TCEB3 CCNH MA monoubiquitinated N-myristoyl GAG CCNT1 POLR2DHIV-1 RNA template POLR2C RTC with tRNA primerRNA templateHIV-1 transcription complex containing 11 nucleotide long transcriptPOLR2H UBCmyristoylated Nef Protein GTF2F2NCBP2 POLR2L p-SUPT5H CDK9 SSRP1 NELFAp-S5-POLR2A GTF2H2 POLR2C HIV-1 RNA template Surface protein gp120 POLR2K POLR2B POLR2L CDK7 ERCC3 p6 POLR2E POLR2B GTF2F2Virion with CD4gp120 bound to CCR5/CXCR4GTP POLR2H ERCC3 POLR2H p6 POLR2DUBBp6 SUPT16H REV POLR2B NC viral PIC proteinsNC Virion with exposed coreceptor binding sitesPOLR2K POLR2A RTC with minus sssDNAtRNA primerRNA templateIN p6 PSIP1 TCEB1 TAF5 RNA Polymerase II TAF13 myristoylated Nef Protein VPU NELFCD TAF9 GTF2H4 Rev multimer-bound HIV-1 mRNACrm1RanGTPCHMP5 TBP Envelope glycoprotein gp160 POLR2FGTF2H1POLR2H GDP TAF11 Transmembrane protein gp41 POLR2G VPS37C CDK7 POLR2I CTDP1 POLR2B RNA Polymerase II POLR2DPOLR2H RPS27ANELFAN-myristoyl GAG POLR2G GTF2BRTC without viral RNA templateGTF2F2POLR2A POLR2L VPR POLR2G CTDP1 NUP214 NUP88 CTP HMGA1 p6 Tat-containing early elongation complex with hyperphosphorylated Pol II CTD p51 TAF6 VIF SSRP1 POLR2A NC POLR2FPOLR2J Surface protein gp120 GTF2F2POLR2G GTF2H3 POLR2E GTP POLR2K POLR2L GTF2H2 POLR2E Immature HIV virionPOLR2DCCNT1 UTP POLR2B p-SUPT5H MA CHMP4A p6 POLR2G GTF2F2POLR2FPOLR2DRNA Polymerase II ATPGTF2F2GTF2F2CDK7 TAF1 POLR2H NELFCD POLR2FTAF4B ELL PiPOLR2B POLR2FELL GTF2H3 GTF2H4 p51 ERCC2 CCR5 GTF2H1p-SUPT5H NELFATCEB3 POLR2J LIG4 NELFB RNA Pol II with phosphorylated CTD CE complexReverse transcriptase/ribonuclease H POLR2B Surface protein gp120 GTF2H2 SUPT4H1 CHMP2A MA POLR2C VPR CTP POLR2DGTF2A1GTF2A2 GTF2F2POLR2E POLR2L p51 PPIA ERCC2 HIV-1 transcription complex containing 9 nucleotide long transcriptCCNT1 POLR2H POLR2I Reverse transcriptase/ribonuclease H GTF2F2ERCC2 GAG-POL Polyprotein myristoylated Nef Protein POLR2K NELFATCEB2 POLR2B POLR2C NC CCNH VPU CDK7 POLR2C NELF complexTFIIDGTF2H4 GTF2F1ERCC3 CTDP1 PPIA VPR IN TBP NELFB CTDP1 NELFCD HIV-1 processive elongation complexVPU p6 UBCCCNT2 TAF1 POLR2L UBA52CCNH UTP POLR2L VTA1 MA CDK7 GTF2F1POLR2DIN GTF2A1NUP98-5 ELL MA NELFAATP IN NucleocapsidPOLR2I TAF9 ATP PPIA N-myristoyl GAG POLR2E GTF2H2 GTF2H4 GTF2F1p51 NC HIV-1 mRNA HMGA1 p6 POLR2I MNAT1 GTF2F1POLR2K GTF2F1GTF2H1POLR2FCTP POLR2G TCEA1 HIV-1 transcription complex with GTF2B TAF1 CCR5 POLR2I CDK9 POLR2B GTF2H3 POLR2B p-S5-POLR2A PSIP1 TCEB1 UBCviral RNA template degraded by RNase-H POLR2J POLR2A Surface protein gp120 CDK7 VPR VPS37D REV NC POLR2K Cap Binding Complex HIV-1 mRNAPOLR2E POLR2H HIV-1 transcription complex containing extruded transcript to +30RANBP2 REV SSRP1 VPR HIV-1 RNA GTF2F2NELFE POLR2H GTF2E1 