HIV Life Cycle (Homo sapiens)

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54, 86121651, 24, 42, 51, 154...121104064, 84, 130145911212, 40, 87, 1601214313211685, 10539, 6568138, 14719, 43, 1068240, 8718, 78, 156101, 11220, 23, 32, 45, 46, 96...65, 1487010113, 36, 59, 881209, 48, 81, 94, 11190113, 15134, 100, 1144038, 83, 134, 140, 149...9, 43, 111587999104, 1071211054372, 9013312, 14, 25, 53, 55...1211588035, 1051211043, 13113, 21, 22, 361215, 12148, 81, 1249112163, 74, 1051209, 43, 1194340, 89101, 1125215, 75, 87, 1554, 44441, 141139401027, 132, 150, 15310513, 369140, 891013, 54, 62, 67, 101...31786512125, 49, 97, 13428, 37, 40, 69, 93...121772, 90101, 1125860, 102, 1289161129152436517, 30, 50, 57, 92...1216, 56, 10934, 98, 108, 114121426, 7733, 68early endosome membranecytosolnucleoplasmGolgi membraneendoplasmic reticulum membranePOLR2E NUP37 CCNH POLR2B NUP214 TAF1L POLR2B GTF2A2 TAF10 SSRP1 VIF (P69723) proteinERCC3 POLR2E CTDP1 CDK9 TBP POLR2G TCEB2 POLR2G viral RNA template extensively digested except in PPT region POLR2G p6 (P04585) protein VPS4B NUP98-5 HIV-1 template DNA:9 nucleotide transcript hybrid UBC(457-532) GTF2H1 GTF2H4 UBB(153-228) XPO1 viral plus strand DNA with sticky 3' end POLR2K Rev multimer-boundHIV-1 mRNA:CRM1complexMA (P04591) protein Elongating HIV-1 transcript in processive Pol II mediated elongation NELFCD IN (Integrase) (P04585) protein VPU (P05919) protein ADPUTP POLR2C minus sssDNA ERCC2 VIF (P69723) protein GTF2H3 other viral genomicRNACCNH TAF2 CCNH NC (P04585) protein GTF2F1 p6 (P04585) protein TAF4B POLR2A POLR2B RCC1GTF2A2 POLR2K UBC(77-152) RNGTT p51 (RT) IN (Integrase) (P04585) protein NCBP2 VPU (P05919) protein MA (P04585) protein MA (P04585) protein POLR2H CXCR4 GTF2F2 GTF2F2 CD4POLR2K PR (Protease) (P04585) protein NELFCD REV (P04618) protein TAF13 Elongating HIV-1 transcript in processive Pol II mediated elongation POLR2I SUPT4H1 POLR2H MNAT1 TAF1L GTF2F1 p-S5-POLR2A TAF10 Tat (P04608) TCEB1 POLR2L POLR2L Elongating HIV-1 transcript in processive Pol II mediated elongation ERCC3 HIV-1 template DNAcontaining promoterwith transcript of 2 or 3 nucleotidesUBA52(1-76) Nef Protein(UniProt:P04601)CD4:Env gp120/gp41hairpincomplex:CCR5/CXCR4IN bound to sticky3' ends of viralDNA in PICReverse transcriptase/ribonuclease H NUP214 MA (P04591) protein POLR2J GTF2H5 NC (P04591) protein RPS27A(1-76) CTDP1 POLR2E NELFA POLR2H IN (Integrase)(P04585) proteinNCBP2 GTF2F1 dNTPMA (P04585) protein POLR2K POLR2B UBC(533-608) p6 (P04591) protein Rev-multimer UBC(609-684) VIF (P69723) protein POLR2E POLR2H SSRP1 GTF2F1 CDK9 NELFB POLR2F NELFA XRCC5 p6 (P04591) protein ERCC2 p6 (P04585) protein p-SUPT5HPPIA p51 (RT) POLR2A AAAS TAF3 NELFB CTP GTF2F1 TFIIHRAN PPIA VPU (P05919) protein dCTP POLR2C viral plus strand DNA after ligation ERCC2 TAF2 CHMP6 NELFA TAF1 POLR2D TAF9 CCNT1 p6 (P04591) protein TAF11 TAF11 POLR2I TFIIHPOLR2J NUP93 GTF2F1 SUPT4H1 CCNH ERCC2 VPU (P05919) protein NELFA VPU (P05919) protein CCNK TAF10 PPIA CCNT1 VIF (P69723) protein Reverse transcriptase/ribonuclease H RAN BANF1 POLR2K POLR2L ERCC2 GTF2H4 POLR2E POLR2B CCNT1 minus strand DNA (extending) p6 (P04591) protein TAF6 TAF4 ATP HIV-1 processiveelongation complexGTF2F1 GTF2H1 TAF2 Ran:GTPPOLR2I GTF2F1 CCNH HIV-1 template:capped HIV-1 transcript hybrid NUP133 CXCR4 p6 (P04591) protein CoA-SHPOLR2E viral minus strand DNA with sticky 3' end POLR2D POLR2I TFIIETAF1 Reverse transcriptase/ribonuclease H POLR2B CDK9 FEN1viral second strand DNA with plus sssDNA (discontinuous) p6 (P04585) protein BANF1 UBC(1-76) CDK9 NC (P04591) protein NC (P04585) protein viral minus strand DNA (ful-length) RNMT GTF2F2 UBB(77-152) PPIA HIV-1 RNA GTF2H3 GTF2H4 Reverse transcriptase/ribonuclease H POLR2E NUP155 GTF2A1(275-376) CCNT2 GTF2F1 VPR (P69726) protein Envelopeglycoprotein gp160PR (Protease) (P04585) protein POLR2C HIV-1 mRNA POM121C p6 (P04585) protein RTC (ReverseTranscriptionComplex) with RNAtemplatemyristoylated Nef Protein (UniProt:P04601) RAN TCEB3 VIF (P69723) protein p-SUPT5H NTPRANBP1UBC(77-152) POLR2C CDK9 CHMP6 GTF2H5 HIV-1 RNA TCEB3 NCBP2 POLR2K POLR2B PPIA POLR2K NEDD4L POLR2G POLR2K TAF13 CDK7 TAF1 ERCC2 