HIV Life Cycle (Homo sapiens)

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14, 6436, 89111, 106, 117, 1658, 55, 109, 14495, 117351101151151110158, 16326, 9521, 30, 9713, 26, 9536396, 34, 51, 53, 67...24, 62, 96, 111149841919174, 16242, 59, 107, 109, 115...14, 16, 36, 65, 89...12, 76, 134, 141118, 128, 13157, 15286, 16136, 899526, 95379, 23, 27, 38, 52...461, 9925, 162, 16840, 127121, 63, 97, 16411154162957916228, 47, 12472110104, 1201102, 1541154, 16687, 119, 15950, 95, 117, 13917, 14515, 48, 54451613, 26, 9596, 11114, 16, 36, 65, 89...14216378, 1571101342, 132, 16736, 89142133, 148, 16315, 122, 1627333, 69, 71, 81, 85...46, 9829, 49, 53, 56, 94...41115415, 31, 60, 119, 159162135163151, 15543, 163220, 75, 96, 1111621810346, 9890804515, 31, 162154114214911234, 32, 53, 83, 140...9536129early endosome membraneendoplasmic reticulum membraneGolgi membranecytosolnucleoplasmRANBP1Nup45 VPR GTF2BHIV-1 RNA NELFCD GTF2F2 POLR2F TAF4 GTF2F2 ELL ATP TAF9 POLR2D VPR VPU (P05919) protein POLR2I Nup45 RTC with annealedcomplementary PBSseqments in +sssDNAand -strand DNACCNT1 SUPT16H VIF (P69723) protein PR (Protease) (P04585) protein BANF1 Surface protein gp120 (P04578) ERCC3 POLR2K p6 (P04585) protein SSRP1 capped HIV-1 pre-mRNA TCEB3CL2 POLR2H viral minus strand DNA after ligation TAF11 MA (P04585) protein UBC(77-152) Multimeric matrix layer HIV-1 RNA NC (P04591) protein p-S5-POLR2A POLR2E GTF2F1 GTF2F2 POLR2E NC (P04585) protein viral plus strand DNA with sticky 3' end NC (P04585) protein UBC(305-380) REV (P04618) protein GTF2F1 MA (P04591) protein VPR VPS4B VPR NELFB viral second strand DNA (plus sss) POLR2A Transmembrane protein gp41 HIV-1 openpre-initiationcomplexTAF1L GTF2F1 POLR2L IN (Integrase) (P04585) protein p-S5-POLR2A p6 (P04591) protein XPO1 PPiGTF2F1 Rev multimer-boundHIV-1 mRNANELFA SUPT4H1 TCEB3CL TAF4B GTF2H2 N-myristoyl GAG tRNA-Lysine3 TAF6 POLR2H MNAT1 tRNA-Lysine3 POLR2A genomic DNA with staggered 5' ends CHMP7 HMGA1 TCEB3CL2 ERCC3 Surface protein gp120 (P04578) Spliced Env mRNAHIV-1 mRNA POLR2C viral RNA template degraded by RNase-H (initial) NCBP2 capped HIV-1 pre-mRNA UBC(457-532) VPU (P05919) protein PIC (PreIntegrationComplex)POLR2B Ran-GDPERCC3 MA (P04585) protein p6 (P04591) protein POLR2L ERCC2 POLR2A POLR2K NUP85 POLR2G VIF (P69723) protein GTF2F2 viral PIC proteinsVIF (P69723) protein POLR2H MA (P04585) protein GTF2B NELFCD NUP214 IN (Integrase) (P04585) protein p51 (RT) RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexTAF6 POLR2K CDK7 UBC(153-228) TCEB3B TFIIDTat:P-TEFb(CyclinT1:Cdk9) complexRTCwithintegrationcompetentviralDNA:BANF1:HMGA1:PSIP1VPS37D Transmembrane protein gp41 p6 (P04591) protein NC (P04585) protein NELFB p6 (P04585) protein POLR2J POLR2E POLR2I POLR2I VPR ERCC2 GTF2F2 VIF (P69723) protein MA (P04585) protein p6 (P04591) protein Virion with CD4bound to gp120POLR2G TAF15 VPU (P05919) protein CTDP1 TAF1 NELFE Multimeric capsid coat PPIA p6 (P04585) protein UBC(381-456) NELFCD VPS37A POLR2H SUPT4H1 GTF2H2 ELLGTF2H2 POLR2E POM121C TCEB2 Rev-multimerNC (P04585) protein NCBP1 VIF (P69723) protein TCEB3C p6 (P04591) protein viral minus strand DNA (full-length) NELFA POLR2I Reverse transcriptase/ribonuclease H POLR2G VPS4A Trimeric gp120:gp41oligomerIN (Integrase) (P04585) protein CTDP1p51 (RT) POLR2F REV (P04618) protein VIF (P69723) protein p-S2,S5-POLR2A PPIA VPU (P05919) protein p6 (P04585) protein POLR2D POLR2K RNAPolII(hypophosphorylated):capped pre-mRNA complexCCNT1 POLR2C POLR2B NEDD4LPOLR2F POLR2F TAF2 ATP RNAPolymeraseII(unphosphorylated):TFIIF complexPPIA HMGA1 GTP POLR2J CTP GTP VPU (P05919) protein POLR2K POLR2J UBC(533-608) IN (Integrase)(P04585) proteinDSIF:NELF:earlyelongation complexafter limitednucleotide additionCTDP1 NTPCHMP5 NELFCD MA (P04585) protein VIF (P69723) protein TAF4B UBC(153-228) POLR2H VPU (P05919) protein HIV-1 mRNANELFA capped HIV-1 pre-mRNA ERCC3 MA (P04591) protein XPO1 POLR2D viral PIC proteinsNELFB SUPT16H GTF2H4 TCEB3CL POLR2D ERCC2 GTF2E1 POLR2I p6 (P04591) protein GTF2H2 PPiNC (P04591) protein VIF (P69723) protein GTF2A1(1-274) POLR2B POLR2C HIV-1 RNA FEN1REV (P04618) protein ELL TCEB3CL POLR2C HIV-1 RNA NUP107 TCEB3CL POLR2L viral plus strand DNA (full-length) GTF2F1 CXCR4 CTP viral plus strand DNA after ligation p6 (P04585) protein Trimeric gp120:gp41oligomerGTF2H5 NELFCD NC (P04591) protein CTDP1 N-myristoyl GAG (P04591) protein p-S2,S5-POLR2A POLR2B CDK7 ERCC3 TAF3 REV (P04618) protein Autointegrated viralDNA as an invertedcircleMNAT1 POLR2I p51 (RT) CHMP2A Tat (P04608) GTF2F1 TBP POLR2L CDK7 GTF2H1 GTF2H3 VPU (P05919) protein POLR2I POLR2D p-S5-POLR2A GTF2H3 CCNH CHMP4A UBC(1-76) RPS27A(1-76) GTF2F2 MNAT1 MA (P04591) protein NCBP2 GTF2E1 NC (P04585) protein POLR2L GTF2H1 RPS27A(1-76) ADPERCC2 MNAT1 POLR2E VPR tRNA-Lysine3 POLR2H TAF3 TAF15 POLR2C POLR2H viral plus strand DNA (full-length) GTF2F2 GTF2E1 TAF9 VIF (P69723) protein ELL ERCC2 POLR2K GTF2E1 NUP155 CCNH TCEB2 UBC(1-76) POLR2J POLR2A CCNT1 RNA Pol II withphosphorylated CTD:CE complex withactivated GTVpr:importin-alphacomplexREV (P04618) protein CDK9 GTF2H4 TFIIHNC (P04591) protein NUP43 TAF11 POLR2G UBC(305-380) p6 (P04591) protein CCNK TAF6 GTF2F1 IntegrationintermediateGTF2H1 myristoylated Nef Protein (UniProt:P04601) GTF2F2 GTF2H3 GTF2BGTP Multimeric capsid coat VIF (P69723) protein CCNH PPIA p6 (P04585) protein Tat-containingelongation complexprior to separationCCNH XRCC5 SUPT4H1 GTF2H4 UBC(77-152) TAF13 TBP UBC(533-608) ATPVirion withCD4:gp120 bound toCCR5/CXCR4Virion BuddingComplexTCEB3CL2 BANF1 IN (Integrase) (P04585) protein POLR2B POLR2B POLR2B GTF2H5 POLR2I GTF2H1 CCNT1 TAF10 CDK7 HIV-1 RNA template MatrixIN (Integrase) (P04585) protein CCR5 p6 (P04591) POLR2C NELFB TCEB3CL RTC with minussssDNA transferredto 3'-end of viralRNA templateGTF2A2 p6 (P04591) protein GAG-POL Polyprotein(P04585)VPU (P05919) protein ATP NC (P04591) protein GTF2F1 POLR2B POLR2F REV (P04618) protein TPR Reverse transcriptase/ribonuclease H POLR2J Reverse transcriptase/ribonuclease H REV (P04618) protein NELFCD Surface protein gp120 ELL CCNH PSIP1 GTF2H2 p6 (P04591) protein minus sssDNA UBC(77-152) TCEB1 myristoylated Nef Protein (UniProt:P04601) POLR2G CTDP1 VPU (P05919)viral PIC proteinsReverse transcriptase/ribonuclease H POLR2E UBC(305-380) p-S5-POLR2A POLR2K TAF1 TCEB1 GTF2H2 POLR2B POLR2J GTF2H2 Integrated provirusMA (P04591) protein myristoylated nefGTF2H3 POLR2J CDK9 CTP GTF2H1 CCNH GTF2F2 NUP160 TAF2 POLR2A POLR2G TCEB3B viral DNA bound withIntegrase in PICMultimeric matrix layer p51 (RT) VPU (P05919) protein POLR2D NC (P04591) protein NUP155 POLR2J GTF2A1(275-376) GTF2F2 NELFB TCEA1 POLR2E TCEA1 POLR2K SUPT4H1 Transmembrane protein gp41 viral RNA template being digested by RNase-H (extensive) POLR2E RNMT GTF2H3 HIV-1 template DNA:30 nt transcript hybrid UBC(609-684) POLR2I HIV-1 RNA template POLR2I UBC(381-456) SEH1L-2 VPS28 NUP50 GTF2H2 Transmembrane protein gp41 POLR2I Reverse transcriptase/ribonuclease H TAF1 BANF1 TCEB2 Tat (P04608) POLR2C POLR2F CDK7 BANF1CHMP7 POLR2H POLR2A MA (P04591) protein p-S2,S5-POLR2A NUP35 POLR2A TAF15 PiNC (P04585) protein GTF2H1 HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotides POLR2J TAF1L POLR2K Multimeric capsidcoatviral minus strand DNA (ful-length) POLR2D GTF2F1 POLR2D POLR2I GTF2F1 POLR2B POLR2I p6 (P04585) protein GTF2H5 TAF7 UTP POLR2C CTDP1 POM121C POLR2H GTF2H3 GTF2A1(1-274) POLR2H TCEB1 POLR2L POLR2H capped HIV-1 pre-mRNA p-S2,S5-POLR2A XPO1 Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPp6 (P04591) protein POLR2L Mature HIV virionPOLR2I RNGTTTAF3 IN (Integrase) (P04585) protein REV (P04618) protein NMT2HIV-1 template DNAcontaining promoterwith transcript of 2 or 3 nucleotidesCTDP1 POLR2F CCNT1 MNAT1 VPU (P05919) protein RTERCC2 p-SUPT5H HIV-1 Tat-containingpaused processiveelongation complexHIV-1 Tat-containingaborted elongationcomplex afterarrestPOLR2K VIF (P69723) protein REV (P04618) protein PPiUBB(153-228) POLR2B minus sssDNA Transmembrane protein gp41 (P04578) GTF2H5 RTC with degradedRNA template andminus sssDNANELFA p51 (RT) RNGTT TAF3 p-NELFE ATPNUP98-3 CTP GTF2B p6 (P04591) protein XPO1IN (Integrase) (P04585) protein Surface protein gp120 (P04578) TCEA1 POLR2L TCEB3CL GTPPOLR2L VPR (P69726) protein GTP TAF4B GTP POLR2J POLR2G TCEB1 MA (P04585) protein CHMP3 TCEB3CL TFIIAmyristoylated Nef Protein (UniProt:P04601) TBP TCEB3CL REV (P04618) protein POLR2H ERCC2 NUPL1-2 TAF3 GTF2H1 p51 (RT) NTPPOLR2D REV (P04618) protein MNAT1 GTF2H1 TAF13 Elongin ComplexNUP205 RANBP1 POLR2H HIV-1 arrestedprocessiveelongation complexPPIA VPS37A POLR2I myristoylated Nef Protein (UniProt:P04601) ERCC3 AAAS REV (P04618) protein POLR2E Transmembrane protein gp41 Multimeric matrix layer POLR2I TCEB3C VPR VIF (P69723) protein POLR2L HIV-1 RNA XRCC5:XRCC6viral plus strand DNA (full-length) IN (Integrase) (P04585) protein POLR2L POLR2C Multimeric capsid coat minus sssDNA Host genomic DNA CTDP1 CHMP2B GTF2H2 UBC(153-228) viral RNA template degraded by RNase-H (initial) POLR2A NELFE p51 (RT) POLR2G RPS27A(1-76) CTDP1 TCEB2 CCR5, CXCR4POLR2H NDC1 SUPT4H1 NUP214 POLR2K POLR2B TAF7L VPR TAF4 VIF (P69723) protein POLR2J ELL IN (Integrase) (P04585) protein POLR2J CTP TAF10 p51 (RT) viral minus strand DNA (full-length) SUPT16H p6 (P04585) protein UBC(381-456) MA (P04591) protein NUP133 UBC(609-684) TAF9B POLR2J CDK7 nefCCNH MA (P04591) protein MNAT1 GTF2F2 POLR2H TFIIERAN GTP TAF11 MA (P04585) protein IN (Integrase) (P04585) protein ATP TCEB3C NUP153 Surface protein gp120 GTF2H1 GTF2F1 GTF2F1 GTP minus sssDNA NELFA SSRP1 GTF2E2 GTF2F2 GTF2H3 POLR2B POLR2E CTDP1 SUPT4H1 REV (P04618) protein CCNT1 TAF7 CDK7 p6 (P04585) protein TCEA1 REV (P04618) protein ATP SSRP1 MNAT1 PSIP1 REV (P04618) protein POLR2L Virion with gp41forming hairpinstructurePOLR2F PSIP1 ELL POLR2G GTF2H5 SUPT16H POLR2K NELFA Reverse transcriptase/ribonuclease H ERCC3 GTF2H5 MA (P04585) protein ERCC2 POLR2I HIV-1 initiationcomplex withphosphodiester-PPiintermediatePOLR2B GTF2F1 REV (P04618) protein TAF10 minus strand DNA (extending) p51 (RT) PSIP1 GTF2F1 SUPT4H1 POLR2B tRNA-Lysine3 CXCR4 CDK9 GTF2H3 BANF1 CCNT2 TCEB3CL2 POLR2F CDK7 SSRP1 UBAP1 POLR2K GTF2F1 TAF3 HIV-1 template DNA:30 nt transcript hybrid N-myristoyl GAG (P04591) protein TAF5 POLR2C ERCC3 POLR2H UTP HIV-1 transcriptioncomplex containing4 nucleotide longtranscriptUBB(1-76) POLR2J CHMP6 TAF3 XPO1 POLR2D PPIA POLR2B TAF5 TAF7 HIV-1 RNA NC (P04591) protein CD4 TAF7 TAF7 Surface protein gp120 PPip-S5-POLR2A NELFA ERCC3 XRCC4 CCNK PPip51 (RT) GTF2A2 POLR2G CCNH NELFCD POLR2K POLR2J TCEB3C GTF2A2 POLR2E GTP TCEB3CL NC (P04585) protein POLR2J CDK7 POLR2A TAF15 POLR2C NUP62 SUPT4H1 REV (P04618) protein POLR2E Autointegrated viralDNA as smallercirclesVIF (P69723) protein RTC with duplex DNAcontainingdiscontinuous plusstrand flapTAF3 REV (P04618) protein XPO1viral minus strand DNA (initial) CCNT2 UTP POLR2F VIF (P69723) proteinMA (P04591) protein TAF1 p6 (P04591) protein PPIA GTF2A1(275-376) UBB(153-228) TAF13 POLR2B PSIP1 ELL UTP HMGA1 VPRVPR (P69726) protein NELFB RNA Pol II withphosphorylated CTD:CE complexp6 (P04585) protein POLR2H TAF10 IN (Integrase) (P04585) protein Host genomic DNAMNAT1 GTF2H5 TAF15 HIV-1 template DNA:30 nt transcript hybrid POLR2K LIG4 POLR2G CDK9 REV (P04618) protein TAF4 GTP POLR2D POLR2D p6 (P04591) GTF2A2 TAF13 POLR2F GTF2F1 Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPUBC(229-304) GTF2E1 POLR2J GTP PPIA GTF2H3 N-myristoyl GAG(P04591) proteinPPIA GTF2F1 IN (Integrase) (P04585) protein SUPT4H1 MNAT1 VPU (P05919) protein POLR2G NUP205 VPU (P05919) protein NELFB TAF15 GTF2E2 PPitRNA-Lysine3 REV (P04618) protein POLR2C VPR UBB(153-228) CDK7 p51 (RT) LIG4 NELFB GTF2F2 POLR2F ERCC2 GTF2A2 Reverse transcriptase/ribonuclease H CTP POLR2F HIV-1 template DNA:30 nt transcript hybrid Reverse transcriptase/ribonuclease H Rev-multimer MNAT1 p6 (P04585) protein BANF1 POLR2L p6 (P04585) protein NELFCD TAF1L HIV-1 earlyelongation complexwithhyperphosphorylatedPol II CTDGTF2H3 TAF13 p-SUPT5H POLR2G GTF2H4 