POLR2E POLR2C POLR2DUbGTF2A1GTF2A2 REV UBCGTF2H4 IN REV Transmembrane protein gp41 REV other viral genomic RNATrimeric gp120gp41 oligomerPOLR2G POLR2G GTF2F2TCEB1 POLR2I TAF9 Transmembrane protein gp41 NCBP1 p6 CDK9 GTF2H4 MA NELFCD VPR VPR PR POLR2C VPR VPR VIF PR MNAT1 TAF6 NC UBCTAF11 CD4Env gp120/gp41 hairpin complexCCR5/CXCR4GTF2F2ERCC2 CCNH TBP HMGA1 GTF2H3 Rev multimer-bound HIV-1 mRNACrm1RanGTPPOLR2FVPR VPU HIV-1 RNA p6 POLR2G UBCNELFANELFE POLR2B POLR2C NUP133 CHMP7 POLR2DPOLR2DPOLR2A GTF2F2UBCNC TAF9 p-S2,S5-POLR2A ERCC3 Reverse transcriptase/ribonuclease H IN GTF2H1POLR2FCCNH POLR2J RNA Pol II GTF2H1viral RNA template extensively digested except in PPT region TAF5 POLR2FPOLR2G REV PIC SUPT4H1 PPIA PSIP1 RPS27APOLR2I GTF2H3 UBBGTF2E2 ATP Surface protein gp120 POLR2G NTPVPU TAF6 UBCPOLR2FIN POLR2K TCEA1 ERCC2 p6 POLR2E TAF13 GDPGTF2H1POLR2E NUP93 NELFATCEA1 IN PPIA POLR2H MYS-CoATAF4B TBP GTF2F1POLR2C POLR2J CDK7 VPR POLR2H POLR2E NC p6 POLR2C GDP POLR2K UBBPOLR2K POLR2K viral RNA template extensively digested except in PPT region RNA Polymerase II TAF10 POLR2B VPS37D MA 1-LTR form of circular viral DNAELL POLR2B VPU POLR2J UBCPOLR2L PPIA p6 GTF2H3 POLR2H NC Trimeric ENV precursorReverse transcriptase/ribonuclease H MNAT1 p6 ATP NELFATAF13 POLR2H POLR2FPOLR2J POLR2I CDK9 CCNH MA UBA52RNGTT NELFB HIV-1 initiation complexERCC3 IN RNA Polymerase II PR Tat-containing elongation complex prior to separationPOLR2L p-S2,S5-POLR2A POLR2H NUP107 GTF2E2 GTF2A2 CHMP4C TAF9 TAF11 TAF5 GTF2H1p-SUPT5H POLR2FGTF2H4 GTF2H2 GTF2F1TAF11 PSIP1 Transmembrane protein gp41 POLR2DPOLR2FGTF2H3 POLR2E p-S2,S5-POLR2A POLR2K RANGAP1POLR2A GTF2F1VPU NUP205POLR2E POLR2A p6 GTF2H1GTF2BHIV-1 RNA template NC HIV-1 early elongation complex with hyperphosphorylated Pol II CTDGTF2H2 REV POLR2G CCNT1 NELFE MNAT1 POLR2B TAF10 TAF5 IN bound to sticky 3' ends of viral DNA in PICHIV-1 transcription complex containing 4 nucleotide long transcriptHIV-1 open pre-initiation complexCCNH MA Nuclear Pore Complex REV FACT complexPOLR2E TCEB3 UTP MA GTF2E1 VPR POLR2G Encapsidated viral corep-S2,S5-POLR2A p6 p6 POLR2C viral RNA template being digested by RNase-H POLR2C p-NELFE IN TCEB3 POLR2I SUPT16H Reverse transcriptase/ribonuclease H VIF POLR2L ERCC3 NELFCD POLR2L ATP GTF2F2VPR GTF2H3 NELFE MNAT1 POLR2J HIV-1 mRNA GTF2F1Elongin ComplexPOLR2G IN bound to sticky 3' ends of viral DNA in PICCDK9 NELFE NCBP1 GTF2H3 VPR IN GTF2E1 HIV-1 Tat-containing arrested processive elongation complexTCEB1 SUPT4H1 IN NUP214 TAF10 CD4 RTGTF2F2CCNT1 CCNH HIV-1 unspliced RNANELFE POLR2FCXCR4 SUPT16H PPIA GTF2H4 VPR GTF2E1 GTF2F1TAF4 GTF2F1p-S5-POLR2A Reverse transcriptase/ribonuclease H HIV-1 Tat-containing