POLR2H HIV-1 RNA homodimerRev-bound HIV-1 mRNAIN (Integrase) (P04585) protein TCEA1 POLR2E SUPT4H1 RNGTT TAF4 POLR2C ESCRT-IIIPOLR2I tRNA-Lysine3 POLR2C GTF2F1 Virion withCD4:gp120 bound toCCR5/CXCR4NELFE LIG4 CCNH Multimeric capsid coat NMT2GTP HMGA1 GTF2F2 MA (P04591) protein NELFE POLR2L TAF1L POLR2E PR (Protease) (P04585) protein ERCC2 POLR2I POM121C POLR2G TAF5 NELFA Mature HIV virionPOLR2B TAF6 VPR (P69726) protein SSRP1 minus sssDNA Ku proteins bound toviral DNAHIV-1 template DNAwith firsttranscriptdinucleotide,opened to +8positionTat (P04608) p-SUPT5H POLR2C HIV-1 template DNA:30 nt transcript hybrid p51 (RT) GTF2H2 VPR POLR2H POLR2H CDK7 POLR2C NTPPOLR2G TAF9B Transmembrane protein gp41 dATP NUP43 TCEB2 UBC(1-76) CTDP1 GTP HIV-1 RNA RANBP1 CDK7 POLR2F POLR2E p-S2,S5-POLR2A MA (P04585) protein TFIIDCDK9 POLR2B TAF1L SSRP1 TCEA1 Nup45 POLR2K REV (P04618) protein p-SUPT5H Reverse transcriptase/ribonuclease H HIV-1 elongationcomplex containingTatviral minus strand DNA (ful-length) POLR2G tRNA-Lysine3 POLR2L viral DNA:Kuproteins:XRCC4:DNAligase IV complexGTF2F2 Trimeric gp120:gp41oligomerPOLR2A VPS4B BANF1TFIIATAF13 HIV-1 arrestedprocessiveelongation complexCDK9 UBC(381-456) UBC(305-380) viral minus strand DNA after ligation UBC(533-608) POLR2C POLR2E NC (P04591) protein Rev-multimer TAF9B POLR2I HIV-1 RNA p6 (P04591) protein Immature HIV virionCTP TAF2 POLR2B Transmembrane protein gp41 (P04578) POLR2L SUPT4H1 ERCC3 SUPT4H1 myristoylated Nef Protein (UniProt:P04601) POLR2I GTP GTF2F1 POLR2J TAF1 Multimeric matrix layer NELF complexTCEB2 GTF2F1 NC (P04585) protein HIV-1 transcriptioncomplexNC (P04585) protein NTPGTF2H1 TFIIHp-SUPT5H REV (P04618) protein GTF2H3 viral plus strand DNA (full-length) MA (P04591) protein POLR2F p6 (P04591) protein IN (Integrase) (P04585) protein tRNA-Lysine3 NELFCD Multimeric capsidcoatVIF (P69723) protein CTP p-S5-POLR2A POLR2F Transmembrane protein gp41 GTF2H4 CDK9 FACT complexGTF2F1 CCNH HIV-1 earlyelongation complexwithhyperphosphorylatedPol II CTDTCEB1 POLR2I VPS28 p-SUPT5H NUP62 POLR2E MA (P04585) protein POLR2E TCEB2 RNGTTUTP ELL Transmembrane protein gp41 TAF5 GTF2A1(275-376) POLR2C minus sssDNA POLR2E POLR2I IN bound to sticky3' ends of viralDNA in PICPOLR2K HMGA1 GTF2H3 POLR2A POLR2A p-S5-POLR2A CDK9 IN (Integrase) (P04585) protein POLR2K Host genomic DNA POLR2E GTF2F2 POLR2H POLR2C POLR2G POLR2B p51 (RT) UBB(153-228) GTF2A1(1-274) POLR2J RTC with integrationcompetent viral DNAPOLR2J REV (P04618) protein IN (Integrase) (P04585) protein MNAT1 TBP GTF2H5 CD4 TCEA1 POLR2H Multimeric matrix layer GTF2H3 p-S2,S5-POLR2A ERCC2 UBA52(1-76) GTF2A1(275-376) POLR2H TAF10 Aborted HIV-1 earlyelongation complexMA (P04591) protein NUP62 p-S2,S5-POLR2A tRNA-Lysine3 ADPUTP NUP50 TFIIHUTP POLR2H ATP p51 (RT) TAF9 Multimeric matrix layer tRNA-Lysine3 UBC(153-228) POLR2F HMGA1CCNT1 GTF2F1 XRCC5 VPU (P05919) protein TBP POLR2G Multimeric capsid coat POLR2C Elongin ComplexNC (P04585) protein POLR2F IN (Integrase) (P04585) protein POLR2F POLR2H POLR2D CDK9 p6 (P04591) NCBP1 NELFA GTF2E2 viral plus strand DNA (full-length) POLR2K NCBP1 NELFE CCR5 POLR2B POLR2L ATP myristoylated Nef Protein (UniProt:P04601) PSIP1 POLR2E GTF2F2 ERCC2 viral PIC proteinsp-S5-POLR2A POLR2K PR (Protease) (P04585) protein p6 (P04585) protein POLR2G RAN Ran-GDPGTF2E2 GTF2F2 POLR2B UBC(533-608) FURINN-myristoyl GAG (P04591) protein CD4 TAF12 POLR2J NELFE CDK7 ATP VPRp6 (P04585) protein PSIP1 viral PIC proteinsTAF10 POLR2C HIV-1 template DNA:4-9 nucleotide transcript hybrid REV (P04618) protein p51 (RT) p51 (RT) REV (P04618) protein ERCC2 CHMP4B POLR2F NELFB NUPL2 POLR2C POLR2C GTF2H5 capped HIV-1 pre-mRNA VPR (P69726) protein viral RNA template extensively digested except in PPT region TAF1 NDC1 TAF4 CTDP1 POLR2I GTF2E1 CDK7 POLR2J TPR VIF (P69723) protein PR (Protease)(P04585) proteinELL POLR2G minus sssDNA CCR5 PPiTCEB1 ELLPOLR2G XPO1 p6 (P04585) protein TCEB1 POLR2H VPR TCEB1 NELFE p6 (P04591) protein p-SUPT5H p-S2,S5-POLR2A CCNK POLR2I TAF13 POLR2D PPIA GTF2H4 Transmembrane protein gp41 (P04578) HIV-1PolymeraseII(phosphorylated):TFIIF:capped pre-mRNATAF4B NELFE POLR2L POLR2C TAF4 MNAT1 CTDP1 GTF2F1 NUP37 