GTF2H3 CDK7 CCNH POLR2F POLR2H GTF2F2 TAF7 CCNH IN (Integrase) (P04585) protein HIV-1 RNA TAF9B SSRP1 VIF (P69723) protein UBB(1-76) CCNK CTDP1 VPU (P05919) protein VPR (P69726) protein p-S2,S5-POLR2A NUP210 CTDP1 HIV-1 transcriptioncomplex containing4-9 nucleotide longtranscriptCCNH GTF2F2 CDK7 GTF2F2 Encapsidated viralcorep6 (P04585) UBB(1-76) GTF2B Elongating HIV-1 transcript in processive Pol II mediated elongation MNAT1 UBC(381-456) GTF2F2 POLR2L minus strand DNA (extending) POLR2J GTF2F2 POLR2H TCEA1 Host genomic DNA POLR2G GTP POLR2D TCEA1 UBB(1-76) POLR2F TAF12 NucleocapsidERCC3 p6 (P04591) GTF2H2 GTF2A1(1-274) HMGA1 ATP MA (P04591) protein CDK9 GTF2F1 POLR2D REV (P04618) protein GTP Rev-multimer NUPL1-2 TCEB3 POLR2D TAF9 NELFCD GTF2A1(1-274) POLR2H UBC(1-76) Vps/Vta1POLR2A HIV-1 RNA P-TEFb complexVPU (P05919) protein TAF7L POLR2D POLR2C BANF1 GTF2H2 GTF2H4 TCEB3CL2 TCEB3CL TAF1L GTF2H3 TCEB3 CCNT2 POLR2C ERCC3 HIV-1 initiationcomplexPOLR2L myristoylated Nef Protein (UniProt:P04601) POLR2B ERCC2 POLR2C NUP43 Multimeric capsid coat POLR2D POLR2L NELFB POLR2H Envelope glycoprotein gp160 minus strand DNA (extending) RNAPolII(hypophosphorylated) complex bound to DSIF proteinCCR5 TCEB3 NUP98-5 POLR2D VPR (P69726) protein UBC(457-532) POLR2F POLR2I NELFCD CD4 ERCC3 POLR2E CCNH p6 (P04591) protein POLR2E POLR2G UBB(153-228) POLR2F POLR2L MNAT1 POLR2B GTF2H2 NELFE REV (P04618) protein CTDP1 IN (Integrase) (P04585) protein POLR2J p6 (P04591) protein viral plus strand DNA with sticky 3' end ERCC3 TAF15 POLR2L UTP POLR2E VPR NC (P04585) protein POLR2I TCEB3CL2 PR (Protease) (P04585) protein POLR2G RAN:GTPSSRP1 GTP NC (P04591) protein POLR2K GTF2H5 p-S2,S5-POLR2A CTDP1 POLR2G GTF2H4 viral plus strand DNA with sticky 3' end ERCC2 POLR2H CXCR4 viral minus strand DNA with sticky 3' end POLR2K viral second strand DNA with plus sssDNA (extending) ERCC3 p6 (P04591) protein p6 (P04591) protein POLR2H POLR2L IN (Integrase) (P04585) protein POLR2G TAF9B GTF2F2 Multimeric capsid coat VPU (P05919) protein 1-LTR form ofcircular viral DNAPPIA NELFA NELFE POLR2E POLR2J GTF2F1 Reverse transcriptase/ribonuclease H Transmembrane protein gp41 (P04578) TAF3 POLR2J NELFCD VPR (P69726) protein TAF1L GTF2A2 POLR2E IN (Integrase) (P04585) protein GTF2F2 POLR2H POLR2C CCNT2 NCBP2 ERCC2 POLR2L POLR2F VPU (P05919) protein TCEB2 genomic DNA with staggered 5' ends VPR VIF (P69723) protein p6 (P04591) VTA1 viral plus strand DNA with sticky 3' end GTF2E1 viral plus strand DNA (full-length) CTP Assembling HIVvirionp-SUPT5H Elongating HIV-1 transcript in processive Pol II mediated elongation VIF (P69723) protein TCEB3B TAF11 HIV-1 RNA template TBP RTC with integrationcompetent viral DNATFIIHGTF2H4 NC (P04591) protein NELFCD POLR2E REV (P04618) protein viral minus strand DNA (ful-length) HIV-1 elongationcomplex containingTatGTF2H4 RNGTT capped HIV-1 pre-mRNA HMGA1 NDC1 TCEB3 p-S5-POLR2A POLR2K TAF9 ATP ATP RAN POLR2G POLR2H XRCC5 POLR2B p51 (RT) XRCC4 ERCC2 GTF2H4 TAF9 POLR2E Nuclear Pore Complex(NPC)TCEB1 PSIP1 GTF2H2 TAF5 POLR2D GTF2A1(275-376) ERCC3 POLR2K TAF5 TAF4 tRNA-Lysine3 CCNT2 POLR2F UBC(1-76) POLR2J TCEA1 TCEB2 GTF2H1 POLR2C HIV-1 template DNA:30 nt transcript hybrid VPU (P05919) protein ELL TAF15 SUPT16H CCNH REV (P04618) protein p6 (P04585) protein SUPT4H1 POLR2J UBC(229-304) TCEB3CL2 POLR2K GTF2H1 POLR2L POLR2C POLR2K CCNK p6 (P04591) protein CCNT1 GTF2H4 NELFA NELFE GTF2H5 CD4:Env gp120/gp41hairpincomplex:CCR5/CXCR4POLR2K VIF (P69723) protein Transmembrane protein gp41 GTF2F2 TAF11 Surface protein gp120 CHMP4C CD4 UBC(153-228) HMGA1 CCNT1 CCNT1 MA (P04591) protein MA (P04585) protein SUPT4H1 ATP tRNA-Lysine3 MA (P04585) protein PSIP1 GTF2E2 TCEB2 p6 (P04585) protein POLR2F NELFCD UBC(609-684) IN (Integrase) (P04585) protein HIV-1 processiveelongation complexPOLR2E TAF9B GTF2F1 ERCC2 UTP myristoylated nefTAF4 ATPp6 (P04591) protein TCEB3 POLR2E TBP ATP POLR2J HIV-1 RNA template GTP TFIIDviral minus strand DNA (ful-length) SUPT4H1 MA (P04585) protein Elongating HIV-1 transcript in processive Pol II mediated elongation MA (P04591) protein GTF2H5 POLR2B NCBP2 VPU (P05919) protein NTPGTF2H1 Reverse transcriptase/ribonuclease H TCEB3CL2 POLR2D GTF2H4 CCNK NELFA POLR2I p6 (P04591) protein p-SUPT5H other viral genomicRNAPR (Protease) (P04585) protein VPR (P69726) protein MNAT1 MNAT1 ATP VPS37C myristoylated nef POLR2C MA (P04585) protein Reverse transcriptase/ribonuclease H POLR2J POLR2J POLR2H MA (P04591) protein CHMP2A VPR (P69726) protein POLR2D GTF2H2 HIV-1 mRNA GTF2A1(1-274) NELF complexTAF9B VPU (P05919)GTF2A1(1-274) POLR2G POLR2E p-S5-POLR2A GTF2H3 UBA52(1-76) GTF2A2 POLR2J POLR2L VIF (P69723) protein POLR2B POLR2H GTF2H5 GTF2H1 HIV-1 abortedelongation complexafter arrestp6 (P04585) protein POLR2A POLR2J POLR2J Ku proteins bound toviral DNAPOLR2G GTF2H2 REV (P04618) protein ERCC2 POLR2L VPU (P05919) protein GTF2F2 p6 (P04585) protein NELFB Surface protein gp120 HMGA1GTF2F2 Rev-multimer NUP85 GTF2A2 GTF2H2 POLR2F POLR2D TAF6 UTP ADPMVB12 Cap Binding Complex(CBC)NELFB minus strand DNA (extending) POLR2F tRNA-Lysine3 VIF (P69723) protein CCNH p51 (RT) p51 (RT) ERCC2 IN (Integrase) (P04585) protein CDK9 POLR2C Reverse transcriptase/ribonuclease H NELFE GTF2F1 TAF7 POLR2D HIV-1PolymeraseII(phosphorylated):TFIIF:capped pre-mRNAMA (P04585) protein CCNT1 TAF10 TAF9 CCR5 VPS37B IN (Integrase) (P04585) protein p-SUPT5H p51 (RT) GTF2H4 tRNA-Lysine3 p-SUPT5H POLR2B p51 (RT) NUP50 NUPL2 NC (P04591) protein TCEB1 N-myristoyl GAG POLR2B VPU (P05919) protein TCEB3 REV (P04618) proteinELL VIF (P69723) protein TCEB3C TAF1 TCEB3 HIV-1 RNA TAF10 POLR2G viral plus strand DNA (full-length) GTF2H4 UBC(381-456) viral minus strand DNA (ful-length) UBC(229-304) NCBP2 HIV-1 Tat-containingarrested processiveelongation complexTAF5 GTF2F1 p6 (P04585) GTF2F2 KPNA1 POLR2K minus sssDNA p-SUPT5H UTP POLR2E viral second strand DNA with plus sssDNA (extending) CXCR4 MA (P04591) protein NUP210 Multimeric capsid coat POLR2D POLR2E NELFE p6 (P04585) protein CCNH CDK7 GTF2E2 ERCC2 TAF9 TAF7L NELFE CDK9 NTPNC (P04591) protein p6 (P04585) protein TAF1 Tat (P04608) REV (P04618) protein CHMP4B HMGA1 POLR2E TAF11 MA (P04591) protein p6 (P04591) protein GTF2A1(275-376) CCNT2 UTP TCEB3C UBC(457-532) POLR2K GTF2F1 TFIIHTCEB3C TCEB2 NCBP1 TCEB3 GTF2H1 VPU (P05919) protein p-SUPT5H TCEB1 TCEB3CL2 viral minus strand DNA (initial) IN (Integrase) (P04585) protein ATP ELL TAF10 NUP133 HIV-1 template:capped HIV-1 transcript hybrid tRNA-Lysine3 XRCC5 UBB(77-152) SUPT4H1 POLR2D BANF1 Trimeric ENVprecursorERCC2 MA (P04585) protein TAF11 SSRP1 NCBP1 POLR2B GTF2H2 POLR2G NELFE CTDP1 TAF4B POLR2F POLR2B HIV-1 transcriptioncomplexCCNH VPR GTF2A1(275-376) tRNA-Lysine3 TAF5 NUP160 GTF2H3 POLR2B CTP POLR2D ATP VPR POLR2K POLR2F TAF12 p6 (P04585) protein POLR2J HIV-1 closedpre-initiationcomplexCDK7 TCEA1 ERCC3 POLR2E p51 (RT) TAF12 Reverse transcriptase/ribonuclease H MNAT1 ERCC3 TAF7L GTF2F1 GTF2A1(275-376) TAF7L GTF2B GTF2E2 GTF2H4 POLR2E MA (P04585) protein Reverse transcriptase/ribonuclease H POLR2E REV (P04618) protein GTF2F2 template DNA:30 nt transcript hybrid viral minus strand DNA (ful-length) TAF7 MVB12 POLR2L ERCC3 POLR2F SUPT16H GTF2F1 CCNT1 POLR2C MA (P04591) protein GTF2H3 POLR2D IN:viral DNA boundto host genomic DNAwith staggered endsPOLR2H POLR2C TAF13 ADPRev-multimer CHMP4B REV (P04618) protein UBC(533-608) RANBP2 p6 (P04585) TFIIHPOLR2G UBC(533-608) ERCC3 POLR2D GTP HIV-1 template DNA with first transcript dinucleotide, opened to +8 position FURINNUP88 p6 (P04585) protein POLR2G Transmembrane protein gp41 (P04578) TCEB3CL2 UBC(609-684) HIV-1 template:capped HIV-1 transcript hybrid GDP NELFE HIV-1 template DNA:9 nucleotide transcript hybrid PPIAGTF2F1 TAF6 viral PIC proteinsCDK7 GTF2H1 NELFB GTP TAF12 TAF1L NUP107 SUPT4H1 VTA1 XRCC6 POLR2B VIF (P69723) protein IN (Integrase) (P04585) protein MA (P04591) protein GTP TBP TCEB2 NUP98-3 UBC(533-608) NUP62 UBC(229-304) ADPVPR (P69726) protein RTC with extensiveRNase-H digestionCDK7 UTP MA (P04591) protein TAF7 CDK9 TAF9 NELFE TAF15 p51 (RT) TCEB3B GTF2H2 NELFCD GTP MA (P04585) protein POLR2G IN (Integrase) (P04585) protein POLR2F MNAT1 TAF1L POLR2F POLR2I GTP ATPVPR MA (P04585) protein CDK7 PPIA POLR2C POLR2J p6 (P04591) protein VIF (P69723) protein POLR2E TCEB2 IN (Integrase) (P04585) protein TAF5 Pol II transcriptioncomplex containingextruded transcriptto +30POLR2F POLR2K UBC(153-228) POLR2E CD4 UTP FACT complexTAF1L GTF2F1 REV (P04618) protein p6 (P04591) protein Virion withfusogenicallyactivated gp41TAF2 TAF4B NUP98-4 POLR2F VPR XRCC6 dNTPHMGA1 CCNT1 IN (Integrase) (P04585) protein GTF2H5 UTP POLR2L SUPT4H1 DSIF:NELF:earlyelongation complexTAF12 NELFA CDK9 Revmultimer-boundHIV-1mRNA:Crm1:Ran:GTP:NPCPOLR2J CCNH CXCR4 POLR2C GTF2F2 GTF2H5 Reverse transcriptase/ribonuclease H minus sssDNA NUP37 TCEB1 CCNT1 POLR2K TAF12 HIV-1 cappedpre-mRNA:CBC:RNAPol II(phosphorylated)complexNELFCD GTF2F1 POLR2F GTF2E2 RTC with minusstrand DNAsynthesis initiatedfrom 3'-endUBC(1-76) TCEB3B POLR2F GTF2H4 RNGTT p6 (P04591) protein POLR2K MA (P04591) protein POLR2H VPR HIV-1 PromoterEscape ComplexPOLR2K NCBP1 POLR2L NCBP1 GTF2H1 CCNT1 VPR (P69726) protein PPIA RNAPolymeraseII(unphosphorylated):TFIIF complexCCNK TAF12 ERCC2 POLR2B TAF9 Multimeric capsid coat TAF1 POLR2D POLR2F REV (P04618) proteinReverse transcriptase/ribonuclease H POLR2K GTF2F2 POLR2B NEDD4L IN (Integrase) (P04585) protein GTF2F1 TAF2 POLR2A UBC(457-532) ERCC3 TAF13 NELFB TCEB3CL2 UTP GTF2H3 CCNH CHMP6 GTF2H3 CDK7 p51 (RT) NCBP2 Tat (P04608) POLR2A VPU (P05919) protein POLR2F ATPp-SUPT5H SSRP1 HIV-1 RNA template MA (P04585) protein Multimeric capsid coat GTF2F1 POLR2C IN (Integrase) (P04585) protein MA (P04591) protein POLR2I GTP GTF2H5 POLR2H GDP POLR2C UBB(77-152) GTF2F1 CCNH POLR2J viral second strand DNA with plus sssDNA (discontinuous) GTF2H5 GTP DSIF complexPPIAp6 (P04591) protein p6 (P04585) GTF2F2 Reverse transcriptase/ribonuclease H SUPT4H1 VIF (P69723) protein NUPL2 NELFA GTF2E2 UBB(1-76) TAF9B UTP p-S2,S5-POLR2A POLR2C viral plus strand DNA (full-length) VPR TAF4 TAF6 POLR2L POLR2F CDK9 CDK7 tRNA-Lysine3 UBC(533-608) ERCC2 HIV-1 transcriptioncomplex containing9 nucleotide longtranscriptPOLR2B IN (Integrase) (P04585) protein POLR2I POLR2F p51 (RT) POLR2B HIV-1 template:capped HIV-1 transcript hybrid POLR2A POLR2D VPR CCNT1 HIV-1 template DNA hybrid with phosphodiester-PPi intermediate TCEB3 SSRP1 GTF2H4 POLR2I TAF12 RAE1 MA (P04585) protein CCR5 NELFE GTF2E2 GTF2H4 monoubiquitinatedN-myristoyl GAG(P04591) proteinRPS27A(1-76) p-SUPT5H TSG101 POLR2B SUPT4H1 NCBP2 POLR2E HIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end GAG-POL Polyprotein (P04585) minus sssDNA HIV-1 template DNA:4 nucleotide transcript hybrid POLR2C TAF5 POLR2K GTF2H4 p-S5-POLR2A GTF2F1 POLR2K POLR2E CCNH GTF2F1 CCNH CCNT1 GTF2H5 CTDP1 POLR2J TBP GTF2F2 GTF2F2 UBB(1-76) POLR2L viral plus strand DNA with sticky 3' end VPR (P69726) protein CTP POLR2L GTF2H5 POLR2F UBC(1-76) MA (P04591) protein CHMP4A HIV-1 template:capped HIV-1 transcript hybrid POLR2L viral plus strand DNA (full-length) UBC(77-152) TCEB2 TCEB3B GTF2E2 POLR2K p6 (P04591) protein minus sssDNA POLR2C VPR UbTAF2 p-SUPT5H p-S5-POLR2A CTP NCBP1 VPU (P05919) protein VIF (P69723) protein PPIA UBC(305-380) GTF2H2 TAF2 TCEB3CL POLR2K PiPOLR2D VPU (P05919) protein CTP NELFB GTF2F1 CE:Pol II CTD:Spt5complexREV (P04618) protein TCEB3B p-S2,S5-POLR2A p6 (P04585) protein NELFA UBAP1 GTP TCEB3C AAAS POLR2A UBC(229-304) POLR2D MNAT1 CCR5 POLR2B p-S2,S5-POLR2A Reverse transcriptase/ribonuclease H TAF3 GTF2H1 HIV-1 RNA template UBB(77-152) p51 (RT) GTF2E2 POLR2E UBB(153-228) Rev-multimerPOLR2L TAF6 GTF2E1 GTF2H5 TFIIDNELFE GTF2F2 GTF2A1(1-274) PDCD6IPHIV-1 transcriptioncomplex containingextruded transcriptto +30TAF12 REV (P04618) protein VPR (P69726) protein TAF9B GTF2H3 POLR2K TAF4B ERCC3 UTP viral minus strand DNA (full-length) POLR2G GTF2F1 ERCC2 Virion with gp41fusion peptide ininsertion complexGTF2H4 VPR (P69726) protein CTP MA (P04591) protein GTF2H5 