aborted elongation complex after arrestPOLR2H SUPT4H1 NUP160 MNAT1 POLR2L VPR SUPT16H ERCC3 HIV-1 RNA template GTF2E1 p51 POLR2J SUPT16H MNAT1 CCNT1 p-SUPT5H VPR POLR2K CDK7 GTF2F2POLR2I GTF2F2CDK7 p-S5-POLR2A VIF LIG4 GTF2F2NCBP2 POLR2C NUP85 Tat POLR2G TAF4 CCNT2 TCEB3 NC SUPT4H1 TCEA1 NUP35 POLR2I HIV-1 RNA template N-myristoyl GAG GTF2A2 POLR2B CCNT1 POLR2H POLR2DTBP CHMP3SSRP1 RAN REV POLR2I PPIAVIF GTF2E2 VPU POLR2L NC UBCREV CDK7 Reverse transcriptase/ribonuclease H NELFB PR UBCIN Host genomic DNARTC with extensive RNase-H digestionp6 PR TCEA1 NC REV POLR2H Envelope glycoprotein gp160POLR2B POLR2C XRCC6 UTP VPU p51 TAF11 VPR p-S2,S5-POLR2A ATPGTF2F1p6 TAF4B ERCC2 VPU UBCPPIA POLR2E CDK9 MNAT1 GTF2H2 NUP43 dNTPmyristoylated Nef Protein POLR2Dp51 PSIP1 POLR2H POLR2L VIF VPU IN CCNT2 UBCPOLR2DPOLR2L Autointegrated viral DNA as an inverted circlePOLR2B POLR2A HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotidesGTF2H3 TAF13 UBCMA POLR2DRAN SUPT4H1 NUP188POLR2K GTF2F1POLR2L TCEA1 ESCRT-IIIIN RAE1 GTF2F1POLR2A POLR2G Transmembrane protein gp41 TAF12 POLR2K GTF2A1SSRP1 p-S2,S5-POLR2A POLR2E DSIFNELFearly elongation complexPOLR2E TAF4 myristoylated Nef Protein POLR2I LIG1GTF2H2 Tat GTF2F2CTDP1 NUP153 UBCGTF2A1POLR2FPOLR2FPOLR2H POLR2B UBCTAF4B RTC with annealed complementary PBS seqments in +sssDNA and -strand DNAPOLR2J TAF9 NUP155 GTF2A2 TFIIHGTF2H3 POLR2K POLR2H VIF UBCPOLR2K POLR2C RTC IN REV CDK9 VIF TAF5 MA POLR2DGTF2H4 VIF POLR2J CDK7 MNAT1 NELFB MNAT1 UBCREV Tat TAF12 GTF2E2 NEDD4LPOLR2A PR p6 GTF2E2 MNAT1 RPS27APiTAF9 POLR2DXRCC6 Reverse transcriptase/ribonuclease H Spliced Env mRNATCEA1 MA NC NUP35 NELFAGTF2H4 REV myristoylated Nef Protein POLR2G NC Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELFERCC2 CCR5 REV MNAT1 POLR2L GTF2H3 GTF2A2 POLR2DGTF2H3 POLR2H Tat PR POLR2FPOLR2L CCR5 CCNH CD4 viral DNAKu proteinsXRCC4DNA ligase IV complexPOLR2I CDK7 GTF2F1NUP43 MA ELL RTC with degraded RNA template and minus sssDNAERCC2 POLR2C GAG-POL Polyprotein UBCCCNH POLR2I GTF2H3 POLR2G POLR2FPOLR2DGTF2F2Viral core surrounded by Matrix layerRANBP1Aborted HIV-1 early elongation complextRNA-Lysine3POLR2C IN POLR2L p6 Tat CHMP5 POLR2K ESCRT-IPR GTF2F2MA POLR2Fp-S5-POLR2A GTP Tat VPU ERCC3 ERCC2 RAN POLR2DTAF12 Nef Protein Assembling HIV virionPOLR2G POLR2J GTF2F1TCEB1 IN TAF13 CXCR4 NUP37 TCEB2 ATP NCBP2 POLR2K POLR2H ERCC2 GTF2H2 CTP CHMP3p-SUPT5H GTF2E2 GTF2H4 MNAT1 VIF RNMT SUPT4H1 NC POLR2C POLR2DTCEA1 CCNH GTP TSG101POLR2I ADPGTF2F2RNGTT NELFCD DSIF complexVPU REV POLR2H Surface protein gp120 VPU POLR2I VPR p-S2,S5-POLR2A POLR2B GTF2F2HMGA1GTF2F1NELFB REV MA POLR2L MA CDK9 POLR2I TatP-TEFbIN XPO1 REV CHMP4B VIF TAF5 p6 POLR2L 6537, 50, 1013480