POLR2F ERCC2 p51 (RT) Multimeric capsid coat CCNT1 GTF2F2 GTF2F2 SUPT16H Surface protein gp120 (P04578) GTF2H5 VIF (P69723) protein p-S5-POLR2A Virion with gp41fusion peptide ininsertion complexp6 (P04585) protein POLR2C RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexPOLR2G SUPT16H NCBP1 PPIA POLR2E Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPGTF2F1 POLR2J GTF2F1 RTC without viralRNA templateGTF2A1(275-376) TAF6 Tat (P04608) myristoylated Nef Protein (UniProt:P04601) p51 (RT) TAF11 Nuclear Pore Complex(NPC)TCEA1 Cap Binding Complex(CBC)GTF2H1 NUP85 GTF2H2 CDK7 CCNT1 UBC(609-684) NELFA NELFB POLR2B POLR2J TAF4B NCBP1 p6 (P04585) protein HIV-1 Tat-containingarrested processiveelongation complexp6 (P04585) protein VPR (P69726) protein NELFB POLR2L POLR2B TAF9 MA (P04591) protein BANF1 NELFB HIV-1 transcriptioncomplex containingextruded transcriptto +30myristoylated Nef Protein (UniProt:P04601) VPR MA (P04585) protein POLR2F UBC(305-380) GTF2H1 NELFE POLR2D Ran GTPase:GDPPOLR2K KPNA1 PR (Protease) (P04585) protein p-S2,S5-POLR2A PPIA ELL NELFCD p6 (P04591) GTP POLR2K CHMP2B viral minus strand DNA (ful-length) POLR2B PPiMNAT1 TAF5 MNAT1 POLR2D capped HIV-1 pre-mRNA NC (P04591) protein viral RNA template being digested by RNase-H (extensive) POLR2F SUPT4H1 UBA52(1-76) HIV-1 initiationcomplexTCEB2 CDK7 POLR2G NUP107 Reverse transcriptase/ribonuclease H GTF2F2 VPR REV (P04618) protein GTF2H3 Early elongationcomplex withseparated abortedtranscriptTAF11 TCEB3 POLR2D p51 (RT) TAF4 minus sssDNA GTF2A2 POLR2I PPIA GTF2H2 CTP POLR2G MA (P04591) protein MA (P04585) protein ESCRT-IUBC(381-456) RANBP1IN (Integrase) (P04585) protein POLR2I GTF2H1 ELL GTF2H4 POLR2G viral minus strand DNA (ful-length) MA (P04585) protein TCEB1 IN (Integrase) (P04585) protein TAF4 VPU (P05919) protein POLR2K UBC(609-684) UBC(381-456) UBC(381-456) GTF2H2 p6 (P04585) protein CHMP5 TAF4B REV (P04618) protein GTF2F1 VIF (P69723) protein GTF2F1 POLR2J POLR2A POLR2A POLR2E ERCC3 CHMP7 p-S2,S5-POLR2A POLR2K GTF2H5 MA (P04591) protein minus sssDNA IN (Integrase) (P04585) protein GTF2BUBC(229-304) TAF6 CCNK CDK7 POLR2A RTC with minussssDNA transferredto 3'-end of viralRNA templateVirion BuddingComplexTAF12 POLR2J GTF2H5 Trimeric ENVprecursorHIV-1 template DNA with first transcript dinucleotide, opened to +8 position POLR2F p-SUPT5H MNAT1 POLR2D tRNA-Lysine3 VPU (P05919) protein GTF2F1 POLR2F UBC(153-228) GTP p6 (P04591) protein HIV-1 RNA template GTF2F1 POLR2E GTF2E2 RTC with extensiveRNase-H digestionGTF2A2 ERCC3 GTF2H1 HIV-1 openpre-initiationcomplexPOLR2D capped HIV-1 pre-mRNA GTP CDK9 POLR2D GTF2H2 Reverse transcriptase/ribonuclease H POLR2G POLR2H HIV-1 Tat-containingprocessiveelongation complexVPU (P05919) protein POLR2H p51 (RT) RNA Pol II withphosphorylated CTD:CE complex withactivated GTGTF2F2 p6 (P04591) NUP35 GTF2F2 GTF2H4 VPR REV (P04618) protein POLR2F minus strand DNA (extending) UTP REV (P04618) proteinviral RNA template degraded by RNase-H (initial) viral plus strand DNA with sticky 3' end SUPT16H POLR2I p51 (RT) GTF2F2 HMGA1 VIF (P69723) protein RAN GTF2F1 viral minus strand DNA with sticky 3' end Multimeric matrix layer CTDP1 TSG101 N-myristoyl GAG p-SUPT5H POLR2H NELFCD CCNT1 VPU (P05919) protein tRNA-Lysine3 GTF2H3 CXCR4 TAF11 VPR (P69726) protein viral minus strand DNA (initial) POLR2D POLR2I GTF2F1 POLR2E REV (P04618) protein REV (P04618) protein viral plus strand DNA with sticky 3' end POLR2K CCNT1 POLR2L ERCC2 POLR2J TAF4B TSG101 PR (Protease) (P04585) protein UBC(1-76) p6 (P04585) protein SEH1L-2 POLR2D POLR2D p51 (RT) NELFB CCNH POLR2H GTF2H4 POLR2G ERCC3 GTP NUPL2 Rev-multimer POLR2B tRNA-Lysine3 POLR2J XRCC5:XRCC6POLR2C CDK9 Elongating HIV-1 transcript in processive Pol II mediated elongation GTF2H1 GTF2F2 POLR2F CCR5 tRNA-Lysine3 ATPPOLR2D TAF3 POLR2C NCBP2 CDK7 POLR2J GTF2H1 Reverse transcriptase/ribonuclease H GTF2F1 GTP SSRP1 ERCC3 NELFCD Spliced Env mRNAcapped HIV-1 pre-mRNA CTP GTP TFIIAPPIA RANBP2 HMGA1 POLR2F CTP POLR2K POLR2H VPU (P05919) protein TCEA1 TAF1 NDC1 MA (P04585) protein VIF (P69723) protein POLR2H HIV-1 template DNA:30 nt transcript hybrid XRCC4 NELFCD HMGA1 NELFB Integrated