SUPT16H GTF2A1(1-274) RNMTHIV-1 Tat-containingprocessiveelongation complexSurface protein gp120 XPO1 TCEA1 HIV-1 RNA homodimerGTF2F2 TCEB3B POLR2L UBC(457-532) TCEB3C UBC(305-380) CTP SUPT4H1 NC (P04585) protein Viral coresurrounded byMatrix layerGTF2F2 PR (Protease) (P04585) protein POLR2D NELFA GTF2A1(1-274) VIF (P69723) protein POLR2D GTF2E2 myristoylated Nef Protein (UniProt:P04601) tRNA-Lysine3 GTF2F1 POLR2B POLR2F NELFE viral plus strand DNA (full-length) POLR2H viral RNA template extensively digested except in PPT region Transmembrane protein gp41 MA (P04585) protein NELFCD POLR2C PPIA TAF9B IN (Integrase) (P04585) protein p6 (P04585) POLR2F RTC without viralRNA templatePOLR2H SUPT16H Tat (P04608) VPS4A CDK7 p-S5-POLR2A p6 (P04585) protein CCNH GTP myristoylated Nef Protein (UniProt:P04601) TAF13 TAF5 Multimeric matrix layer Elongating HIV-1 transcript in processive Pol II mediated elongation TAF2 SSRP1 Multimeric matrix layer POLR2D TCEB1 IN (Integrase) (P04585) protein BANF1 NELFA HIV-1 template DNA:3 nucleotide transcript hybrid ERCC3 POLR2F MA (P04591) protein GTF2H5 GTF2E1 CDK9 SUPT4H1 viral minus strand DNA with sticky 3' end GTF2B POLR2K TCEB1 NTPGTF2F2 GTF2H3 monoubiquitinatedN-myristoyl GAG(P04591) proteinREV (P04618) protein POLR2H POLR2I ERCC3 POLR2C VPR (P69726) protein SUPT4H1 SEH1L-2 viral plus strand DNA (full-length) RANBP2 ESCRT-IIIPPIA POLR2G POLR2L POLR2C POLR2J TSG101 POLR2L POLR2I CCNH Elongating HIV-1 transcript in processive Pol II mediated elongation POLR2F PPiPOLR2L NTPVIF (P69723) protein POLR2B TCEB3CL2 Tat (P04608) TAF7 GTF2A1(275-376) NELFB POLR2J NELFA p-S5-POLR2A GTF2F1 GTF2E1 NUP93 TFIIEPPIA NUP54 GTF2A2 POLR2C IN (Integrase) (P04585) protein TAF4B CDK9 POLR2C XRCC4:LIG4GDPSurface protein gp120 POLR2F HIV-1 RNA template CCR5 UBA52(1-76) TAF10 VPU (P05919) protein CCNK p51 (RT) ERCC2 POLR2C CD4 PPIA SUPT16H Surface protein gp120 CD4 IN bound to sticky3' ends of viralDNA in PICTBP PPIA IN bound to sticky3' ends of viralDNA in PICPOLR2D tRNA-Lysine3 TAF7L UBA52(1-76) PPIA p-SUPT5H NC (P04585) protein GTF2H5 POLR2G MA (P04591) protein POLR2I TCEB3C TCEB3CL2 GTF2E1 RNAPolymeraseII(unphosphorylated):TFIIF complexPOLR2I GTF2H1 POLR2D p-S5-POLR2A p-SUPT5H GTF2H1 POLR2C SUPT4H1 POLR2B ATP p-S2,S5-POLR2A Transmembrane protein gp41 MNAT1 UBC(381-456) VPS28 POLR2K GTF2H2 POLR2D viral plus strand DNA (full-length) HIV-1 template DNA:4-9 nucleotide transcript hybrid POLR2I POLR2D REV (P04618) protein p-S2,S5-POLR2A TAF11 GTF2H3 POLR2H GTF2H2 VPS37B RTGTF2F2 Rev multimer-boundHIV-1 mRNA:CRM1complexTAF9B Elongating HIV-1 transcript in processive Pol II mediated elongation GAG-POL Polyprotein (P04585) Tat (P04608) TAF1L HIV-1 transcriptioncomplex containing3 nucleotide longtranscriptPPIA p-SUPT5H Tat (P04608) GTF2H4 Reverse transcriptase/ribonuclease H TAF6 HIV-1 templateDNA:4-9 nucleotidetranscript hybridPOLR2I Multimeric matrix layer p6 (P04585) protein GTF2H2 GTF2F2 GTF2F1 POLR2B POLR2A TCEA1 GTF2H1 p6 (P04585) protein POLR2L PDCD6IP POLR2L Transmembrane protein gp41 TAF11 tRNA-Lysine3 NELFCD GTF2A1(275-376) PPIA POLR2H ERCC2 REV (P04618) protein POLR2H MNAT1 CTP POLR2E POLR2J POLR2G RAN Reverse transcriptase/ribonuclease H p6 (P04591) protein VPR (P69726) protein GTF2H2 SUPT16H TAF13 CDK7 viral plus strand DNA (full-length) POLR2F TAF1 POLR2I UBA52(1-76) VIF (P69723) protein CTDP1 GTF2F1 CTP POLR2D POLR2L NTPPOLR2E Cap Binding Complex(CBC)TAF7L POLR2G TAF6 HIV-1 template DNAwith firsttranscriptdinucleotide,opened to +8positionRAN p6 (P04585) protein TBP ELL ELL PSIP1 Tat (P04608) RTC with extendingsecond-strand DNAGTF2H3 TCEB3B MNAT1 MA (P04585) protein monoubiquitinatedN-myristoyl GAG(P04591) proteinTAF11 PSIP1 PPIA POLR2C POLR2I NUP93 minus strand DNA (extending) GTF2A2 POLR2G GTP POLR2A PPIA GTF2F1 TAF2 RNAPolymeraseII(unphosphorylated):TFIIF complexPOLR2H POLR2L p6 (P04591) protein MA (P04591) protein POLR2J GTF2B PPIA TAF9B GTF2A1(1-274) UBB(153-228) ERCC3 ATP POLR2K p6 (P04591) IN (Integrase) (P04585) protein POLR2I POLR2D GTF2H1 UTP GTF2H3 POLR2H tRNA-Lysine3 POLR2K HIV-1 template:capped HIV-1 transcript hybrid TAF1 Reverse transcriptase/ribonuclease H POM121 POLR2J POLR2C POLR2K TFIIATCEB3C POLR2B POLR2K GTF2H5 TCEB3B PR (Protease) (P04585) protein POLR2C REV (P04618) protein POLR2C NELFA POLR2B P-TEFb(CyclinT1:Cdk9)-containingelongation complexwith separated anduncleavedtranscriptTBP POLR2C Tat (P04608)GTF2H1 POLR2F HIV-1 elongationcomplexVIF (P69723) protein POLR2I TAF11 ERCC2 viral plus strand DNA (full-length) GTF2E1 VPU (P05919) protein GTF2H4 tRNA-Lysine3 MA (P04585) protein RTC with nickedminus sssDNA:tRNAprimer:RNA templateTAF15 TAF1L GTF2F2 POLR2I HIV-1 template DNA:11 nucleotide transcript hybrid ESCRT-IERCC2 CDK7 GTF2F2 VPU (P05919) protein POLR2B GTF2F1 GTF2H4 CCR5 TAF7L GTF2F2 GTF2H3 TAF10 VPS37D CDK9 VIF (P69723) protein GTF2H1 VIF (P69723) protein VIF (P69723) protein GTF2H4 POLR2B NUP37 TCEB1 p-SUPT5H VPU (P05919) protein tRNA-Lysine3 POLR2H RPS27A(1-76) MNAT1 HIV-1 transcriptioncomplex containingtranscript to +30Reverse transcriptase/ribonuclease H TCEA1 PR (Protease) (P04585) protein POLR2F IN (Integrase) (P04585) protein POLR2I PR (Protease) (P04585) protein GTF2H2 POLR2G GTF2H5 CD4 HMGA1 POLR2H POLR2G GTF2E2 VPR (P69726) protein p6 (P04585) protein GTF2F2 TAF2 GTF2E1 POLR2L TAF2 IN (Integrase) (P04585) protein POLR2G NCBP2 p51 (RT) HIV-1 RNA template CDK9 POLR2I GTF2H4 POLR2K myristoylated Nef Protein (UniProt:P04601) tRNA-Lysine3POM121 CoA-SHNELFB CTDP1 N-myristoyl GAG (P04591) protein HIV-1 transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30POLR2D IN (Integrase) (P04585) protein NELFA CDK9 GTF2H1 CDK7 RAN VPR viral minus strand DNA with sticky 3' end p-S2,S5-POLR2A POLR2J MA (P04591) protein CDK7 VPU (P05919) protein viral minus strand DNA (ful-length) POLR2I TCEB1 viral minus strand DNA with sticky 3' end TFIIHMA (P04585) protein VPU (P05919) protein CCNH p-S2,S5-POLR2A CDK7 RTC with tRNAprimer:RNA templateReverse transcriptase/ribonuclease H POLR2I UBC(77-152) GTF2F1 TAF5 BANF1 POLR2E ERCC3 MA (P04585) protein Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD andphospho-NELFSurface protein gp120 NELFCD VIF (P69723) protein POLR2J GTF2F2 CCNT1 p6 (P04591) protein TCEB3CL UBC(153-228) POLR2E POLR2B XRCC6 tRNA-Lysine3 VIF (P69723) protein POLR2D p-SUPT5H POLR2H CDK7 CCNT1 RNAPolymeraseII(unphosphorylated):TFIIF complexGTF2A1(275-376) POLR2B TAF12 SUPT16H POLR2H GTF2H4 NUP153 TAF2 p-SUPT5H CDK9 RAN CCNT2 MNAT1 HIV-1 pausedprocessiveelongation complexPOLR2E NELFB POLR2E TFIIHTPR RAN:GTPCHMP2B Glycosylated Envelope glycoprotein gp160 p6 (P04585) protein POLR2E UBB(77-152) CDK7 GTF2H5 CTP capped HIV-1 pre-mRNA p-S2,S5-POLR2A POLR2K CDK9 GTF2F1 RCC1NELFA PPIA NELFE GTF2H3 CTDP1 UBA52(1-76) Ran GTPase:GDPNELFE CCNH GTF2F1 NTPATP HIV-1 template DNA:30 nt transcript hybrid POLR2K NUP98-5 PR (Protease) (P04585) protein CDK9 POLR2J tRNA-Lysine3 REV (P04618) protein REV (P04618) protein Virion with exposedcoreceptor bindingsitesPR (Protease)(P04585) proteinGTF2A1(275-376) POLR2L TAF10 TAF4 TAF7L GTF2H2 viral minus strand DNA with sticky 3' end HIV-1 unspliced RNAPOLR2G PPIA TCEB3B REV (P04618) protein TAF6 POLR2L GTF2H5 POLR2E TCEB3 TAF7 POLR2I VPR (P69726) protein UBC(229-304) viral minus strand DNA (full-length) RAE1 viral minus strand DNA (ful-length) MNAT1 POLR2B UBC(457-532) POLR2G UBC(305-380) CDK9 VPU (P05919) protein CD4VPU (P05919) protein CTDP1 TCEB3 POLR2C POLR2E POLR2J POLR2F p6 (P04591) protein UBB(77-152) IN (Integrase)(P04585) proteinP-TEFb(CyclinT1:Cdk9) complexXRCC6 SSRP1 GTF2H3 p-SUPT5H HIV-1 mRNA GTF2B NELFB POLR2G GTF2H3 POLR2G POLR2J NELFCD POLR2G NTPSSRP1 NUP54 TCEA1 TBP POLR2B UBC(609-684) RAN GTF2H4 NELFCD POLR2L myristoylated nef TCEB3 Elongating HIV-1 transcript prior to separation viral minus strand DNA (ful-length) UBA52(1-76) POLR2F ERCC2 CHMP4C GTF2F1 Reverse transcriptase/ribonuclease H TAF4 GTF2F1 Ku proteins bound toviral DNAp51 (RT) POLR2C TAF4B TFIIEuncoated viralcomplexTAF7L Immature HIV virionSUPT16H GTF2A1(1-274) POLR2I p51 (RT) RTC with extendingminus strand DNALIG1GTF2A2 HIV-1 mRNA ATP POLR2H TCEB3CL myristoylated Nef Protein (UniProt:P04601) VPU (P05919)PPIA 2-LTR form ofcircular viral DNATAF7L TAF4 ATP VPU (P05919) protein p6 (P04585) protein REV (P04618) protein NUP188 IN (Integrase) (P04585) protein NELFB Elongating HIV-1 transcript in processive Pol II mediated elongation TAF3 TAF9 CD4 HIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end NELFE p-SUPT5H POLR2J HIV-1 mRNA POLR2H TAF1L viral DNA:Kuproteins:XRCC4:DNAligase IV complexCTDP1 p-NELFE XRCC5 NUP35 GTF2H4 POLR2G GTF2H3 VIF (P69723) protein TAF4B REV (P04618) protein REV (P04618) protein POLR2D MNAT1 CCNH POLR2C p-SUPT5H TAF9B p-S2,S5-POLR2A Multimeric matrix layer TCEB3B GTF2E1 CCNH p-SUPT5H VPR CCNH TCEB3 TCEB1 POLR2J TAF10 POLR2G TAF1 POLR2K MA (P04591) protein TCEA1REV (P04618) protein GTF2F2 Tat (P04608) GTF2E2 VIF (P69723) protein POLR2G GTF2A1(275-376) p-SUPT5H ERCC3 POLR2L p6 (P04591) protein GTF2H1 TFIIHGTF2Bp-NELFE GTF2H5 CXCR4 ERCC2 CDK7 PR (Protease) (P04585) protein TAF13 POLR2C tRNA-Lysine3 Envelopeglycoprotein gp160Multimeric capsid coat GTF2F1 POLR2D TCEB2 TAF13 MNAT1 NMT 1CTDP1 tRNA-Lysine3POLR2L POLR2H MA (P04585) protein PR (Protease) (P04585) protein HMGA1 NCBP1 VPU (P05919) protein POLR2I NCBP1 minus sssDNA Virion with gp41exposedGTF2H1 GTF2H1 p51 (RT) POLR2A Early elongationcomplex withseparated abortedtranscriptNC (P04585) protein POLR2I RANGAP1POLR2D PR (Protease) (P04585) protein ERCC3 MNAT1 POLR2H p-SUPT5HTCEB3B POLR2L POLR2D POLR2K CTDP1 POLR2I POLR2E Elongating HIV-1 transcript prior to cleavage p-SUPT5H CTP GTF2H4 p6 (P04585) protein POLR2I NELFB VPS4B GTF2F2 TAF4 POLR2F POLR2H TAF4 VIF (P69723) protein CHMP5 p51 (RT) POLR2K HIV-1 mRNA TCEB3C POLR2A REV (P04618) protein REV (P04618) protein VPS37C NELFE RAN SUPT16H VPU (P05919) protein GTF2F2 TAF1 POLR2I Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD (phospho-NELFphospho DSIF)VPU (P05919) protein NCBP2 TCEB3C GAG-POL Polyprotein(P04585)Transmembrane protein gp41 CCNT1 POLR2B Multimeric matrix layer HIV-1 mRNA TAF12 POLR2C CTP PSIP1UBC(609-684) tRNA-Lysine3 Elongating HIV-1 transcript in processive Pol II mediated elongation p6 (P04585) protein NUP98-4 MA (P04585) protein tRNA-Lysine3 GTF2H1 TFIIHTAF5 Multimeric capsid coat CXCR4 POLR2L MA (P04591) protein TAF4B MNAT1 TFIIAGTF2H5 POLR2J minus sssDNA NELFA Reverse transcriptase/ribonuclease H NELFB ERCC3 Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTDUTP GTF2H2 Rev-bound HIV-1 mRNAMA (P04585) protein POLR2I POLR2E GTF2F2 POLR2C POLR2H MYS-CoASSRP1 RTC with minussssDNA:tRNAprimer:RNA templateUTP Rev-multimer RPS27A(1-76) UBC(77-152) RNAPolymeraseII(unphosphorylated):TFIIF complexNELFCD POLR2G GTF2H2 capped HIV-1 pre-mRNA NELFA capped HIV-1 pre-mRNA TFIIEPOLR2E SUPT4H1 NC (P04591) protein p-S2,S5-POLR2A GAG Polyprotein(P04591)Reverse transcriptase/ribonuclease H NUP188 POLR2A POLR2B POLR2K POLR2L POLR2G GTF2H5 POLR2G POLR2G Rev-multimer minus sssDNA TAF15 TAF9 Surface protein gp120 POLR2C POLR2J PSIP1 Multimeric matrix layer NUP88 ERCC2 tRNA-Lysine3 GTF2F2 Host genomic DNA CHMP3 Reverse transcriptase/ribonuclease H Reverse transcriptase/ribonuclease H POLR2F GTF2F2 HIV-1 transcriptioncomplex containing11 nucleotide longtranscriptPOLR2G NC (P04585) protein UBB(77-152) PPIA GTF2H2 POLR2E Trimeric ENVprecursorPOLR2E POLR2D RTC (ReverseTranscriptionComplex) with RNAtemplateNCBP1 ADPPOLR2E TCEB2 POLR2I TAF6 BANF1 TAF4B GTF2F2 IN (Integrase) (P04585) protein viral RNA template extensively digested except in PPT region p51 (RT) HIV-1 RNA template Tat (P04608) Aborted HIV-1 earlyelongation complexGTF2H3 VPU (P05919) protein HIV-1 template:capped HIV-1 transcript hybrid GTF2F1 70105, 113, 1387070105, 113, 13870701307013, 22, 82, 125, 150...105, 113, 1387044, 68, 114, 137105, 113, 138713, 22, 82, 125, 150...707070141105, 113, 13870105, 113, 13879105, 113, 138917013, 22, 82, 125, 150...105, 113, 1389158, 66, 93, 1437010707070