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Wikipathways-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.

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  171. Jacob GA, Luse SW, Luse DS.; ''Abortive initiation is increased only for the weakest members of a set of down mutants of the adenovirus 2 major late promoter.''; PubMed Europe PMC Scholia
  172. Mak J, Jiang M, Wainberg MA, Hammarskjöld ML, Rekosh D, Kleiman L.; ''Role of Pr160gag-pol in mediating the selective incorporation of tRNA(Lys) into human immunodeficiency virus type 1 particles.''; PubMed Europe PMC Scholia

History

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

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1-LTR form of circular viral DNAComplexREACT_9361 (Reactome)
2-LTR form of circular viral DNAComplexREACT_9104 (Reactome)
AAAS 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)
CTDP1mim-catalysisREACT_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_163632 (Reactome)
ESCRT-Imim-catalysisREACT_115855 (Reactome)
ESCRT-Imim-catalysisREACT_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)
FURINmim-catalysisREACT_163905 (Reactome)
GAG Polyprotein REACT_115774 (Reactome)
GAG-POL Polyprotein REACT_163644 (Reactome)
GAG-POL Polyprotein mim-catalysisREACT_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 viral DNA bound to host genomic DNA with staggered endsmim-catalysisREACT_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)
NMT1mim-catalysisREACT_116143 (Reactome)
NMT2mim-catalysisREACT_115774 (Reactome)
NTPArrowREACT_6158 (Reactome)
NTPArrowREACT_6357 (Reactome)
NTPREACT_6158 (Reactome)
NTPREACT_6172 (Reactome)
NTPREACT_6184 (Reactome)
NTPREACT_6192 (Reactome)
NTPREACT_6208 (Reactome)
NTPREACT_6240 (Reactome)
NTPREACT_6278 (Reactome)
NTPREACT_6325 (Reactome)
NTPREACT_6349 (Reactome)
NTPREACT_6357 (Reactome)
Nef Protein REACT_116143 (Reactome)
Nuclear Pore Complex ArrowREACT_6340 (Reactome)
Nuclear Pore Complex REACT_6337 (Reactome)
NucleocapsidArrowREACT_8994 (Reactome)
P-TEFb complexREACT_6297 (Reactome)
P-TEFb complexmim-catalysisREACT_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)
RCC1mim-catalysisREACT_9507 (Reactome)
REACT_115708 (Reactome) Cytosolic N-myristoyl Gag polyprotein is conjugated with a single molecule of ubiquitin. Conjugation is typically to one of two lysine residues in the p6 domain of Gag but can be to lysine residues in the MA, CA, NC, and SP2 domains of the protein. The specific host cell E2 and E3 proteins that mediate Gag ubiquitination have not been identified. The same studies that first identified the p6 ubiquitination sites in Gag also called the biological significance of Gag ubiquitination into question by demonstrating that Gag proteins in which the p6 ubiquitination sites had been removed by mutagenesis could still assemble efficiently into infectious viral particles (Ott et al. 1998, 2000). More recent work, however, has identified additional ubiquitination sites throughout the carboxyterminal region of the Gag polyprotein, and when all of these sites are removed by mutagenesis, both viral assembly involving the mutant Gag polyprotein and infectivity of the resulting viral particles are sharply reduced (Gottwein et al. 2006).
REACT_115774 (Reactome) The amino terminal glycine residue of HIV-1 Gag polyprotein is myristoylated (Henderson et al. 1992). Myristoylation of newly synthesized Gag occurs in the cytosol of the infected host cell, with myristoyl-CoA as the myristate donor and the host cell NMT2 enzyme as the catalyst. Human cells express two isoforms of N-myristoyl transferase (NMT) (Giang and Cravatt 1998). The argumant that the second isoform catalyzes this reaction is indirect, based on the the observations that a stable enzyme:substrate complex forms transiently during the reaction (Farazi et al. 2001), and that Gag polyprotein can be found complexed with NMT2 (but not NMT1) in HIV-1-infected human cells (Hill and Skowronski 2005).
REACT_115855 (Reactome) Monoubiquitinated N-myristoyl Gag polyprotein associates with the ESCRT-1 complex at an endosomal membrane (Eastman et al. 2005; Martin-Serrano et al. 2003; Stuchell et al. 2004).
REACT_115916 (Reactome) Gag is translated from the unspliced viral RNA on free ribosomes in the cytoplasm. The products of the pro and pol genes are also synthesized from the unspliced viral RNA, but never as parts of an independent polyprotein. They are initially contained within the Gag-Pro or Gag-Pro-Pol fusion protein, the product of translational readthrough
REACT_116143 (Reactome) Nef amino terminal myristoylation has been shown to be critical for many of Nef's functions. As expected myristoylated Nef can be identified as co-fractionating with cell membranes and cytoskeletal components.