provirusGTF2F1 NELFCD HMGA1 NUPL1-2 TBP IN (Integrase) (P04585) protein POLR2E POLR2B CXCR4 TAF5 GTF2F1 NELFE POLR2I CCNH PSIP1 Elongating HIV-1 transcript in processive Pol II mediated elongation POLR2B XPO1 POLR2E TAF4B genomic DNA with staggered 5' ends POLR2D RPS27A(1-76) NC (P04585) protein p6 (P04585) protein VPR (P69726) protein GTF2F2 PPIA POLR2H REV (P04618) protein POLR2H VPR GTF2A1(1-274) POLR2F Reverse transcriptase/ribonuclease H GTF2F2 ERCC3 p6 (P04591) protein MA (P04591) protein POLR2J POLR2F CDK9 VPS37C NUP98-3 SUPT4H1 GTF2H2 NELFB RNAPolymeraseII(unphosphorylated):TFIIF complexTAF9 REV (P04618) protein POLR2L RTC with minusstrand DNAsynthesis initiatedfrom 3'-endNC (P04591) protein POLR2J POLR2F Rev-multimer GTF2H5 POLR2D RTC with nickedminus sssDNA:tRNAprimer:RNA templateERCC2 RNAPolymeraseII(unphosphorylated):TFIIF complextRNA-Lysine3 GTF2H3 VPS37A POLR2I UTP tRNA-Lysine3 POLR2G UBB(1-76) IN (Integrase)(P04585) proteinCCR5 Surface protein gp120 CTP PPIA UBC(305-380) POLR2I GAG-POL Polyprotein(P04585)GTF2H2 GTF2H3 HMGA1 VPU (P05919) protein VPU (P05919)POLR2H TAF4B NUP210 Reverse transcriptase/ribonuclease H POLR2F POLR2E TAF3 PR (Protease) (P04585) protein POLR2L CCNT1 UBC(77-152) ERCC3 NELFB UBC(153-228) TAF1 NUP210 VPR (P69726) protein GTF2H5 RAN p-S2,S5-POLR2A POLR2L TAF9 NUP205 POLR2C POLR2L p-S2,S5-POLR2A MA (P04585) protein GTF2H3 POLR2B POLR2L POLR2H REV (P04618) protein POLR2C CDK7 IN (Integrase) (P04585) protein Transmembrane protein gp41 ATP Reverse transcriptase/ribonuclease H NUP54 POLR2H POLR2B POLR2A TAF5 MA (P04591) protein ERCC2 CTDP1 POLR2D POLR2I GTF2H2 POLR2H Transmembrane protein gp41 (P04578) HIV-1 transcriptioncomplex containing4-9 nucleotide longtranscriptviral minus strand DNA (initial) MA (P04585) protein VPR TAF2 GTF2A1(275-376) GTF2E2 GTF2H1 NELFCD TAF1L GTF2A1(1-274) GAG Polyprotein(P04591)Multimeric capsid coat HIV-1 elongationcomplexNCBP1 Multimeric matrix layer GTF2H1 p6 (P04585) protein GTF2H4 UTP Autointegrated viralDNA as smallercirclesSUPT16H POLR2H p-S5-POLR2A IN (Integrase) (P04585) protein NELFE SUPT4H1 GTF2A1(1-274) p6 (P04591) RTC with tRNAprimer:RNA templatePOLR2K CHMP5 myristoylated Nef Protein (UniProt:P04601) NCBP2 POLR2E NELFA UBB(1-76) MNAT1 Vpr:importin-alphacomplexVPU (P05919) protein POLR2L RAE1 capped HIV-1 pre-mRNA CHMP3 POLR2J POLR2F Tat:P-TEFb(CyclinT1:Cdk9) complexPOLR2B CCNH MA (P04591) protein POLR2L POLR2D TPR POLR2L TBP POLR2B Transmembrane protein gp41 POLR2K UBC(305-380) GTF2B POLR2G Nup45 POLR2B CCNH CXCR4 POLR2K SUPT4H1 N-myristoyl GAG(P04591) proteinUBC(457-532) POLR2C REV (P04618) protein NC (P04591) protein REV (P04618) protein CCR5, CXCR4Trimeric ENVprecursorVPU (P05919) protein NC (P04591) protein TAF6 NELFCD VPR (P69726) protein NELFA TAF11 PPIA UTP GTF2H2 POLR2F CCNK CD4 TAF12 TAF6 REV (P04618) protein Rev-multimer capped HIV-1 pre-mRNA myristoylated NefProtein(UniProt:P04601)CXCR4 ERCC3 MNAT1 TAF5 POLR2J GTF2H5 GTF2F2 minus sssDNA PSIP1 TAF9B GTF2E1 GTF2H5 CCNT2 REV (P04618) protein TAF2 POLR2I NELFE NUP98-4 GTF2H5 POLR2K POLR2F POLR2E monoubiquitinatedN-myristoyl GAG(P04591) proteinGAG-POL Polyprotein (P04585) NucleocapsidNELFA POLR2H ELL MA (P04591) protein POLR2G POLR2D POLR2E CE:Pol II CTD:Spt5complexPOLR2L GTF2A2 viral minus strand DNA (full-length) POLR2B VIF (P69723) protein GTP TCEB2 dGTP Reverse transcriptase/ribonuclease H ATP ERCC2 VIF (P69723) protein POLR2G POLR2J CTP p51 (RT) GTF2H5 CCR5 MA (P04591) protein CCNH REV (P04618) protein POLR2K NTPCHMP4C GTF2F2 GTF2F1 CCNT1 Tat-containingelongation complexprior to separationTAF3 HIV-1 RNA template ADPGTF2H4 CCNT1 p6 (P04585) protein Tat (P04608) RNA Pol II withphosphorylated CTD:CE complexPOLR2G GTF2F2 CTP UBC(609-684) NELFCD GTF2H5 GTF2F2 GTF2H1 TAF11 CDK7 RTTCEA1 TAF5 TCEB3 POLR2B TAF2 myristoylated NefProtein(UniProt:P04601)p-S5-POLR2A PIC (PreIntegrationComplex)TAF4 POLR2L GTF2E1 GTF2H5 GTF2H1 MNAT1 UBC(457-532) POLR2G UBC(77-152) NUP153 UBB(153-228) NELFB VIF (P69723) protein RTC with annealedcomplementary PBSseqments in +sssDNAand -strand DNACHMP2A viral plus strand DNA (full-length) GTF2F1 POLR2D POLR2K GTF2H5 CTDP1 NC (P04591) protein BANF1 GTF2A2 