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. View original pathway at:Reactome.

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Pathway is converted from Reactome ID: 162587
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Reactome version: 66
Reactome Author 
Reactome Author: Bukrinsky, M, D'Eustachio, Peter, Gillespie, Marc E, Gopinathrao, G, Iordanskiy, Sergey, Morrow, Matthew P, Matthews, Lisa, Rice, Andrew P

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Bibliography

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  133. Yi R, Bogerd HP, Cullen BR.; ''Recruitment of the Crm1 nuclear export factor is sufficient to induce cytoplasmic expression of incompletely spliced human immunodeficiency virus mRNAs.''; PubMed Europe PMC Scholia
  134. Wild C, Oas T, McDanal C, Bolognesi D, Matthews T.; ''A synthetic peptide inhibitor of human immunodeficiency virus replication: correlation between solution structure and viral inhibition.''; PubMed Europe PMC Scholia
  135. Conaway RC, Conaway JW.; ''ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.''; PubMed Europe PMC Scholia
  136. Farazi TA, Waksman G, Gordon JI.; ''The biology and enzymology of protein N-myristoylation.''; PubMed Europe PMC Scholia
  137. Charneau P, Alizon M, Clavel F.; ''A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication.''; PubMed Europe PMC Scholia
  138. Ehrlich LS, Liu T, Scarlata S, Chu B, Carter CA.; ''HIV-1 capsid protein forms spherical (immature-like) and tubular (mature-like) particles in vitro: structure switching by pH-induced conformational changes.''; PubMed Europe PMC Scholia
  139. Rabut G, Doye V, Ellenberg J.; ''Mapping the dynamic organization of the nuclear pore complex inside single living cells.''; PubMed Europe PMC Scholia
  140. Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JA, Glavy JS, Hurt E, Beck M.; ''Molecular architecture of the inner ring scaffold of the human nuclear pore complex.''; PubMed Europe PMC Scholia
  141. Pal M, Luse DS.; ''Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA.''; PubMed Europe PMC Scholia
  142. Dubay JW, Roberts SJ, Brody B, Hunter E.; ''Mutations in the leucine zipper of the human immunodeficiency virus type 1 transmembrane glycoprotein affect fusion and infectivity.''; PubMed Europe PMC Scholia
  143. McDougal JS, Nicholson JK, Cross GD, Cort SP, Kennedy MS, Mawle AC.; ''Binding of the human retrovirus HTLV-III/LAV/ARV/HIV to the CD4 (T4) molecule: conformation dependence, epitope mapping, antibody inhibition, and potential for idiotypic mimicry.''; PubMed Europe PMC Scholia
  144. Kilby JM, Eron JJ.; ''Novel therapies based on mechanisms of HIV-1 cell entry.''; PubMed Europe PMC Scholia
  145. Rizzuto CD, Wyatt R, Hernández-Ramos N, Sun Y, Kwong PD, Hendrickson WA, Sodroski J.; ''A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding.''; PubMed Europe PMC Scholia
  146. Fiedler U, Marc Timmers HT.; ''Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.''; PubMed Europe PMC Scholia
  147. Goodrich JA, Tjian R.; ''Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.''; PubMed Europe PMC Scholia
  148. Melikyan GB, Markosyan RM, Hemmati H, Delmedico MK, Lambert DM, Cohen FS.; ''Evidence that the transition of HIV-1 gp41 into a six-helix bundle, not the bundle configuration, induces membrane fusion.''; PubMed Europe PMC Scholia
  149. Zhang W, Canziani G, Plugariu C, Wyatt R, Sodroski J, Sweet R, Kwong P, Hendrickson W, Chaiken I.; ''Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic.''; PubMed Europe PMC Scholia
  150. Brown PO, Bowerman B, Varmus HE, Bishop JM.; ''Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein.''; PubMed Europe PMC Scholia
  151. Miller MD, Farnet CM, Bushman FD.; ''Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition.''; PubMed Europe PMC Scholia
  152. Meng B, Lever AM.; ''Wrapping up the bad news: HIV assembly and release.''; PubMed Europe PMC Scholia
  153. Cramer P, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.''; PubMed Europe PMC Scholia
  154. Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H.; ''NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  155. Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR.; ''Identification of a major co-receptor for primary isolates of HIV-1.''; PubMed Europe PMC Scholia
  156. Chen H, Engelman A.; ''The barrier-to-autointegration protein is a host factor for HIV type 1 integration.''; PubMed Europe PMC Scholia
  157. Julias JG, McWilliams MJ, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.; ''Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage.''; PubMed Europe PMC Scholia
  158. Kati WM, Johnson KA, Jerva LF, Anderson KS.; ''Mechanism and fidelity of HIV reverse transcriptase.''; PubMed Europe PMC Scholia
  159. Sackett K, Shai Y.; ''The HIV-1 gp41 N-terminal heptad repeat plays an essential role in membrane fusion.''; PubMed Europe PMC Scholia
  160. Gonatopoulos-Pournatzis T, Cowling VH.; ''Cap-binding complex (CBC).''; PubMed Europe PMC Scholia
  161. Hill BT, Skowronski J.; ''Human N-myristoyltransferases form stable complexes with lentiviral nef and other viral and cellular substrate proteins.''; PubMed Europe PMC Scholia
  162. Rausch JW, Le Grice SF.; '''Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus.''; PubMed Europe PMC Scholia
  163. Dalgleish AG, Beverley PC, Clapham PR, Crawford DH, Greaves MF, Weiss RA.; ''The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus.''; PubMed Europe PMC Scholia
  164. Martin-Serrano J, Zang T, Bieniasz PD.; ''Role of ESCRT-I in retroviral budding.''; PubMed Europe PMC Scholia
  165. Iordanskiy S, Berro R, Altieri M, Kashanchi F, Bukrinsky M.; ''Intracytoplasmic maturation of the human immunodeficiency virus type 1 reverse transcription complexes determines their capacity to integrate into chromatin.''; PubMed Europe PMC Scholia
  166. Zhang H, Dornadula G, Orenstein J, Pomerantz RJ.; ''Morphologic changes in human immunodeficiency virus type 1 virions secondary to intravirion reverse transcription: evidence indicating that reverse transcription may not take place within the intact viral core.''; PubMed Europe PMC Scholia
  167. Bushman FD, Fujiwara T, Craigie R.; ''Retroviral DNA integration directed by HIV integration protein in vitro.''; PubMed Europe PMC Scholia
  168. Pullen KA, Ishimoto LK, Champoux JJ.; ''Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase.''; PubMed Europe PMC Scholia
  169. Holstege FC, Fiedler U, Timmers HT.; ''Three transitions in the RNA polymerase II transcription complex during initiation.''; PubMed Europe PMC Scholia
  170. Carr CM, Kim PS.; ''A spring-loaded mechanism for the conformational change of influenza hemagglutinin.''; PubMed Europe PMC Scholia
  171. Jacob GA, Luse SW, Luse DS.; ''Abortive initiation is increased only for the weakest members of a set of down mutants of the adenovirus 2 major late promoter.''; PubMed Europe PMC Scholia
  172. Mak J, Jiang M, Wainberg MA, Hammarskjöld ML, Rekosh D, Kleiman L.; ''Role of Pr160gag-pol in mediating the selective incorporation of tRNA(Lys) into human immunodeficiency virus type 1 particles.''; PubMed Europe PMC Scholia

History

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

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1-LTR form of circular viral DNAComplexR-HIV-175558 (Reactome)
2-LTR form of circular viral DNAComplexR-HIV-175242 (Reactome)
AAAS ProteinQ9NRG9 (Uniprot-TrEMBL)
ADPMetaboliteCHEBI:16761 (ChEBI)
ATP MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted HIV-1 early elongation complexComplexR-HSA-167467 (Reactome)
Assembling HIV virionComplexR-HSA-3149451 (Reactome)
Autointegrated viral