REACT_163632 (Reactome) The human ESCRT pathway comprises more than 30 different proteins, and this complexity is expanded further by associated regulatory and ubiquitylation machinery. Functional studies have identified a minimal core set of human ESCRT proteins, machinery that is essential for HIV-1 budding. ESCRT-1 recruitment follows an unusal path. The PTAP motif in p6 mimics the ESCRT-1 recruitment motif, bypassing the need for ESCRT-0. The TSG101/ ESCRT-I and ALIX both function by recruiting downstream ESCRT-III and VPS4 complexes, which in turn mediate membrane fission and ESCRT factor recycling.
REACT_163644 (Reactome) Gag assembly leads to formation of the immature lattice. The Gag molecules in the immature virion are extended and oriented radially, with their amino-terminal MA domains bound to the inner membrane leaflet and their carboxy- terminal p6 domains facing the interior of the particle. The GAGPol Pro molecules have arrived at the site of viral assembly in fewer numbers than the Gag protein (20:1). The trimeric gp41:gp120 complex is brought to the plasma membrane by the host vesicular transport system. Only 7-14 trimers per virion. VPU has followed the same ER:Golgi path. Vif, Nef, and Vpr are packaged along with the the HIV genome.
REACT_163666 (Reactome) The VPU protein is produced
REACT_163732 (Reactome) VPU is shuttled through the ER:Golgi protein expression pathway.
REACT_163787 (Reactome) The ENV precursor protein gp160 is synthesized.
REACT_163798 (Reactome) There are numerous N-linked glycosylation sites that are important for infectivity of human immunodeficiency virus type 1. With more than 20 consensus N-linked glycosylation sites in gp120 it is expected that a number are important for virion function.
REACT_163803 (Reactome) The events that lead to the viral component assembly and the recruitment of the ESCRT host machinery are well-characterized. The exact steps that release the immature viral particle are not. Membrane fission is an energy intensive process and an active area of study.
REACT_163807 (Reactome) The proteolytic events that cleave Gag and Gag-Pro-Pol are well characterized, but the event that triggers the protease is not well characterized. The PRGag, that is assembled in the immature virion weakly dimerizes, once PR is cleaved from the proprotein PR dimerizes and becomes an efficient protease. This assembly step may be part of the switch. Once the protease becomes active in the immature virion MA, CA, SP1, NC, SP2, P6, PR, RT, and IN are produced. This event, the production of these fragments would be the switch from immature to mature.
REACT_163857 (Reactome) The cleaved and assembled gp41:gp121 complexes are transport to teh plasma membrane. This complex ultimately arrives via the cellular secretion pathway. Env is an integral membrane protein shuttled through the ER and Golgi where it was glycosylated and cleaved into the gp41 and gp120 subunits. The trimeric complex is brought to the plasma membrane by the host vesicular transport system. Only 7-14 trimers are present per virion.
REACT_163863 (Reactome) Once transported to the plasma membrane the VPU protein will be incorporated into the assembling virus. The Vpu accessory protein is found to be required for efficient virion release from some cell lines but completely dispensible in others.
REACT_163872 (Reactome) Assembling Gag molecules are largely derived from the rapidly diffusing cytoplasmic pool. Gag membrane targeting requires myristoylation and a subset of GAG molecules are shuttled to the plasma membrane in this way.
REACT_163888 (Reactome) The trimeric ENV precursor complex is transported from the ER to the Golgi.
REACT_163905 (Reactome) The trimeric gp160 complexes are cleaved into the gp41 and gp120 subunits by the cellular protease furin.
REACT_163952 (Reactome) The monomeric GP160 ENV precursor protein assembles into a trimer.
REACT_163953 (Reactome) HIV is characterized by the production of multiple-spliced RNA species. The genomic fragmant is processesed creating multiple mRNA fragments.
REACT_6134 (Reactome) After assembly of the complete RNA polymerase II-preinitiation complex, the next step is separation of the two DNA strands. This isomerization step is known as the closed-to-open complex transition and occurs prior to the initiation of mRNA synthesis. In the RNA polymerase II system this step requires the hydrolysis of ATP or dATP into Pi and ADP or dADP (in contrast to the other RNA polymerase systems) and is catalyzed by the XPB subunit of TFIIH. The region of the promoter, which becomes single-stranded , spans from –10 to +2 relative to the transcription start site.