ERCC2 GTP CTDP1 Reverse transcriptase/ribonuclease H GTF2B GTF2H4 LIG1POLR2F viral minus strand DNA (ful-length) POLR2I SUPT4H1 UBA52(1-76) IN (Integrase) (P04585) protein TAF4B p51 (RT) NELFB MNAT1 ATPGTF2H4 p51 (RT) CDK7 DSIF:NELF:earlyelongation complexafter limitednucleotide additionTAF1 p-NELFE MA (P04591) protein POLR2L MA (P04591) protein NUP153 p-SUPT5H VPS37B POLR2I POLR2E GTP GTF2F1 POLR2D POLR2C POLR2D GTF2H2 GTP REV (P04618) protein GTF2H2 SUPT4H1 HIV-1 mRNA GTF2H3 RTC with minussssDNA:tRNAprimer:RNA templateELL PDCD6IPMA (P04585) protein VPU (P05919) protein POLR2H POLR2H VIF (P69723) protein CTP PPIA p-SUPT5H MA (P04591) protein POLR2C VPU (P05919) protein AAAS Reverse transcriptase/ribonuclease H POLR2I CCNT1 p6 (P04585) protein NELFA POLR2D POLR2I HIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end GTF2H5 PPIA TCEA1 SUPT16H ERCC3 POLR2F HIV-1 template:capped HIV-1 transcript hybrid GTF2H4 CHMP2B REV (P04618) proteinCTDP1 HIV-1 mRNA p6 (P04585) NELFB GTF2F2 POLR2B p-SUPT5H GTF2F2 PPIA POLR2J UBB(77-152) VIF (P69723) protein TAF4 GTF2E2 Multimeric capsid coat GTF2F2 ERCC3 BANF1 VPU (P05919) protein GTP tRNA-Lysine3 TBP POLR2K Ku proteins bound toviral DNANELFCD GTF2H2 GTF2A1(275-376) GTF2F2 VPR (P69726) protein POLR2C TCEB1 P-TEFb(CyclinT1:Cdk9)-containingelongation complexwith separated anduncleavedtranscriptTCEB2 POLR2J Tat (P04608) IN (Integrase) (P04585) protein RNAPolymeraseII(unphosphorylated):TFIIF complexMA (P04585) protein POLR2C tRNA-Lysine3 ERCC3 Surface protein gp120 POLR2G NELFA UBC(381-456) p6 (P04591) protein p6 (P04591) GTF2F1 POLR2G NUP50 CTP NELFE POLR2F VPU (P05919) protein TAF13 GTP p6 (P04591) protein GTF2E2 p6 (P04591) protein IN (Integrase) (P04585) protein POLR2J POLR2J UTP ERCC3 REV (P04618) protein REV (P04618) protein NUP188 HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotides p-SUPT5H POLR2D CDK7 PPIAPOLR2K CTP GTF2H5 POLR2E CDK7 POLR2I CCNT1 CXCR4 tRNA-Lysine3 NUP54 CCNK Transmembrane protein gp41 NELFB GTF2F1 MA (P04591) protein ERCC3 NELFB POLR2I ERCC2 TAF1L SSRP1 POLR2I NELFCD p-S2,S5-POLR2A VIF (P69723) protein SSRP1 POLR2L UBC(457-532) minus sssDNA CHMP4C GTF2F2 p6 (P04591) protein TAF9 POLR2E POLR2D SUPT4H1 NELFCD POLR2L GTF2H1 monoubiquitinatedN-myristoyl GAG(P04591) proteinp6 (P04591) protein ELL MA (P04591) protein CCNH viral second strand DNA (plus sss) NELFA p6 (P04591) protein Multimeric capsid coat NUP88 POLR2H POLR2C capped HIV-1 pre-mRNA CD4 TCEB2 p51 (RT) POLR2I POLR2J viral plus strand DNA (full-length) TAF13 PPiPOLR2G GTF2H4 POLR2J Surface protein gp120 POLR2L p-SUPT5H MNAT1 POLR2H TBP VPR (P69726) protein VIF (P69723) protein MA (P04585) protein NUP93 VPU (P05919) protein VPR BANF1 TAF13 PPiGTF2F2 POLR2D POLR2J GAG-POL Polyprotein(P04585)UBB(153-228) NUP155 Reverse transcriptase/ribonuclease H VPU (P05919) protein TCEB3 CTDP1 Multimeric matrix layer GTF2B POLR2I DSIF:NELF:earlyelongation complexPOLR2C UBB(1-76) NELFA CCNT2 HIV-1 template DNA:30 nt transcript hybrid POLR2H IN (Integrase) (P04585) protein GTF2A1(275-376) POLR2G minus strand DNA (extending) POLR2J POLR2C Surface protein gp120 POLR2H POLR2H PPIA VIF (P69723) protein POLR2K VPU (P05919) protein POLR2K TAF12 Pip6 (P04591) protein GTF2H3 VIF (P69723) protein p-NELFE TBP UBB(153-228) POLR2F UBC(457-532) RAN ERCC3 PPIA HIV-1 template:capped HIV-1 transcript hybrid POLR2I RNMTVPU (P05919) protein POLR2J POLR2D GTF2F1 PSIP1 HIV-1 transcriptioncomplex containing4 nucleotide longtranscriptPOLR2G GTF2F2 TCEB3 GTF2F1 UBC(229-304) VIF (P69723) protein GTF2B ERCC3 POLR2B HIV-1 RNA template TAF4 POLR2F NUP43 p-SUPT5H POLR2I GTF2H1 POLR2E NTPCTDP1 GTF2F1 CDK9 IN (Integrase) (P04585) protein VTA1 REV (P04618) protein Virion withfusogenicallyactivated gp41POLR2D POLR2E p-SUPT5H GTF2E1 REV (P04618) protein TAF10 TAF1 viral plus strand DNA (full-length) PPIA viral plus strand DNA (full-length) GDPRNGTT p51 (RT) POLR2F TAF9B HIV-1 transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30HIV-1 pausedprocessiveelongation complexNUP98-5 MA (P04591) protein NELFA TFIIHGTP ELL HMGA1 tRNA-Lysine3 IN (Integrase) (P04585) protein minus sssDNA Multimeric matrix layer POLR2B POLR2L POLR2J