DNA as smaller

circles
ComplexR-HIV-175037 (Reactome)
Autointegrated viral

DNA as an inverted

circle
ComplexR-HIV-175415 (Reactome)
BANF1 ProteinO75531 (Uniprot-TrEMBL)
BANF1ProteinO75531 (Uniprot-TrEMBL)
CCNH ProteinP51946 (Uniprot-TrEMBL)
CCNK ProteinO75909 (Uniprot-TrEMBL)
CCNT1 ProteinO60563 (Uniprot-TrEMBL)
CCNT2 ProteinO60583 (Uniprot-TrEMBL)
CCR5 ProteinP51681 (Uniprot-TrEMBL)
CCR5, CXCR4ComplexR-HSA-175536 (Reactome)
CD4 ProteinP01730 (Uniprot-TrEMBL)
CD4:Env gp120/gp41

hairpin

complex:CCR5/CXCR4
ComplexR-HSA-171297 (Reactome)
CD4ProteinP01730 (Uniprot-TrEMBL)
CDK7 ProteinP50613 (Uniprot-TrEMBL)
CDK9 ProteinP50750 (Uniprot-TrEMBL)
CE:Pol II CTD:Spt5 complexComplexR-HSA-167139 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CHMP2A ProteinO43633 (Uniprot-TrEMBL)
CHMP2B ProteinQ9UQN3 (Uniprot-TrEMBL)
CHMP3 ProteinQ9Y3E7 (Uniprot-TrEMBL)
CHMP4A ProteinQ9BY43 (Uniprot-TrEMBL)
CHMP4B ProteinQ9H444 (Uniprot-TrEMBL)
CHMP4C ProteinQ96CF2 (Uniprot-TrEMBL)
CHMP5 ProteinQ9NZZ3 (Uniprot-TrEMBL)
CHMP6 ProteinQ96FZ7 (Uniprot-TrEMBL)
CHMP7 ProteinQ8WUX9 (Uniprot-TrEMBL)
CTDP1 ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP MetaboliteCHEBI:17677 (ChEBI)
CXCR4 ProteinP61073 (Uniprot-TrEMBL)
Cap Binding Complex (CBC)ComplexR-HSA-77088 (Reactome)
CoA-SHMetaboliteCHEBI:15346 (ChEBI)
DSIF complexComplexR-HSA-112420 (Reactome)
DSIF:NELF:early

elongation complex after limited

nucleotide addition
ComplexR-HSA-170726 (Reactome)
DSIF:NELF:early elongation complexComplexR-HSA-167078 (Reactome)
ELL ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 ProteinP18074 (Uniprot-TrEMBL)
ERCC3 ProteinP19447 (Uniprot-TrEMBL)
ESCRT-IIIComplexR-HSA-917723 (Reactome)
ESCRT-IComplexR-HSA-184398 (Reactome)
Early elongation

complex with separated aborted

transcript
ComplexR-HSA-170736 (Reactome)
Elongating HIV-1 transcript in processive Pol II mediated elongation R-HIV-167069 (Reactome)
Elongating HIV-1 transcript prior to cleavage R-ALL-167142 (Reactome)
Elongating HIV-1 transcript prior to separation R-ALL-167145 (Reactome)
Elongin ComplexComplexR-HSA-112425 (Reactome)
Encapsidated viral coreComplexR-HSA-188943 (Reactome)
Envelope glycoprotein gp160ProteinP04578 (Uniprot-TrEMBL)
Envelope glycoprotein gp160 ProteinP04578 (Uniprot-TrEMBL)
FACT complexComplexR-HSA-112417 (Reactome)
FEN1ProteinP39748 (Uniprot-TrEMBL)
FURINProteinP09958 (Uniprot-TrEMBL)
GAG Polyprotein (P04591)ProteinP04591 (Uniprot-TrEMBL)
GAG-POL Polyprotein (P04585)ProteinP04585 (Uniprot-TrEMBL)
GAG-POL Polyprotein (P04585) ProteinP04585 (Uniprot-TrEMBL)
GDP MetaboliteCHEBI:17552 (ChEBI)
GDPMetaboliteCHEBI:17552 (ChEBI)
GTF2A1(1-274) ProteinP52655 (Uniprot-TrEMBL)
GTF2A1(275-376) ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 ProteinP52657 (Uniprot-TrEMBL)
GTF2B ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 ProteinP29084 (Uniprot-TrEMBL)
GTF2F1 ProteinP35269 (Uniprot-TrEMBL)
GTF2F2 ProteinP13984 (Uniprot-TrEMBL)
GTF2H1 ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 ProteinQ92759 (Uniprot-TrEMBL)
GTF2H5 ProteinQ6ZYL4 (Uniprot-TrEMBL)
GTP MetaboliteCHEBI:15996 (ChEBI)
GTPMetaboliteCHEBI:15996 (ChEBI)
Glycosylated Envelope glycoprotein gp160 ProteinP04578 (Uniprot-TrEMBL)
HIV-1

Polymerase II

(phosphorylated):TFIIF:capped pre-mRNA
ComplexR-HSA-167088 (Reactome)
HIV-1 Promoter Escape ComplexComplexR-HSA-167472 (Reactome)
HIV-1 RNA ProteinAF033819 (EMBL)
HIV-1 RNA homodimerComplexR-HIV-174985 (Reactome)
HIV-1 RNA template ProteinAF033819 (EMBL)
HIV-1 Tat-containing

aborted elongation complex after

arrest
ComplexR-HSA-167460 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
ComplexR-HSA-167091 (Reactome)
HIV-1 Tat-containing

paused processive

elongation complex
ComplexR-HSA-167071 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ComplexR-HSA-167184 (Reactome)
HIV-1 aborted

elongation complex

after arrest
ComplexR-HSA-167482 (Reactome)
HIV-1 arrested

processive

elongation complex
ComplexR-HSA-167286 (Reactome)
HIV-1 capped

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

complex
ComplexR-HSA-167080 (Reactome)
HIV-1 closed

pre-initiation

complex
ComplexR-HSA-167125 (Reactome)
HIV-1 early

elongation complex with hyperphosphorylated

Pol II CTD
ComplexR-HSA-167075 (Reactome)
HIV-1 elongation

complex containing

Tat
ComplexR-HSA-167185 (Reactome)
HIV-1 elongation complexComplexR-HSA-167082 (Reactome)
HIV-1 initiation

complex with phosphodiester-PPi

intermediate
ComplexR-HSA-167106 (Reactome)
HIV-1 initiation complexComplexR-HSA-167129 (Reactome)
HIV-1 mRNA ProteinAF033819 (EMBL)
HIV-1 mRNARnaAF033819 (EMBL)
HIV-1 open

pre-initiation

complex
ComplexR-HSA-167137 (Reactome)
HIV-1 paused

processive

elongation complex
ComplexR-HSA-167283 (Reactome)
HIV-1 processive elongation complexComplexR-HSA-167081 (Reactome)
HIV-1 template

DNA:4-9 nucleotide

transcript hybrid
R-HIV-167470 (Reactome)
HIV-1 template DNA

containing promoter with transcript of

2 or 3 nucleotides
R-HIV-167475 (Reactome)
HIV-1 template DNA

with first transcript dinucleotide, opened to +8

position
R-HIV-167096 (Reactome)
HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotides R-HIV-167475 (Reactome)
HIV-1 template DNA hybrid with phosphodiester-PPi intermediate R-HIV-167109 (Reactome)
HIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end R-HIV-167138 (Reactome)
HIV-1 template DNA with first transcript dinucleotide, opened to +8 position R-HIV-167096 (Reactome)
HIV-1 template DNA:11 nucleotide transcript hybrid R-HIV-167112 (Reactome)
HIV-1 template DNA:3 nucleotide transcript hybrid R-HIV-167114 (Reactome)
HIV-1 template DNA:30 nt transcript hybrid R-HIV-167131 (Reactome)
HIV-1 template DNA:4 nucleotide transcript hybrid R-HIV-167122 (Reactome)
HIV-1 template DNA:4-9 nucleotide transcript hybrid R-HIV-167470 (Reactome)
HIV-1 template DNA:9 nucleotide transcript hybrid R-HIV-167105 (Reactome)
HIV-1 template:capped HIV-1 transcript hybrid R-HIV-167074 (Reactome)
HIV-1 transcription

complex containing 11 nucleotide long

transcript
ComplexR-HSA-167132 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
ComplexR-HSA-167119 (Reactome)
HIV-1 transcription

complex containing 4 nucleotide long

transcript
ComplexR-HSA-167124 (Reactome)
HIV-1 transcription

complex containing 4-9 nucleotide long

transcript
ComplexR-HSA-167471 (Reactome)
HIV-1 transcription

complex containing 9 nucleotide long

transcript
ComplexR-HSA-167100 (Reactome)
HIV-1 transcription

complex containing extruded transcript

to +30
ComplexR-HSA-167102 (Reactome)
HIV-1 transcription

complex containing

transcript to +30
ComplexR-HSA-167120 (Reactome)
HIV-1 transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
ComplexR-HSA-167127 (Reactome)
HIV-1 transcription complexComplexR-HSA-167101 (Reactome)
HIV-1 unspliced RNARnaAF033819 (EMBL)
HMGA1 ProteinP17096 (Uniprot-TrEMBL)
HMGA1ProteinP17096 (Uniprot-TrEMBL)
Host genomic DNA R-HSA-175158 (Reactome)
Host genomic DNAR-HSA-175158 (Reactome)
IN (Integrase) (P04585) proteinProteinP04585 (Uniprot-TrEMBL)
IN (Integrase) (P04585) protein ProteinP04585 (Uniprot-TrEMBL)
IN bound to sticky

3' ends of viral

DNA in PIC
ComplexR-HSA-175416 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
ComplexR-HSA-177526 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
ComplexR-HSA-175224 (Reactome)
Immature HIV virionComplexR-HSA-3139025 (Reactome)
Integrated provirusComplexR-HSA-175486 (Reactome)
Integration intermediateComplexR-HSA-175148 (Reactome)
KPNA1 ProteinP52294 (Uniprot-TrEMBL)
Ku proteins bound to viral DNAComplexR-HSA-175247 (Reactome)
LIG1ProteinP18858 (Uniprot-TrEMBL)
LIG4 ProteinP49917 (Uniprot-TrEMBL)
MA (P04585) protein ProteinP04585 (Uniprot-TrEMBL)
MA (P04591) protein ProteinP04591 (Uniprot-TrEMBL)
MNAT1 ProteinP51948 (Uniprot-TrEMBL)
MVB12 R-HSA-8959998 (Reactome)
MYS-CoAMetaboliteCHEBI:15532 (ChEBI)
MatrixComplexR-HIV-173120 (Reactome)
Mature HIV virionComplexR-HSA-175514 (Reactome)
Multimeric capsid coatR-HIV-175314 (Reactome)
Multimeric capsid coat R-HIV-173644 (Reactome)
Multimeric capsid coat R-HIV-175314 (Reactome)
Multimeric matrix layer R-HIV-173641 (Reactome)
Multimeric matrix layer R-HIV-175338 (Reactome)
N-myristoyl GAG (P04591) proteinProteinP04591 (Uniprot-TrEMBL)
N-myristoyl GAG (P04591) protein ProteinP04591 (Uniprot-TrEMBL)
N-myristoyl GAG ProteinP04591 (Uniprot-TrEMBL)
NC (P04585) protein ProteinP04585 (Uniprot-TrEMBL)
NC (P04591) protein ProteinP04591 (Uniprot-TrEMBL)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NDC1 ProteinQ9BTX1 (Uniprot-TrEMBL)
NEDD4L ProteinQ96PU5 (Uniprot-TrEMBL)
NEDD4LProteinQ96PU5 (Uniprot-TrEMBL)
NELF complexComplexR-HSA-112432 (Reactome)
NELFA ProteinQ9H3P2 (Uniprot-TrEMBL)
NELFB ProteinQ8WX92 (Uniprot-TrEMBL)
NELFCD ProteinQ8IXH7 (Uniprot-TrEMBL)
NELFE ProteinP18615 (Uniprot-TrEMBL)
NMT 1ProteinP30419 (Uniprot-TrEMBL)
NMT2ProteinO60551 (Uniprot-TrEMBL)
NTPComplexR-ALL-30595 (Reactome)
NUP107 ProteinP57740 (Uniprot-TrEMBL)
NUP133 ProteinQ8WUM0 (Uniprot-TrEMBL)
NUP153 ProteinP49790 (Uniprot-TrEMBL)
NUP155 ProteinO75694 (Uniprot-TrEMBL)
NUP160 ProteinQ12769 (Uniprot-TrEMBL)
NUP188 ProteinQ5SRE5 (Uniprot-TrEMBL)
NUP205 ProteinQ92621 (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)
NUP98-3 ProteinP52948-3 (Uniprot-TrEMBL)
NUP98-4 ProteinP52948-4 (Uniprot-TrEMBL)
NUP98-5 ProteinP52948-5 (Uniprot-TrEMBL)
NUPL1-2 ProteinQ9BVL2-1 (Uniprot-TrEMBL)
NUPL2 ProteinO15504 (Uniprot-TrEMBL)
Nuclear Pore Complex (NPC)ComplexR-HSA-157689 (Reactome)
NucleocapsidComplexR-HIV-175167 (Reactome)
Nup45 ProteinQ9BVL2-2 (Uniprot-TrEMBL)
P-TEFb complexComplexR-HSA-112431 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complexComplexR-HSA-167183 (Reactome)
P-TEFb(Cyclin

T1:Cdk9)-containing elongation complex with separated and uncleaved

transcript
ComplexR-HSA-167199 (Reactome)
PDCD6IP ProteinQ8WUM4 (Uniprot-TrEMBL)
PDCD6IPProteinQ8WUM4 (Uniprot-TrEMBL)
PIC (PreIntegration Complex)ComplexR-HSA-175143 (Reactome)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2D ProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2F ProteinP61218 (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)
POM121C ProteinA8CG34 (Uniprot-TrEMBL)
PPIA ProteinP62937 (Uniprot-TrEMBL)
PPIAProteinP62937 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
PR (Protease) (P04585) proteinProteinP04585 (Uniprot-TrEMBL)
PR (Protease) (P04585) protein ProteinP04585 (Uniprot-TrEMBL)
PSIP1 ProteinO75475 (Uniprot-TrEMBL)
PSIP1ProteinO75475 (Uniprot-TrEMBL)
PiMetaboliteCHEBI:18367 (ChEBI)
Pol II transcription

complex containing extruded transcript

to +30
ComplexR-HSA-157171 (Reactome)
RAE1 ProteinP78406 (Uniprot-TrEMBL)
RAN ProteinP62826 (Uniprot-TrEMBL)
RAN:GTPComplexR-HSA-180686 (Reactome)
RAN:GTPComplexR-HSA-180738 (Reactome)
RANBP1 ProteinP43487 (Uniprot-TrEMBL)
RANBP1ProteinP43487 (Uniprot-TrEMBL)
RANBP2 ProteinP49792 (Uniprot-TrEMBL)
RANGAP1ProteinP46060 (Uniprot-TrEMBL)
RCC1ProteinP18754 (Uniprot-TrEMBL)
REV (P04618) protein ProteinP04618 (Uniprot-TrEMBL)
REV (P04618) proteinProteinP04618 (Uniprot-TrEMBL)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein
ComplexR-HSA-167070 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex
ComplexR-HSA-167086 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ComplexR-HSA-71307 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
ComplexR-HSA-167123 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
ComplexR-HSA-167107 (Reactome)
RNGTT ProteinO60942 (Uniprot-TrEMBL)
RNGTTProteinO60942 (Uniprot-TrEMBL)
RNMT ProteinO43148 (Uniprot-TrEMBL)
RNMTProteinO43148 (Uniprot-TrEMBL)
RPS27A(1-76) ProteinP62979 (Uniprot-TrEMBL)
RTC

with integration competent viral

DNA:BANF1:HMGA1:PSIP1
ComplexR-HSA-9608475 (Reactome)
RTC (Reverse

Transcription Complex) with RNA

template
ComplexR-HSA-173814 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
ComplexR-HSA-173792 (Reactome)
RTC with degraded