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

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

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

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

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

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

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

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

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

REACT_9040 (Reactome) As the reverse transcriptase activity of the HIV-1 RT heterodimer catalyzes the extension of the minus-strand DNA, the RNaseH activity catalyzes the degradation of the complementary viral genomic RNA sequences. Telesnitsky and Goff (1993) observed that two defective forms of reverse transcriptase can complement to restore retroviral infectivity. The RNase H active site is positioned within the HIV-1 RT heterodimer so as to attack the RNA strand of the RNA:DNA duplex at a point 18 bases behind the site of reverse transcription (Furfine and Reardon 1991; Ghosh et al. 1995; Gopalakrishnan et al. 1992; Wohrl and Moelling 1990). The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis and the level of its activity in vivo is unclear, however (Kati et al. 1992). The product of these combined DNA synthesis and RNA degradation events is a DNA strand still duplexed with extended viral genomic RNA fragments.
REACT_9042 (Reactome) XRCC4 and DNA ligase 4 are recruited to the complex containing viral DNA.
REACT_9044 (Reactome) After fusion of the viral membrane with the target cell membrane, the viral core, which is surrounded by a layer of Matrix (p17) proteins, is exposed to the cytoplasm. Disintegration of the Matrix layer allows for the conical-shaped viral core to be fully released, and allow for viral capsid dissociation and eventually reverse transcription. Dissociation of the Matrix layer is not well characterized, but is believed to occur due to disruption of protein-protein interactions as a result of the conditions of the cytoplasm (including pH), which differ from that of the internal viral structure.
REACT_9045 (Reactome) The 1-LTR circle can be formed by either of two pathways. The first involves a failure to complete reverse transcription; the second, annotated here, follows the completion of reverse transcription and is mediated by cellular enzymes. In this pathway, the action of host cell homologous recombination enzymes on the long terminal repeat (LTR) termini of the viral DNA results in formation of a single LTR. This reaction probably takes place after partial or complete disassembly of the PIC to expose the viral DNA. Repair of this intermediate as in the late stages of homologous recombination pathways results in formation of the 1-LTR circle. Mutations in the Mre11/Rad50/NBS pathway influence the formation of 1-LTR circles.
REACT_9046 (Reactome) As the reverse transcriptase activity of the HIV-1 RT heterodimer catalyzes the synthesis of minus-strand strong stop DNA (-sssDNA), the RNaseH activity of the same RT heterodimer catalyzes the degradation of the complementary viral genomic RNA sequences. Degradation of this RNA is required for the efficient transfer of the -sssDNA to the 5' end of the viral genomic RNA. The RNase H active site is positioned within the HIV-1 RT heterodimer so as to attack the RNA strand of the RNA:DNA duplex at a point 18 bases behind the site of reverse transcription (Furfine and Reardon 1991; Ghosh et al. 1995; Gopalakrishnan et al. 1992; Wohrl and Moelling 1990). The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis, however (Kati et al. 1992), and may further depend on RT stalling and structural features of the viral genomic RNA template. The product of these combined DNA synthesis and RNA degradation events is a DNA strand still duplexed with extended viral genomic RNA fragments.
REACT_9048 (Reactome) The first chemical step of integration involves a single step transesterification, in which the recessed 3' hydroxyl of the viral DNA becomes covalently joined to a protruding 5' end in the target DNA. This step at the same time cleaves the target DNA.
REACT_9049 (Reactome) Synthesis of minus-strand DNA proceeds toward the 5' end of the PBS motif of the template HIV genomic RNA.