RNA template and

minus sssDNA
ComplexR-HSA-173773 (Reactome)
RTC with duplex DNA

containing discontinuous plus

strand flap
ComplexR-HSA-188560 (Reactome)
RTC with extending minus strand DNAComplexR-HSA-173764 (Reactome)
RTC with extending second-strand DNAComplexR-HSA-182880 (Reactome)
RTC with extensive RNase-H digestionComplexR-HSA-173789 (Reactome)
RTC with integration competent viral DNAComplexR-HSA-175254 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
ComplexR-HSA-173779 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
ComplexR-HSA-173774 (Reactome)
RTC with minus

strand DNA synthesis initiated

from 3'-end
ComplexR-HSA-173786 (Reactome)
RTC with nicked

minus sssDNA:tRNA

primer:RNA template
ComplexR-HSA-182804 (Reactome)
RTC with tRNA primer:RNA templateComplexR-HSA-173801 (Reactome)
RTC without viral RNA templateComplexR-HSA-173824 (Reactome)
RTComplexR-HIV-173772 (Reactome)
Ran GTPase:GDPComplexR-HSA-165549 (Reactome)
Ran-GDPComplexR-HSA-180701 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexComplexR-HSA-180718 (Reactome)
Rev

multimer-bound HIV-1

mRNA:Crm1:Ran:GTP:NPC
ComplexR-HSA-165531 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ComplexR-HSA-165537 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ComplexR-HSA-165552 (Reactome)
Rev multimer-bound

HIV-1 mRNA:CRM1

complex
ComplexR-HSA-180873 (Reactome)
Rev multimer-bound HIV-1 mRNAComplexR-HIV-165532 (Reactome)
Rev-bound HIV-1 mRNAComplexR-HIV-165535 (Reactome)
Rev-multimer R-HIV-165542 (Reactome)
Rev-multimer R-HIV-165543 (Reactome)
Rev-multimerR-HIV-165542 (Reactome)
Rev-multimerR-HIV-165543 (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 (P04578) ProteinP04578 (Uniprot-TrEMBL)
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)
TAF15 ProteinQ92804 (Uniprot-TrEMBL)
TAF1L ProteinQ8IZX4 (Uniprot-TrEMBL)
TAF2 ProteinQ6P1X5 (Uniprot-TrEMBL)
TAF3 ProteinQ5VWG9 (Uniprot-TrEMBL)
TAF4 ProteinO00268 (Uniprot-TrEMBL)
TAF4B ProteinQ92750 (Uniprot-TrEMBL)
TAF5 ProteinQ15542 (Uniprot-TrEMBL)
TAF6 ProteinP49848 (Uniprot-TrEMBL)
TAF7 ProteinQ15545 (Uniprot-TrEMBL)
TAF7L ProteinQ5H9L4 (Uniprot-TrEMBL)
TAF9 ProteinQ16594 (Uniprot-TrEMBL)
TAF9B ProteinQ9HBM6 (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)
TCEB3B ProteinQ8IYF1 (Uniprot-TrEMBL)
TCEB3C ProteinQ8NG57 (Uniprot-TrEMBL)
TCEB3CL ProteinQ3SY89 (Uniprot-TrEMBL)
TCEB3CL2 ProteinA6NLF2 (Uniprot-TrEMBL)
TFIIAComplexR-HSA-109629 (Reactome)
TFIIDComplexR-HSA-109626 (Reactome)
TFIIEComplexR-HSA-109633 (Reactome)
TFIIHComplexR-HSA-109634 (Reactome)
TPR ProteinP12270 (Uniprot-TrEMBL)
TSG101 ProteinQ99816 (Uniprot-TrEMBL)
Tat (P04608) ProteinP04608 (Uniprot-TrEMBL)
Tat (P04608)ProteinP04608 (Uniprot-TrEMBL)
Tat-containing

elongation complex

prior to separation
ComplexR-HSA-167193 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF

phospho DSIF)
ComplexR-HSA-170710 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
ComplexR-HSA-170707 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
ComplexR-HSA-167182 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexComplexR-HSA-167237 (Reactome)
Transmembrane protein gp41 (P04578) ProteinP04578 (Uniprot-TrEMBL)
Transmembrane protein gp41 ProteinP04578 (Uniprot-TrEMBL)
Trimeric ENV precursorComplexR-HIV-189843 (Reactome)
Trimeric ENV precursorComplexR-HIV-3149446 (Reactome)
Trimeric gp120:gp41 oligomerComplexR-HIV-189281 (Reactome)
Trimeric gp120:gp41 oligomerComplexR-HIV-189840 (Reactome)
UBA52(1-76) ProteinP62987 (Uniprot-TrEMBL)
UBAP1 ProteinQ9NZ09 (Uniprot-TrEMBL)
UBB(1-76) ProteinP0CG47 (Uniprot-TrEMBL)
UBB(153-228) ProteinP0CG47 (Uniprot-TrEMBL)
UBB(77-152) ProteinP0CG47 (Uniprot-TrEMBL)
UBC(1-76) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(153-228) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(229-304) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(305-380) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(381-456) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(457-532) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(533-608) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(609-684) ProteinP0CG48 (Uniprot-TrEMBL)
UBC(77-152) ProteinP0CG48 (Uniprot-TrEMBL)
UTP MetaboliteCHEBI:15713 (ChEBI)
UbComplexR-HSA-113595 (Reactome)
VIF (P69723) protein ProteinP69723 (Uniprot-TrEMBL)
VIF (P69723) proteinProteinP69723 (Uniprot-TrEMBL)
VPR (P69726) protein ProteinP69726 (Uniprot-TrEMBL)
VPR ProteinP69726 (Uniprot-TrEMBL)
VPRProteinP69726 (Uniprot-TrEMBL)
VPS28 ProteinQ9UK41 (Uniprot-TrEMBL)
VPS37A ProteinQ8NEZ2 (Uniprot-TrEMBL)
VPS37B ProteinQ9H9H4 (Uniprot-TrEMBL)
VPS37C ProteinA5D8V6 (Uniprot-TrEMBL)
VPS37D ProteinQ86XT2 (Uniprot-TrEMBL)
VPS4A ProteinQ9UN37 (Uniprot-TrEMBL)
VPS4B ProteinO75351 (Uniprot-TrEMBL)
VPU (P05919) protein ProteinP05919 (Uniprot-TrEMBL)
VPU (P05919)ProteinP05919 (Uniprot-TrEMBL)
VTA1 ProteinQ9NP79 (Uniprot-TrEMBL)
Viral core

surrounded by

Matrix layer
ComplexR-HSA-173664 (Reactome)
Virion Budding ComplexComplexR-HSA-3211408 (Reactome)
Virion with

CD4:gp120 bound to

CCR5/CXCR4
ComplexR-HSA-173663 (Reactome)
Virion with

fusogenically

activated gp41
ComplexR-HSA-173639 (Reactome)
Virion with CD4 bound to gp120ComplexR-HSA-173650 (Reactome)
Virion with exposed

coreceptor binding

sites
ComplexR-HSA-173648 (Reactome)
Virion with gp41 exposedComplexR-HSA-173665 (Reactome)
Virion with gp41

forming hairpin

structure
ComplexR-HSA-173649 (Reactome)
Virion with gp41

fusion peptide in

insertion complex
ComplexR-HSA-173656 (Reactome)
Vpr:importin-alpha complexComplexR-HSA-180623 (Reactome)
Vps/Vta1ComplexR-HSA-917724 (Reactome)
XPO1 ProteinO14980 (Uniprot-TrEMBL)
XPO1ProteinO14980 (Uniprot-TrEMBL)
XRCC4 ProteinQ13426 (Uniprot-TrEMBL)
XRCC4:LIG4ComplexR-HSA-75912 (Reactome)
XRCC5 ProteinP13010 (Uniprot-TrEMBL)
XRCC5:XRCC6ComplexR-HSA-75905 (Reactome)
XRCC6 ProteinP12956 (Uniprot-TrEMBL)
capped HIV-1 pre-mRNA R-HIV-167079 (Reactome)
dNTPMetaboliteCHEBI:16516 (ChEBI)
genomic DNA with staggered 5' ends R-HSA-175520 (Reactome)
minus sssDNA R-HIV-173823 (Reactome)
minus strand DNA (extending) R-HIV-173767 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ComplexR-HSA-184369 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ComplexR-HSA-184475 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ComplexR-HSA-3149449 (Reactome)
myristoylated Nef Protein (UniProt:P04601) ProteinP04601 (Uniprot-TrEMBL)
myristoylated nef ProteinP04601 (Uniprot-TrEMBL)
myristoylated nefProteinP04601 (Uniprot-TrEMBL)
nefProteinP04601 (Uniprot-TrEMBL)
other viral genomic RNARnaAF033819 (EMBL)
p-NELFE ProteinP18615 (Uniprot-TrEMBL)
p-S2,S5-POLR2A ProteinP24928 (Uniprot-TrEMBL) The C-terminal domain (CTD) of POLR2A contains about 52 repeats of the consensus heptad YSPTSPS. Serines-2 and 5 of the heptads are phosphorylated in RNA polymerase II initiating transcription of protein coding genes. The exact repeats that are phosphorylated are not known.
p-S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-SUPT5H ProteinO00267 (Uniprot-TrEMBL)
p-SUPT5HProteinO00267 (Uniprot-TrEMBL)
p51 (RT) ProteinP04585 (Uniprot-TrEMBL)
p6 (P04585) ProteinP04585 (Uniprot-TrEMBL)
p6 (P04585) protein ProteinP04585 (Uniprot-TrEMBL)
p6 (P04591) ProteinP04591 (Uniprot-TrEMBL)
p6 (P04591) protein ProteinP04591 (Uniprot-TrEMBL)
tRNA-Lysine3 R-HSA-173782 (Reactome)
tRNA-Lysine3 R-HSA-177833 (Reactome)
tRNA-Lysine3R-HSA-173782 (Reactome)
template DNA:30 nt transcript hybrid R-ALL-111260 (Reactome)
uncoated viral complexComplexR-HSA-173653 (Reactome)
viral DNA bound with Integrase in PICComplexR-HSA-177532 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
ComplexR-HSA-175440 (Reactome)
viral PIC proteinsComplexR-HSA-177527 (Reactome)
viral RNA template being digested by RNase-H (extensive) ProteinAF033819 (EMBL)
viral RNA template degraded by RNase-H (initial) ProteinAF033819 (EMBL)
viral RNA template extensively digested except in PPT region ProteinAF033819 (EMBL)
viral minus strand DNA (ful-length) R-HIV-175411 (Reactome)
viral minus strand DNA (full-length) R-HIV-173821 (Reactome)
viral minus strand DNA (initial) R-HIV-173832 (Reactome)
viral minus strand DNA after ligation R-HIV-175013 (Reactome)
viral minus strand DNA with sticky 3' end R-HIV-175079 (Reactome)
viral minus strand DNA with sticky 3' end R-HIV-177533 (Reactome)
viral plus strand DNA (full-length) R-HIV-173762 (Reactome)
viral plus strand DNA (full-length) R-HIV-175036 (Reactome)
viral plus strand DNA after ligation R-HIV-174981 (Reactome)
viral plus strand DNA with sticky 3' end R-HIV-175429 (Reactome)
viral plus strand DNA with sticky 3' end R-HIV-177540 (Reactome)
viral second strand DNA (plus sss) R-HIV-173826 (Reactome)
viral second strand DNA with plus sssDNA (discontinuous) R-HIV-188559 (Reactome)
viral second strand DNA with plus sssDNA (extending) R-HIV-173833 (Reactome)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
1-LTR form of circular viral DNAArrowR-HSA-175117 (Reactome)
2-LTR form of circular viral DNAArrowR-HSA-175258 (Reactome)
ADPArrowR-HSA-167084 (Reactome)
ADPArrowR-HSA-167097 (Reactome)
ADPArrowR-HSA-167098 (Reactome)
ADPArrowR-HSA-170704 (Reactome)
ADPArrowR-HSA-170706 (Reactome)
ATPR-HSA-167084 (Reactome)
ATPR-HSA-167097 (Reactome)
ATPR-HSA-167098 (Reactome)
ATPR-HSA-170704 (Reactome)
ATPR-HSA-170706 (Reactome)
Aborted HIV-1 early elongation complexArrowR-HSA-167478 (Reactome)
Assembling HIV virionArrowR-HSA-3149454 (Reactome)
Assembling HIV virionR-HSA-3159227 (Reactome)
Autointegrated viral

DNA as smaller

circles
ArrowR-HSA-175250 (Reactome)
Autointegrated viral

DNA as an inverted

circle
ArrowR-HSA-164845 (Reactome)
BANF1R-HSA-8951690 (Reactome)
CCR5, CXCR4R-HSA-164507 (Reactome)
CD4:Env gp120/gp41

hairpin

complex:CCR5/CXCR4
ArrowR-HSA-164524 (Reactome)
CD4R-HSA-164509 (Reactome)
CE:Pol II CTD:Spt5 complexArrowR-HSA-167153 (Reactome)
CTDP1R-HSA-167072 (Reactome)
CTDP1mim-catalysisR-HSA-167072 (Reactome)
Cap Binding Complex (CBC)ArrowR-HSA-167084 (Reactome)
Cap Binding Complex (CBC)ArrowR-HSA-167191 (Reactome)
Cap Binding Complex (CBC)R-HSA-167089 (Reactome)
CoA-SHArrowR-HSA-162914 (Reactome)
CoA-SHArrowR-HSA-184392 (Reactome)
DSIF complexR-HSA-167083 (Reactome)
DSIF:NELF:early

elongation complex after limited

nucleotide addition
ArrowR-HSA-167087 (Reactome)
DSIF:NELF:early

elongation complex after limited

nucleotide addition
R-HSA-167147 (Reactome)
DSIF:NELF:early elongation complexArrowR-HSA-167085 (Reactome)
DSIF:NELF:early elongation complexR-HSA-167084 (Reactome)
DSIF:NELF:early elongation complexR-HSA-167087 (Reactome)
DSIF:NELF:early elongation complexR-HSA-167191 (Reactome)
DSIF:NELF:early elongation complexR-HSA-167478 (Reactome)
ELLR-HSA-167077 (Reactome)
ELLR-HSA-167196 (Reactome)
ESCRT-IIIR-HSA-3159232 (Reactome)
ESCRT-IR-HSA-3159232 (Reactome)
ESCRT-Imim-catalysisR-HSA-184269 (Reactome)
ESCRT-Imim-catalysisR-HSA-3149434 (Reactome)
Early elongation

complex with separated aborted

transcript
ArrowR-HSA-167147 (Reactome)
Elongin ComplexR-HSA-167077 (Reactome)
Elongin ComplexR-HSA-167196 (Reactome)
Encapsidated viral coreArrowR-HSA-173642 (Reactome)
Encapsidated viral coreR-HSA-173111 (Reactome)
Envelope glycoprotein gp160ArrowR-HSA-174493 (Reactome)
Envelope glycoprotein gp160ArrowR-HSA-174494 (Reactome)
Envelope glycoprotein gp160R-HSA-171291 (Reactome)
Envelope glycoprotein gp160R-HSA-174493 (Reactome)
FACT complexR-HSA-167077 (Reactome)
FACT complexR-HSA-167196 (Reactome)
FEN1ArrowR-HSA-182876 (Reactome)
FURINmim-catalysisR-HSA-171288 (Reactome)
GAG Polyprotein (P04591)ArrowR-HSA-187213 (Reactome)
GAG Polyprotein (P04591)R-HSA-184392 (Reactome)
GAG-POL Polyprotein (P04585)R-HSA-3149454 (Reactome)
GAG-POL Polyprotein (P04585)mim-catalysisR-HSA-3139027 (Reactome)
GDPArrowR-HSA-180687 (Reactome)
GTF2BArrowR-HSA-167113 (Reactome)
GTF2BArrowR-HSA-167474 (Reactome)
GTF2BArrowR-HSA-167477 (Reactome)
GTPR-HSA-180687 (Reactome)
HIV-1