REACT_9054 (Reactome) How the PIC finds favored sites on target DNA has not been fully clarified. Active genes are favored for integration, and favored sequences at the site of integration also influence the reaction. Studies of cells depeleted in PSIP1/LEDGF/p75 suggest that this protein acts as a tethering factor binding HIV PICs near integration target DNA. Access of PICs to sites on chromosomes may be significant, since centromeric alphoid repeats are disfavored for integration, perhaps due to wrapping in compact centromeric heterochromatin. Nucleosomes bound to the integration template also affect target site selection and integration complex binding.
REACT_9056 (Reactome) With the removal of all viral genomic RNA and tRNA, the PBS sequence at the 3' end of the plus-strand strong-stop DNA (+sssDNA) is free to pair with the complementary PBS sequence at the 3' end of the minus-strand DNA, to generate a circular structure (Telesnitsky and Goff 1997).
REACT_9066 (Reactome) The rate of RNase H cleavage is substantially lower than the rate of DNA synthesis (Kati et al. 1992), so the product of the combined DNA synthesis and RNA degradation events catalyzed by the RT heterodimer mediating minus-strand DNA synthesis is a DNA segment still duplexed with extended viral genomic RNA fragments. Other RT heterodimers bind the remaining RNA:DNA heteroduplexes and their RNase H domains further degrade the viral genomic RNA (Wisniewski et al. 2000a, b). Two PPT (polypurine tract) sequence motifs in the template, one immediately 5' to the U3 sequence and one located within the pol gene in the center of the viral genome, are spared from degradation (Charneau et al. 1992; Julias et al. 2004; Pullen et al. 1993).
REACT_9069 (Reactome) Prior to integration, two nucleotides are removed from each 3' end of the linear viral DNA, thereby exposing recessed 3' hydroxyls. This reaction may serve to remove heterogenous extra bases from the viral DNA end, and to stabilize the IN-DNA complex. The chemistry of cleavage is a simple hydrolysis by single-step transesterification.
REACT_9073 (Reactome) Viral DNA that does not become integrated can undergo another fate, which is to have the two viral DNA ends joined together to form a 2-LTR circle. This reaction requires Ku, XRCC4 and ligase 4.
REACT_9074 (Reactome) Upon completion of reverse transcription, the viral integrase protein (IN) becomes bound to the ends of the viral DNA. This is inferred by the fact that this is the site of integrase action, and several biochemical studies have documented integrase interactions with the terminal DNA.
REACT_9075 (Reactome) HIV-1 genomic RNA contains a centrally located PPT (cPPT) within the pol gene that, like 3'PPT, is spared by RNase H during minus-strand DNA synthesis and persists to prime plus-strand DNA synthesis. This ribonucleotide primes the synthesis of a plus-strand DNA extending through the U3 and R regions of the HIV sequence and terminating in the PBS region (the tRNA primer-binding site). This DNA segment is known as plus-strand strong-stop DNA (+sssDNA) (Telesnitsky and Goff 1997; Pullen et al. 1993; Huber and Richardson 1990). cPPT priming is important for efficient viral replication (Alizon et al. 1992; Rausch and Le Grice 2004). Several features of cPPT priming in vivo remain to be clarified.
REACT_9478 (Reactome) Upon translocation to the cytoplasm, RanBP1 associates with Ran-GTP in the Rev-CRM1-Ran-GTP complex.
REACT_9507 (Reactome) Free, nuclear RanGTP is required for export processes out of the nucleus. RCC1 catalyses the conversion of Ran-GDP to Ran-GTP in the nucleus.
REACT_9530 (Reactome) CRM1 associates directly with Rev through the Rev nuclear export signal (NES) domain and acts as the nuclear export receptor for the Rev-RRE ribonucleoprotein complex.
REV 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 mim-catalysisREACT_6172 (Reactome)
RNA Polymerase II mim-catalysisREACT_6184 (Reactome)
RNA Polymerase II mim-catalysisREACT_6208 (Reactome)
RNA Polymerase II mim-catalysisREACT_6240 (Reactome)
RNA Polymerase II mim-catalysisREACT_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 DNAmim-catalysisREACT_8992 (Reactome)
RTC with extending minus strand DNAmim-catalysisREACT_9075 (Reactome)
RTC with extending second-strand DNAmim-catalysisREACT_8999 (Reactome)
RTC with extensive RNase-H digestionmim-catalysisREACT_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		mim-catalysisREACT_9046 (Reactome)
RTC with minus sssDNA transferred to 3'-end of viral RNA templatemim-catalysisREACT_9049 (Reactome)
RTC with minus strand DNA synthesis initiated from 3'-endmim-catalysisREACT_9040 (Reactome)
RTC with tRNA primer RNA templateREACT_9039 (Reactome)
RTC with tRNA primer RNA templatemim-catalysisREACT_9039 (Reactome)
RTmim-catalysisREACT_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_6337 (Reactome)
Rev multimer-bound HIV-1 mRNA

Crm1 Ran

GTP		REACT_9478 (Reactome)
Rev multimer-bound HIV-1 mRNA

Crm1 Ran

GTP		mim-catalysisREACT_6171 (Reactome)
Rev multimer-bound HIV-1 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_6206 (Reactome)
TFIIHREACT_6275 (Reactome)
TFIIHREACT_6358 (Reactome)
TFIIHmim-catalysisREACT_6134 (Reactome)
TFIIHmim-catalysisREACT_6184 (Reactome)
TFIIHmim-catalysisREACT_6234 (Reactome)
TFIIHmim-catalysisREACT_6325 (Reactome)
Tat P-TEFbREACT_6170 (Reactome)
Tat P-TEFbmim-catalysisREACT_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 CTD and phospho-NELFmim-catalysisREACT_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 early elongation complex with hyperphosphorylated Pol II CTDmim-catalysisREACT_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		mim-catalysisREACT_9073 (Reactome)
viral PIC proteinsArrowREACT_9001 (Reactome)
viral PIC proteinsArrowREACT_9006 (Reactome)
viral PIC proteinsArrowREACT_9022 (Reactome)
viral PIC proteinsArrowREACT_9025 (Reactome)
viral PIC proteinsArrowREACT_9045 (Reactome)
viral PIC proteinsArrowREACT_9048 (Reactome)
viral PIC proteinsArrowREACT_9054 (Reactome)
viral PIC proteinsREACT_9001 (Reactome)
viral PIC proteinsREACT_9048 (Reactome)
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