Polymerase II

(phosphorylated):TFIIF:capped pre-mRNA
R-HSA-167089 (Reactome)
HIV-1 Promoter Escape ComplexR-HSA-167474 (Reactome)
HIV-1 RNA homodimerR-HSA-3149454 (Reactome)
HIV-1 Tat-containing

aborted elongation complex after

arrest
ArrowR-HSA-167459 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
ArrowR-HSA-167090 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
R-HSA-167148 (Reactome)
HIV-1 Tat-containing

arrested processive

elongation complex
R-HSA-167459 (Reactome)
HIV-1 Tat-containing

paused processive

elongation complex
ArrowR-HSA-167076 (Reactome)
HIV-1 Tat-containing

paused processive

elongation complex
R-HSA-167150 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ArrowR-HSA-167148 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ArrowR-HSA-167150 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
ArrowR-HSA-167181 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
R-HSA-167076 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
R-HSA-167090 (Reactome)
HIV-1 Tat-containing

processive

elongation complex
R-HSA-167192 (Reactome)
HIV-1 aborted

elongation complex

after arrest
ArrowR-HSA-167481 (Reactome)
HIV-1 arrested

processive

elongation complex
ArrowR-HSA-167284 (Reactome)
HIV-1 arrested

processive

elongation complex
R-HSA-167288 (Reactome)
HIV-1 arrested

processive

elongation complex
R-HSA-167481 (Reactome)
HIV-1 capped

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

complex
ArrowR-HSA-167089 (Reactome)
HIV-1 capped

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

complex
R-HSA-167072 (Reactome)
HIV-1 closed

pre-initiation

complex
ArrowR-HSA-167484 (Reactome)
HIV-1 closed

pre-initiation

complex
R-HSA-167097 (Reactome)
HIV-1 early

elongation complex with hyperphosphorylated

Pol II CTD
ArrowR-HSA-167084 (Reactome)
HIV-1 early

elongation complex with hyperphosphorylated

Pol II CTD
R-HSA-167077 (Reactome)
HIV-1 elongation

complex containing

Tat
ArrowR-HSA-167196 (Reactome)
HIV-1 elongation

complex containing

Tat
R-HSA-167181 (Reactome)
HIV-1 elongation complexArrowR-HSA-167077 (Reactome)
HIV-1 initiation

complex with phosphodiester-PPi

intermediate
ArrowR-HSA-167130 (Reactome)
HIV-1 initiation

complex with phosphodiester-PPi

intermediate
R-HSA-167134 (Reactome)
HIV-1 initiation complexArrowR-HSA-167118 (Reactome)
HIV-1 initiation complexR-HSA-167130 (Reactome)
HIV-1 mRNAR-HSA-165027 (Reactome)
HIV-1 mRNAR-HSA-187211 (Reactome)
HIV-1 open

pre-initiation

complex
ArrowR-HSA-167097 (Reactome)
HIV-1 open

pre-initiation

complex
R-HSA-167118 (Reactome)
HIV-1 open

pre-initiation

complex
R-HSA-167484 (Reactome)
HIV-1 paused

processive

elongation complex
ArrowR-HSA-167282 (Reactome)
HIV-1 paused

processive

elongation complex
R-HSA-167292 (Reactome)
HIV-1 processive elongation complexArrowR-HSA-167288 (Reactome)
HIV-1 processive elongation complexArrowR-HSA-167292 (Reactome)
HIV-1 processive elongation complexR-HSA-167282 (Reactome)
HIV-1 processive elongation complexR-HSA-167284 (Reactome)
HIV-1 template

DNA:4-9 nucleotide

transcript hybrid
ArrowR-HSA-167468 (Reactome)
HIV-1 template DNA

containing promoter with transcript of

2 or 3 nucleotides
ArrowR-HSA-167474 (Reactome)
HIV-1 template DNA

with first transcript dinucleotide, opened to +8

position
ArrowR-HSA-167477 (Reactome)
HIV-1 transcription

complex containing 11 nucleotide long

transcript
ArrowR-HSA-167117 (Reactome)
HIV-1 transcription

complex containing 11 nucleotide long

transcript
R-HSA-167115 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
ArrowR-HSA-167121 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
ArrowR-HSA-9613490 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
R-HSA-167113 (Reactome)
HIV-1 transcription

complex containing 3 nucleotide long

transcript
R-HSA-9613490 (Reactome)
HIV-1 transcription

complex containing 4 nucleotide long

transcript
ArrowR-HSA-167113 (Reactome)
HIV-1 transcription

complex containing 4 nucleotide long

transcript
R-HSA-167136 (Reactome)
HIV-1 transcription

complex containing 4-9 nucleotide long

transcript
R-HSA-167468 (Reactome)
HIV-1 transcription

complex containing 9 nucleotide long

transcript
ArrowR-HSA-167136 (Reactome)
HIV-1 transcription

complex containing 9 nucleotide long

transcript
R-HSA-167117 (Reactome)
HIV-1 transcription

complex containing extruded transcript

to +30
ArrowR-HSA-167111 (Reactome)
HIV-1 transcription

complex containing extruded transcript

to +30
R-HSA-167098 (Reactome)
HIV-1 transcription

complex containing

transcript to +30
ArrowR-HSA-167115 (Reactome)
HIV-1 transcription

complex containing

transcript to +30
R-HSA-167111 (Reactome)
HIV-1 transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
ArrowR-HSA-167098 (Reactome)
HIV-1 transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30
R-HSA-167128 (Reactome)
HIV-1 transcription complexArrowR-HSA-167134 (Reactome)
HIV-1 transcription complexArrowR-HSA-9613498 (Reactome)
HIV-1 transcription complexR-HSA-167121 (Reactome)
HIV-1 transcription complexR-HSA-167477 (Reactome)
HIV-1 transcription complexR-HSA-9613498 (Reactome)
HIV-1 unspliced RNAArrowR-HSA-165028 (Reactome)
HIV-1 unspliced RNAR-HSA-187213 (Reactome)
HMGA1R-HSA-8951690 (Reactome)
Host genomic DNAR-HSA-175108 (Reactome)
IN (Integrase) (P04585) proteinArrowR-HSA-164506 (Reactome)
IN (Integrase) (P04585) proteinArrowR-HSA-164845 (Reactome)
IN (Integrase) (P04585) proteinArrowR-HSA-175117 (Reactome)
IN (Integrase) (P04585) proteinArrowR-HSA-175250 (Reactome)
IN (Integrase) (P04585) proteinArrowR-HSA-175258 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
ArrowR-HSA-162590 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
ArrowR-HSA-164522 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
R-HSA-162590 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
R-HSA-164845 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
R-HSA-175108 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
R-HSA-175117 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
R-HSA-175174 (Reactome)
IN bound to sticky

3' ends of viral

DNA in PIC
R-HSA-175250 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
ArrowR-HSA-175108 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
R-HSA-164523 (Reactome)
IN:viral DNA bound

to host genomic DNA

with staggered ends
mim-catalysisR-HSA-164523 (Reactome)
Immature HIV virionArrowR-HSA-3159227 (Reactome)
Immature HIV virionR-HSA-3139027 (Reactome)
Integrated provirusArrowR-HSA-164506 (Reactome)
Integration intermediateArrowR-HSA-164523 (Reactome)
Integration intermediateR-HSA-164506 (Reactome)
Ku proteins bound to viral DNAArrowR-HSA-175174 (Reactome)
Ku proteins bound to viral DNAR-HSA-175177 (Reactome)
LIG1ArrowR-HSA-182876 (Reactome)
MYS-CoAR-HSA-162914 (Reactome)
MYS-CoAR-HSA-184392 (Reactome)
MatrixArrowR-HSA-173642 (Reactome)
Mature HIV virionArrowR-HSA-3139027 (Reactome)
Mature HIV virionR-HSA-164509 (Reactome)
Multimeric capsid coatArrowR-HSA-173111 (Reactome)
N-myristoyl GAG (P04591) proteinArrowR-HSA-184392 (Reactome)
N-myristoyl GAG (P04591) proteinR-HSA-184323 (Reactome)
NEDD4LR-HSA-3159232 (Reactome)
NELF complexR-HSA-167085 (Reactome)
NMT 1mim-catalysisR-HSA-162914 (Reactome)
NMT2mim-catalysisR-HSA-184392 (Reactome)
NTPArrowR-HSA-167085 (Reactome)
NTPArrowR-HSA-167192 (Reactome)
NTPR-HSA-167085 (Reactome)
NTPR-HSA-167087 (Reactome)
NTPR-HSA-167113 (Reactome)
NTPR-HSA-167115 (Reactome)
NTPR-HSA-167117 (Reactome)
NTPR-HSA-167118 (Reactome)
NTPR-HSA-167121 (Reactome)
NTPR-HSA-167136 (Reactome)
NTPR-HSA-167181 (Reactome)
NTPR-HSA-167192 (Reactome)
NTPR-HSA-9613490 (Reactome)
NTPR-HSA-9613498 (Reactome)
Nuclear Pore Complex (NPC)ArrowR-HSA-165047 (Reactome)
Nuclear Pore Complex (NPC)R-HSA-165043 (Reactome)
NucleocapsidArrowR-HSA-173771 (Reactome)
P-TEFb complexR-HSA-167084 (Reactome)
P-TEFb complexmim-catalysisR-HSA-167084 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complexR-HSA-167234 (Reactome)
P-TEFb(Cyclin

T1:Cdk9)-containing elongation complex with separated and uncleaved

transcript
ArrowR-HSA-167197 (Reactome)
PDCD6IPR-HSA-3159232 (Reactome)
PIC (PreIntegration Complex)ArrowR-HSA-173115 (Reactome)
PIC (PreIntegration Complex)R-HSA-164514 (Reactome)
PPIAArrowR-HSA-173115 (Reactome)
PPIAR-HSA-3149454 (Reactome)
PPiArrowR-HSA-164504 (Reactome)
PPiArrowR-HSA-167113 (Reactome)
PPiArrowR-HSA-167115 (Reactome)
PPiArrowR-HSA-167117 (Reactome)
PPiArrowR-HSA-167121 (Reactome)
PPiArrowR-HSA-167134 (Reactome)
PPiArrowR-HSA-167136 (Reactome)
PPiArrowR-HSA-9613490 (Reactome)
PPiArrowR-HSA-9613498 (Reactome)
PR (Protease) (P04585) proteinArrowR-HSA-173771 (Reactome)
PSIP1R-HSA-8951690 (Reactome)
PiArrowR-HSA-165055 (Reactome)
PiArrowR-HSA-167097 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30
mim-catalysisR-HSA-167098 (Reactome)
R-HSA-162590 (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.

R-HSA-162914 (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.
R-HSA-164500 (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.
R-HSA-164503 (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).
R-HSA-164504 (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).

R-HSA-164505 (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.
R-HSA-164506 (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.

R-HSA-164507 (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.

R-HSA-164508 (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.

R-HSA-164509 (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.
R-HSA-164510 (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).
R-HSA-164512 (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).
R-HSA-164513 (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.
R-HSA-164514 (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.
R-HSA-164515 (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.
R-HSA-164519 (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.
R-HSA-164520 (Reactome) Synthesis of minus-strand DNA proceeds toward the 5' end of the PBS motif of the template HIV genomic RNA.
R-HSA-164521 (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.
R-HSA-164522 (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.
R-HSA-164523 (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.
R-HSA-164524 (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.
R-HSA-164527 (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).
R-HSA-164528 (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.
R-HSA-164845 (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.
R-HSA-165027 (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.
R-HSA-165028 (Reactome) The association of RanBp1 with RanGTP:CRM1:Rev promotes disassembly of the complex and release of the Rev:RNA cargo (Mahboobi et al. 2015).
R-HSA-165033 (Reactome) In order for Rev to function, multiple molecules must bind sequentiallly to the RRE (Malim and Cullen 1991).
R-HSA-165034 (Reactome) RanGTP binds to a preformed Rev-CRM1 complex.
R-HSA-165043 (Reactome) The Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP complex associates with the NPC (Askjaer et al. 1998; Daugherty et al. 2010).
R-HSA-165047 (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).
R-HSA-165055 (Reactome) Ran-GAP, a Ran-specific GTPase-activating protein converts Ran-GTP to Ran-GDP, producing a Ran-GTP gradient across the nuclear membrane.
R-HSA-167072 (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).
R-HSA-167076 (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).
R-HSA-167077 (Reactome) Eongation factors are recruited to form the HIV-1 elongation complex (Hill and Sundquist 2013).
R-HSA-167083 (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).
R-HSA-167084 (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).
R-HSA-167085 (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.
R-HSA-167087 (Reactome) In the absence of Tat, transcriptional elongation beyond position +59 does not occur (Kao et al., 1987).
R-HSA-167089 (Reactome) The cap binding complex binds to the methylated GMP cap on the nascent mRNA transcript (Gonatopoulos-Pournatzis & Cowling 2014).
R-HSA-167090 (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).
R-HSA-167097 (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

R-HSA-167098 (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 (Buratowski 2009).
R-HSA-167111 (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' (Buratowski 2009).
R-HSA-167113 (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.
R-HSA-167115 (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.
R-HSA-167117 (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.
R-HSA-167118 (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'.

R-HSA-167121 (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.

R-HSA-167128 (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'.

R-HSA-167130 (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'.

R-HSA-167133 (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'.

R-HSA-167134 (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'.

R-HSA-167136 (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.

R-HSA-167147 (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'.

R-HSA-167148 (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).
R-HSA-167150 (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).
R-HSA-167153 (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 (Gonatopoulos-Pournatzis et al.2011).
R-HSA-167181 (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.

R-HSA-167191 (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).
R-HSA-167192 (Reactome) This event was inferred from the corresponding human Poll II transcription elongation event.
R-HSA-167196 (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'.

R-HSA-167197 (Reactome) This event was inferred from the corresponding human Poll II transcription elongation event.
R-HSA-167234 (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).
R-HSA-167282 (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).
R-HSA-167284 (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).
R-HSA-167288 (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).
R-HSA-167292 (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).
R-HSA-167459 (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'.
R-HSA-167468 (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'.

R-HSA-167474 (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'.

R-HSA-167477 (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'.

R-HSA-167478 (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 ).
R-HSA-167481 (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'.

R-HSA-167484 (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'.

R-HSA-170704 (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).
R-HSA-170706 (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)
R-HSA-171288 (Reactome) The trimeric gp160 complexes are cleaved into the gp41 and gp120 subunits by the cellular protease furin.
R-HSA-171291 (Reactome) The monomeric GP160 ENV precursor protein assembles into a trimer.
R-HSA-173111 (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).
R-HSA-173115 (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.
R-HSA-173642 (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.
R-HSA-173647 (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.
R-HSA-173769 (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).

R-HSA-173771 (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).
R-HSA-174491 (Reactome) The trimeric ENV precursor complex is transported from the ER to the Golgi.
R-HSA-174493 (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.
R-HSA-174494 (Reactome) The ENV precursor protein gp160 is synthesized.
R-HSA-175108 (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.
R-HSA-175117 (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.
R-HSA-175174 (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.
R-HSA-175177 (Reactome) XRCC4 and DNA ligase 4 are recruited to the complex containing viral DNA.
R-HSA-175250 (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.
R-HSA-175258 (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.
R-HSA-180687 (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.
R-HSA-180739 (Reactome) Upon translocation to the cytoplasm, RanBP1 associates with Ran-GTP in the Rev-CRM1-Ran-GTP complex.
R-HSA-180885 (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.
R-HSA-182795 (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).
R-HSA-182859 (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).
R-HSA-182876 (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.
R-HSA-184269 (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).
R-HSA-184323 (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).
R-HSA-184392 (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).
R-HSA-187211 (Reactome) HIV is characterized by the production of multiple-spliced RNA species. The genomic fragmant is processesed creating multiple mRNA fragments.
R-HSA-187213 (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
R-HSA-3139027 (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.
R-HSA-3149432 (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.
R-HSA-3149433 (Reactome) As the Rev protein accumulates, nuclear export of the singly and unspliced mRNAs is facilitated. These mRNAs express the Vif, Vpr, Vpu, Env proteins and the Gag and Gag-Pol polyproteins, respectively, and require Rev, which overcomes the restriction of nuclear export of intron-containing transcripts by accessing the CRM1 nuclear export pathway
R-HSA-3149434 (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.
R-HSA-3149440 (Reactome) VPU is shuttled through the ER:Golgi protein expression pathway.
R-HSA-3149454 (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.
R-HSA-3159227 (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.
R-HSA-3159232 (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.
R-HSA-8951690 (Reactome) The DNA in the Pre-initiation complex 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.
R-HSA-9613490 (Reactome) The human BTF2 basic transcription factor (also called TFIIH), is required for class1 gene transcription of the second round of HIV transcripts. TFIIH has an adenosine triphosphate-dependent DNA helicase activity. The helicase activity is closely associated with the multi-subunit BTF2/TFIIH transcription factor which also has a CTD protein kinase activity.
R-HSA-9613498 (Reactome) The human BTF2 basic transcription factor (also called TFIIH), is required for class1 gene transcription of HIV transcripts. TFIIH has an adenosine triphosphate-dependent DNA helicase activity. The helicase activity is closely associated with the multi-subunit BTF2/TFIIH transcription factor which also has a CTD protein kinase activity.
RAN:GTPArrowR-HSA-165028 (Reactome)
RAN:GTPArrowR-HSA-180687 (Reactome)
RAN:GTPR-HSA-165034 (Reactome)
RAN:GTPR-HSA-165055 (Reactome)
RANBP1ArrowR-HSA-165028 (Reactome)
RANBP1ArrowR-HSA-165055 (Reactome)
RANBP1R-HSA-180739 (Reactome)
RANGAP1ArrowR-HSA-165055 (Reactome)
RCC1mim-catalysisR-HSA-180687 (Reactome)
REV (P04618) proteinArrowR-HSA-165028 (Reactome)
REV (P04618) proteinR-HSA-165027 (Reactome)
REV (P04618) proteinR-HSA-3149454 (Reactome)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein
ArrowR-HSA-167083 (Reactome)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein
R-HSA-167085 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex
ArrowR-HSA-167072 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex
R-HSA-167083 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ArrowR-HSA-167468 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ArrowR-HSA-167474 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
ArrowR-HSA-167477 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-167113 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-167115 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-167117 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-167121 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex
mim-catalysisR-HSA-167136 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
ArrowR-HSA-167133 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT
R-HSA-167153 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
ArrowR-HSA-167128 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex
R-HSA-167133 (Reactome)
RNGTTR-HSA-167128 (Reactome)
RNMTR-HSA-167153 (Reactome)
RTArrowR-HSA-173115 (Reactome)
RTC

with integration competent viral

DNA:BANF1:HMGA1:PSIP1
ArrowR-HSA-8951690 (Reactome)
RTC

with integration competent viral

DNA:BANF1:HMGA1:PSIP1
R-HSA-173115 (Reactome)
RTC (Reverse

Transcription Complex) with RNA

template
ArrowR-HSA-173771 (Reactome)
RTC (Reverse

Transcription Complex) with RNA

template
R-HSA-164527 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
ArrowR-HSA-164512 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
R-HSA-164505 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

and -strand DNA
mim-catalysisR-HSA-164505 (Reactome)
RTC with degraded

RNA template and

minus sssDNA
ArrowR-HSA-182859 (Reactome)
RTC with degraded

RNA template and

minus sssDNA
R-HSA-164503 (Reactome)
RTC with duplex DNA

containing discontinuous plus

strand flap
ArrowR-HSA-164505 (Reactome)
RTC with duplex DNA

containing discontinuous plus

strand flap
R-HSA-182876 (Reactome)
RTC with extending minus strand DNAArrowR-HSA-182795 (Reactome)
RTC with extending minus strand DNAR-HSA-164513 (Reactome)
RTC with extending minus strand DNAmim-catalysisR-HSA-164513 (Reactome)
RTC with extending second-strand DNAArrowR-HSA-164513 (Reactome)
RTC with extending second-strand DNAR-HSA-173769 (Reactome)
RTC with extending second-strand DNAmim-catalysisR-HSA-173769 (Reactome)
RTC with extensive RNase-H digestionArrowR-HSA-164528 (Reactome)
RTC with extensive RNase-H digestionR-HSA-182795 (Reactome)
RTC with extensive RNase-H digestionmim-catalysisR-HSA-182795 (Reactome)
RTC with integration competent viral DNAArrowR-HSA-182876 (Reactome)
RTC with integration competent viral DNAR-HSA-8951690 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
ArrowR-HSA-164503 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
R-HSA-164520 (Reactome)
RTC with minus

sssDNA transferred to 3'-end of viral

RNA template
mim-catalysisR-HSA-164520 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
ArrowR-HSA-164504 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
R-HSA-164519 (Reactome)
RTC with minus

sssDNA:tRNA

primer:RNA template
mim-catalysisR-HSA-164519 (Reactome)
RTC with minus

strand DNA synthesis initiated

from 3'-end
ArrowR-HSA-164520 (Reactome)
RTC with minus

strand DNA synthesis initiated

from 3'-end
R-HSA-164528 (Reactome)
RTC with minus

strand DNA synthesis initiated

from 3'-end
mim-catalysisR-HSA-164528 (Reactome)
RTC with nicked

minus sssDNA:tRNA

primer:RNA template
ArrowR-HSA-164519 (Reactome)
RTC with nicked

minus sssDNA:tRNA

primer:RNA template
R-HSA-182859 (Reactome)
RTC with tRNA primer:RNA templateArrowR-HSA-164527 (Reactome)
RTC with tRNA primer:RNA templateR-HSA-164504 (Reactome)
RTC with tRNA primer:RNA templatemim-catalysisR-HSA-164504 (Reactome)
RTC without viral RNA templateArrowR-HSA-173769 (Reactome)
RTC without viral RNA templateR-HSA-164512 (Reactome)
RTmim-catalysisR-HSA-182859 (Reactome)
Ran GTPase:GDPArrowR-HSA-165055 (Reactome)
Ran-GDPR-HSA-180687 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexArrowR-HSA-180739 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexR-HSA-165028 (Reactome)
Rev

multimer-bound HIV-1

mRNA:Crm1:Ran:GTP:NPC
ArrowR-HSA-165043 (Reactome)
Rev

multimer-bound HIV-1

mRNA:Crm1:Ran:GTP:NPC
R-HSA-165047 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ArrowR-HSA-165034 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
ArrowR-HSA-165047 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
R-HSA-165043 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
R-HSA-180739 (Reactome)
Rev multimer-bound

HIV-1

mRNA:Crm1:Ran:GTP
mim-catalysisR-HSA-165055 (Reactome)
Rev multimer-bound

HIV-1 mRNA:CRM1

complex
ArrowR-HSA-180885 (Reactome)
Rev multimer-bound

HIV-1 mRNA:CRM1

complex
R-HSA-165034 (Reactome)
Rev multimer-bound HIV-1 mRNAArrowR-HSA-165033 (Reactome)
Rev multimer-bound HIV-1 mRNAR-HSA-180885 (Reactome)
Rev-bound HIV-1 mRNAArrowR-HSA-165027 (Reactome)
Rev-bound HIV-1 mRNAR-HSA-165033 (Reactome)
Rev-multimerArrowR-HSA-165028 (Reactome)
Rev-multimerR-HSA-165033 (Reactome)
Spliced Env mRNAArrowR-HSA-187211 (Reactome)
Spliced Env mRNAR-HSA-174494 (Reactome)
Spliced Env mRNAR-HSA-3149433 (Reactome)
TCEA1R-HSA-167077 (Reactome)
TCEA1R-HSA-167196 (Reactome)
TFIIAArrowR-HSA-167136 (Reactome)
TFIIAArrowR-HSA-167474 (Reactome)
TFIIAArrowR-HSA-167477 (Reactome)
TFIIDArrowR-HSA-167136 (Reactome)
TFIIDArrowR-HSA-167474 (Reactome)
TFIIDArrowR-HSA-167477 (Reactome)
TFIIEArrowR-HSA-167136 (Reactome)
TFIIEArrowR-HSA-167468 (Reactome)
TFIIEArrowR-HSA-167474 (Reactome)
TFIIEArrowR-HSA-167477 (Reactome)
TFIIHArrowR-HSA-167072 (Reactome)
TFIIHArrowR-HSA-167181 (Reactome)
TFIIHArrowR-HSA-167468 (Reactome)
TFIIHArrowR-HSA-167474 (Reactome)
TFIIHArrowR-HSA-167477 (Reactome)
TFIIHR-HSA-167072 (Reactome)
TFIIHR-HSA-167077 (Reactome)
TFIIHR-HSA-167196 (Reactome)
TFIIHmim-catalysisR-HSA-167097 (Reactome)
TFIIHmim-catalysisR-HSA-9613490 (Reactome)
TFIIHmim-catalysisR-HSA-9613498 (Reactome)
Tat (P04608)R-HSA-167234 (Reactome)
Tat-containing

elongation complex

prior to separation
ArrowR-HSA-167192 (Reactome)
Tat-containing

elongation complex

prior to separation
R-HSA-167197 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF

phospho DSIF)
ArrowR-HSA-170704 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF

phospho DSIF)
R-HSA-167196 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
ArrowR-HSA-170706 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
R-HSA-170704 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated Pol II CTD and

phospho-NELF
mim-catalysisR-HSA-170704 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
ArrowR-HSA-167191 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
R-HSA-170706 (Reactome)
Tat-containing early

elongation complex with hyperphosphorylated

Pol II CTD
mim-catalysisR-HSA-170706 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexArrowR-HSA-167234 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexR-HSA-167191 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complexmim-catalysisR-HSA-167191 (Reactome)
Trimeric ENV precursorArrowR-HSA-171291 (Reactome)
Trimeric ENV precursorArrowR-HSA-174491 (Reactome)
Trimeric ENV precursorR-HSA-171288 (Reactome)
Trimeric ENV precursorR-HSA-174491 (Reactome)
Trimeric gp120:gp41 oligomerArrowR-HSA-171288 (Reactome)
Trimeric gp120:gp41 oligomerArrowR-HSA-173647 (Reactome)
Trimeric gp120:gp41 oligomerR-HSA-173647 (Reactome)
Trimeric gp120:gp41 oligomerR-HSA-3149454 (Reactome)
UbR-HSA-184323 (Reactome)
VIF (P69723) proteinR-HSA-3149454 (Reactome)
VPRR-HSA-3149454 (Reactome)
VPU (P05919)ArrowR-HSA-3149432 (Reactome)
VPU (P05919)ArrowR-HSA-3149433 (Reactome)
VPU (P05919)ArrowR-HSA-3149440 (Reactome)
VPU (P05919)R-HSA-3149432 (Reactome)
VPU (P05919)R-HSA-3149440 (Reactome)
VPU (P05919)R-HSA-3149454 (Reactome)
Viral core

surrounded by

Matrix layer
ArrowR-HSA-164524 (Reactome)
Viral core

surrounded by

Matrix layer
R-HSA-173642 (Reactome)
Virion Budding ComplexArrowR-HSA-3159227 (Reactome)
Virion Budding ComplexArrowR-HSA-3159232 (Reactome)
Virion with

CD4:gp120 bound to

CCR5/CXCR4
ArrowR-HSA-164507 (Reactome)
Virion with

CD4:gp120 bound to

CCR5/CXCR4
R-HSA-164500 (Reactome)
Virion with

fusogenically

activated gp41
ArrowR-HSA-164515 (Reactome)
Virion with

fusogenically

activated gp41
R-HSA-164521 (Reactome)
Virion with CD4 bound to gp120ArrowR-HSA-164509 (Reactome)
Virion with CD4 bound to gp120R-HSA-164510 (Reactome)
Virion with exposed

coreceptor binding

sites
ArrowR-HSA-164510 (Reactome)
Virion with exposed

coreceptor binding

sites
R-HSA-164507 (Reactome)
Virion with gp41 exposedArrowR-HSA-164500 (Reactome)
Virion with gp41 exposedR-HSA-164515 (Reactome)
Virion with gp41

forming hairpin

structure
ArrowR-HSA-164508 (Reactome)
Virion with gp41

forming hairpin

structure
R-HSA-164524 (Reactome)
Virion with gp41

fusion peptide in

insertion complex
ArrowR-HSA-164521 (Reactome)
Virion with gp41

fusion peptide in

insertion complex
R-HSA-164508 (Reactome)
Vpr:importin-alpha complexArrowR-HSA-162590 (Reactome)
Vps/Vta1R-HSA-3159232 (Reactome)
XPO1ArrowR-HSA-165028 (Reactome)
XPO1R-HSA-180885 (Reactome)
XRCC4:LIG4ArrowR-HSA-175258 (Reactome)
XRCC4:LIG4R-HSA-175177 (Reactome)
XRCC5:XRCC6ArrowR-HSA-175258 (Reactome)
XRCC5:XRCC6R-HSA-175174 (Reactome)
dNTPR-HSA-164504 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ArrowR-HSA-184269 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ArrowR-HSA-184323 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
ArrowR-HSA-3149434 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
R-HSA-184269 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
R-HSA-3149434 (Reactome)
monoubiquitinated

N-myristoyl GAG

(P04591) protein
R-HSA-3149454 (Reactome)
myristoylated nefArrowR-HSA-162914 (Reactome)
myristoylated nefArrowR-HSA-173642 (Reactome)
myristoylated nefR-HSA-3149454 (Reactome)
nefR-HSA-162914 (Reactome)
other viral genomic RNAArrowR-HSA-173771 (Reactome)
p-SUPT5HR-HSA-167153 (Reactome)
tRNA-Lysine3R-HSA-164527 (Reactome)
tRNA-Lysine3R-HSA-3149454 (Reactome)
uncoated viral complexArrowR-HSA-173111 (Reactome)
uncoated viral complexR-HSA-173771 (Reactome)
viral DNA bound with Integrase in PICArrowR-HSA-164514 (Reactome)
viral DNA bound with Integrase in PICR-HSA-164522 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
ArrowR-HSA-175177 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
R-HSA-175258 (Reactome)
viral DNA:Ku

proteins:XRCC4:DNA

ligase IV complex
mim-catalysisR-HSA-175258 (Reactome)
viral PIC proteinsArrowR-HSA-164845 (Reactome)
viral PIC proteinsArrowR-HSA-175108 (Reactome)
viral PIC proteinsArrowR-HSA-175117 (Reactome)
viral PIC proteinsArrowR-HSA-175174 (Reactome)
viral PIC proteinsArrowR-HSA-175250 (Reactome)
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