p6 (P04585) protein POLR2K IN (Integrase) (P04585) protein GTF2BUBC(153-228) p-S5-POLR2A TTP p6 (P04591) protein Transmembrane protein gp41 p6 (P04585) protein GTF2H2 POLR2L GTF2F2 SSRP1 XRCC4:LIG4GTF2E2 POLR2A TAF2 MA (P04591) protein GTF2E2 TCEB1 Surface protein gp120 TCEB2 ELL TCEB3 POLR2E XRCC6 VPU (P05919) protein CHMP4B PSIP1 p6 (P04591) protein GTF2F1 RPS27A(1-76) POLR2E ERCC2 GTF2H2 Surface protein gp120 (P04578) MNAT1 GTF2F2 VPR Viral coresurrounded byMatrix layerGTF2H3 viral PIC proteinsPOLR2F NELFE ERCC2 UBC(533-608) ATP HIV-1 RNA template GTF2H2 GTF2A1(275-376) CCNT2 viral plus strand DNA (full-length) Multimeric capsid coat RPS27A(1-76) MNAT1 ATP PPIA POLR2K UBC(305-380) POLR2G p51 (RT) GTF2B POLR2C POLR2B ATP TAF12 Revmultimer-boundHIV-1mRNA:Crm1:Ran:GTP:NPCVPR GTF2H4 MA (P04585) protein NCBP1 UBC(1-76) CTDP1 POLR2F POLR2F SUPT4H1 XPO1POLR2G tRNA-Lysine3POLR2K IN (Integrase) (P04585) protein HIV-1 unspliced RNAPOLR2L UbPOLR2J P-TEFb(CyclinT1:Cdk9) complexMA (P04591) protein POM121 GTF2F2 POLR2J RTGTF2F2 NCBP2 TAF10 POLR2L CDK9 NELFE POLR2K viral minus strand DNA (ful-length) CDK7 VIF (P69723) protein POLR2G POLR2L POLR2C UBB(77-152) GTP VPU (P05919) protein tRNA-Lysine3GTF2H2 POLR2G UBC(305-380) POLR2F POLR2I VPS4A SUPT4H1 CD4 POLR2E CDK7 viral plus strand DNA (full-length) POLR2E monoubiquitinatedN-myristoyl GAG(P04591) proteinPOLR2K viral RNA template degraded by RNase-H (initial) 2-LTR form ofcircular viral DNAVPR NELFA UBC(229-304) POLR2F POLR2A ERCC3 VPU (P05919) protein GTF2F2 TCEB3 p-S2,S5-POLR2A VPS37D POLR2L NUP85 POLR2L POLR2L POLR2I REV (P04618) protein VPR REV (P04618) protein POLR2L POLR2K TAF4 VPU (P05919) protein tRNA-Lysine3 NELFB IN (Integrase) (P04585) protein POLR2K CDK7 TCEB1 UBC(1-76) POLR2J CCNH POLR2F p-SUPT5H Reverse transcriptase/ribonuclease H p-S2,S5-POLR2A Tat (P04608) REV (P04618) protein POLR2D RTC with extendingminus strand DNAGTF2A1(1-274) SSRP1 1-LTR form ofcircular viral DNATAF13 POLR2L VPR (P69726) protein HIV-1 template:capped HIV-1 transcript hybrid IN (Integrase) (P04585) protein CDK7 Reverse transcriptase/ribonuclease H Surface protein gp120 HIV-1 Tat-containingaborted elongationcomplex afterarrestUBC(533-608) UBC(229-304) NELFE UBC(153-228) p6 (P04591) protein GTF2H1 TCEB3 UBC(229-304) GTF2F2 Virion with gp41forming hairpinstructurePOLR2G HIV-1 template DNA:30 nt transcript hybrid SUPT4H1 TAF2 NELFA CDK7 POLR2L POLR2B MA (P04591) protein VPS28 MNAT1 CDK7 TAF3 NELFE GTF2H1 TAF6 POLR2K VIF (P69723) protein VPU (P05919)GTF2H5 VPS37C VPU (P05919) protein CD4 TCEA1 Surface protein gp120 p51 (RT) PPIA TCEA1 GTF2F2 VPU (P05919) protein POLR2C Elongating HIV-1 transcript in processive Pol II mediated elongation HIV-1 RNA template TAF11 MNAT1 POLR2L Host genomic DNA REV (P04618) protein Rev multimer-boundHIV-1 mRNATat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD andphospho-NELFmyristoylated Nef Protein (UniProt:P04601) CCNT1 CDK9 POLR2I Assembling HIVvirionPOLR2F GTF2F2 CTDP1 REV (P04618) protein CTDP1 POLR2L SUPT4H1 POLR2I viral minus strand DNA (full-length) minus strand DNA (extending) p-SUPT5H GTF2H4 p-S2,S5-POLR2A genomic DNA with staggered 5' ends Surface protein gp120 (P04578) Transmembrane protein gp41 POLR2B HIV-1 PromoterEscape ComplexHIV-1 transcriptioncomplex containingtranscript to +30POLR2J MNAT1 UBC(457-532) GTF2H3 CCNH GTF2H1 POLR2J p-SUPT5H SUPT4H1 VPU (P05919) protein Reverse transcriptase/ribonuclease H GTF2E1 p-NELFE CHMP3 ELL POLR2J GTF2F2 TAF11 CHMP2A MA (P04585) protein RPS27A(1-76) HIV-1 transcriptioncomplex containing9 nucleotide longtranscriptIN (Integrase) (P04585) protein TAF1L p-S2,S5-POLR2A GTF2H1 HIV-1 closedpre-initiationcomplexXRCC6 POLR2B POLR2D HIV-1 RNA template PR (Protease) (P04585) protein GTF2A1(275-376) TAF1 NELFCD NUP98-3 XRCC6 HIV-1 template:capped HIV-1 transcript hybrid VIF (P69723) protein HIV-1 template:capped HIV-1 transcript hybrid POLR2C POLR2G POLR2C NC (P04591) protein MatrixReverse transcriptase/ribonuclease H PSIP1 VPS37D UBA52(1-76) CDK7 p6 (P04591) protein viral DNA bound withIntegrase in PICtRNA-Lysine3 Surface protein gp120 MA (P04591) protein DSIF complexMA (P04591) protein VIF (P69723) protein HIV-1 RNA template PPIA TAF5 p-SUPT5H GTF2H4 VPS4A VPR (P69726) protein ERCC3 RNAPolII(hypophosphorylated) complex bound to DSIF proteinCHMP7 NCBP1 POLR2C capped HIV-1 pre-mRNA HIV-1 mRNACDK9 POLR2B VPU (P05919) protein GTF2H4 VPS37A Multimeric capsid coat POLR2H POLR2K NC (P04591) protein POLR2G POLR2C VIF (P69723) protein myristoylated Nef Protein (UniProt:P04601) NMT 1NELFB GTF2H3 VPR XRCC5 XPO1 HIV-1 RNA template HIV-1 RNA template POLR2K TAF13 REV (P04618) protein POLR2L HIV-1 template DNA:30 nt transcript hybrid SEH1L-2 Rev-multimer HIV-1 template DNA hybrid with phosphodiester-PPi intermediate Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTDPOLR2H POLR2C NELFA GTF2H3 GTF2H4 Tat (P04608) RAE1 MNAT1 POLR2D POLR2D GTF2F1 TCEA1 NUP188 HIV-1 transcriptioncomplex containing3 nucleotide longtranscriptVIF (P69723) protein GTF2H1 Reverse transcriptase/ribonuclease H POLR2H TCEB3 NELFB TAF9B CTDP1 GTF2E1 p6 (P04585) protein CTDP1 ERCC3 VPR (P69726) protein GTF2E2 GTF2E1 TCEB2 NELFE NUP205 myristoylated Nef Protein (UniProt:P04601) Tat (P04608) UTP POLR2K NCBP1 TAF4B TAF6 p-S2,S5-POLR2A GTF2H2 POLR2A GTF2H1 GTF2F2 VPU (P05919) protein POLR2E POLR2D HIV-1 template DNA:11 nucleotide transcript hybrid ELL IN (Integrase) (P04585) protein TCEA1TAF3 POLR2E CDK7 CDK7 GTP minus sssDNA Transmembrane protein gp41 REV (P04618) protein GTF2F2 GTF2F2 GTF2F2 REV (P04618) protein POLR2D POLR2I p51 (RT) GTF2E2 p6 (P04585) protein NUP160 p-S5-POLR2A TAF13 p6 (P04585) protein POLR2A CCNH VPS37B REV (P04618) protein p51 (RT) TCEB1 POLR2E p6 (P04585) protein UBB(77-152) NELFCD GTF2A2 CTDP1 IN (Integrase) (P04585) protein CCNH GTF2F1 p-S5-POLR2A GTF2A2 viral minus strand DNA with sticky 3' end Ran-GTPIN (Integrase) (P04585) protein MNAT1 REV (P04618) protein NCBP2 REV (P04618) protein REV (P04618) protein POLR2D GTF2B p6 (P04585) protein VPR CCNT1 POLR2A NCBP1 TFIIDHIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end POLR2C viral second strand DNA with plus sssDNA (extending) SSRP1 ERCC2 POLR2I Transmembrane protein gp41 NELFE RAN GTF2H3 POLR2L UBB(1-76) SUPT4H1 Trimeric gp120:gp41oligomerGTF2F1 GTF2H2 PPIA CHMP4A ERCC3 MNAT1 VPU (P05919) protein MA (P04585) protein GTF2A1(1-274) ELL p-SUPT5H UBC(77-152) HIV-1 mRNA PSIP1CCNH p6 (P04585) POLR2B p6 (P04585) protein NELFE POLR2J GTF2F1 BANF1 Reverse transcriptase/ribonuclease H POLR2J p-SUPT5H POLR2E Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPRTC with degradedRNA template andminus sssDNAPOLR2A uncoated viralcomplexGTF2A1(1-274) POLR2G LIG4 p6 (P04591) protein NCBP2 UBC(609-684) VPU (P05919)p51 (RT) TAF3 RPS27A(1-76) MA (P04585) protein CDK7 TAF9B POLR2E Reverse transcriptase/ribonuclease H UBC(609-684) SUPT16H NC (P04585) protein VPR Surface protein gp120 POLR2G p51 (RT) GTF2H2 Reverse transcriptase/ribonuclease H CCNH UBB(1-76) Reverse transcriptase/ribonuclease H POLR2J GTF2H5 POLR2D GTF2F1 p6 (P04585) protein Tat (P04608) IN (Integrase) (P04585) protein GTF2A2 TAF12 POLR2I NC (P04585) protein POLR2J POM121 UBC(77-152) POLR2D POLR2D IN (Integrase) (P04585) protein Glycosylated Envelope glycoprotein gp160 CCR5 Host genomic DNAPOLR2D CCNH POLR2K viral plus strand DNA with sticky 3' end POLR2E PPIA GTF2H1 GTF2E1 NELFB POLR2F GTF2H4 GTF2F2 PR (Protease) (P04585) protein POLR2G ATP NC (P04585) protein HIV-1 initiationcomplex withphosphodiester-PPiintermediatePOLR2F NC (P04591) protein MNAT1 POLR2B Virion with gp41exposedTBP HIV-1 mRNA POLR2E POLR2L POLR2B POLR2G GTF2H1 TBP VIF (P69723) protein HIV-1 template DNA:3 nucleotide transcript hybrid TCEB1 CCNT2 CCNT2 UTP ATPviral plus strand DNA (full-length) SUPT4H1 GTF2H4 NELFA TCEA1 TAF1L UBC(153-228) POLR2G UBB(77-152) POLR2G POLR2B HIV-1 Tat-containingpaused processiveelongation complexNCBP2 p6 (P04591) protein CCNH CTDP1 GTF2H3 POLR2I CTDP1viral minus strand DNA with sticky 3' end GTF2H5 Encapsidated viralcoreERCC3 viral PIC proteinsTCEB1 SUPT16H GTF2H1 POLR2B TAF12 viral plus strand DNA (full-length) TAF1L POLR2K TAF9 VPR POLR2D ATP CTP ERCC2 POLR2I GTF2H4 NELFA UTP SUPT4H1 POLR2L GTP POLR2G PPIA TAF9B POLR2C VIF (P69723) protein GTF2H5 CCNT1 CTDP1 GTF2H5 viral second strand DNA with plus sssDNA (extending) POLR2J GTF2F1 TFIIHTAF4B CCNH RNAPolymeraseII(unphosphorylated):TFIIF complexp6 (P04591) protein POLR2B POLR2L p51 (RT) CTP tRNA-Lysine3 POLR2H POLR2L UBC(533-608) ERCC2 GTF2H2 UBC(229-304) POLR2F CTP POLR2B GTF2H3 GTF2H3 GTF2H3 POLR2B POLR2J POLR2K CD4 NELFCD MA (P04585) protein Autointegrated viralDNA as an invertedcircleIN (Integrase) (P04585) protein TAF10 p6 (P04585) POLR2A TAF9B SUPT16H PPiGTF2F1 CCR5 minus strand DNA (extending) POLR2B VPU (P05919) protein BANF1 viral plus strand DNA (full-length) GTF2E1 CCNT2 Rev-multimerMNAT1 XRCC5 POLR2F UBB(77-152) VPR (P69726) protein POLR2H tRNA-Lysine3 HIV-1 RNA POLR2H VIF (P69723) protein UBB(153-228) IN (Integrase) (P04585) protein GTF2H4 POLR2C POLR2L CCNH NUP107 POLR2D MA (P04585) protein GTPCDK9 GTF2F1 UBC(381-456) CTDP1 RNAPolII(hypophosphorylated):capped pre-mRNA complexp51 (RT) TCEB3 TAF9 POLR2L POLR2F Multimeric capsid coat N-myristoyl GAG (P04591) protein viral minus strand DNA (full-length) TAF12 NELFCD RNAPolymeraseII(unphosphorylated):TFIIF complexTAF3 GTF2H3 GTF2B Cap Binding Complex(CBC)PSIP1 POLR2H viral minus strand DNA with sticky 3' end REV (P04618) protein GTF2H2 IN (Integrase) (P04585) protein TCEA1 Reverse transcriptase/ribonuclease H SUPT4H1 GTF2H1 CHMP4A VPR POLR2F PR (Protease) (P04585) protein PPiCCNT1 POLR2G POLR2E Elongating HIV-1 transcript prior to separation POLR2F POLR2I TAF12 p51 (RT) TAF1L GTP NUP98-4 TCEB3 MA (P04585) protein GTF2H5 TAF6 VIF (P69723) protein Reverse transcriptase/ribonuclease H POLR2A Tat (P04608) XRCC6 Elongating HIV-1 transcript in processive Pol II mediated elongation POLR2K GTF2H1 GTP HIV-1 cappedpre-mRNA:CBC:RNAPol II(phosphorylated)complexp6 (P04585) protein TAF2 GTF2H4 PPIAp-S5-POLR2A ERCC2 MA (P04585) protein TAF9B NC (P04585) protein myristoylated Nef Protein (UniProt:P04601) POLR2I POLR2C RTC with duplex DNAcontainingdiscontinuous plusstrand flapHIV-1 mRNA GTF2F2 HIV-1 RNA POLR2E TAF6 GAG-POL Polyprotein (P04585) POLR2B POLR2B HIV-1 abortedelongation complexafter arrestRTC with extendingsecond-strand DNAPOLR2B MA (P04591) protein viral minus strand DNA (ful-length) TAF10 TFIIHSSRP1 GTF2A1(1-274) MA (P04585) protein IN (Integrase) (P04585) protein p6 (P04591) protein p6 (P04591) protein POLR2D POLR2B TAF5 POLR2C GDP VIF (P69723) protein MA (P04591) protein HIV-1 template DNA:30 nt transcript hybrid HIV-1 RNA NUP160 POLR2L GTF2A1(1-274) TCEB2 POLR2H CDK7 ERCC2 POLR2J POLR2J p6 (P04585) CD4 GTF2H2 POLR2G MNAT1 tRNA-Lysine3 SUPT16H POLR2G VPR (P69726) protein VIF (P69723) protein REV (P04618) protein POLR2I GTF2E1 POLR2J UBB(1-76) POLR2H VIF (P69723) protein GTF2H2 p6 (P04591) protein Elongating HIV-1 transcript prior to cleavage GTF2F1 NELFCD VIF (P69723) protein ERCC3 HIV-1 RNA RANGAP1GTF2H3 Envelope glycoprotein gp160 SSRP1 ERCC2 VPU (P05919) protein GTF2A2 ERCC3 GTF2E2 tRNA-Lysine3 p-SUPT5H HIV-1 RNA POLR2F NUP35 CCNH GTF2A1(1-274) GTF2H2 tRNA-Lysine3 Virion with exposedcoreceptor bindingsitesUBA52(1-76) p-S2,S5-POLR2A SUPT16H POLR2C NC (P04585) protein TAF9 p-SUPT5H TFIIEGTF2F2 Surface protein gp120 PSIP1 TAF9 HIV-1 mRNA POLR2J REV (P04618) protein POLR2C GTF2E1 POLR2C TAF10 POLR2C PPiNELFA GTF2H4 HIV-1 transcriptioncomplex containing11 nucleotide longtranscriptPOLR2L Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD (phospho-NELFphospho DSIF)tRNA-Lysine3 VPU (P05919) protein HIV-1 templateDNA:4-9 nucleotidetranscript hybridMA (P04585) protein CCNH p-S2,S5-POLR2A POLR2A VTA1 POLR2D p6 (P04585) protein NELFCD BANF1 NELFB myristoylated Nef Protein (UniProt:P04601) TCEB2 VPR (P69726) protein TCEB2 PR (Protease) (P04585) protein p6 (P04585) protein NC (P04585) protein POLR2G CCNT1 POLR2K CDK9 POLR2D XPO1 UTP PDCD6IP NTPHIV-1 template DNA:4 nucleotide transcript hybrid N-myristoyl GAG (P04591) protein POLR2H NELFCD ATP POLR2F POLR2K SUPT16H UBC(1-76) NUPL1-2 GTF2F2 GTF2H5 CDK7 MNAT1 GTF2H3 CCNK Host genomic DNA XPO1REV (P04618) protein TAF9B Multimeric matrix layer REV (P04618) protein Multimeric matrix layer POLR2F VIF (P69723) protein ERCC3 TAF3 GTF2F1 p6 (P04585) Multimeric capsid coat VIF (P69723) protein XRCC4 TAF12 ATP UTP Rev-multimerPOLR2H GTF2H3 POLR2E GTF2F2 VPR CTDP1 tRNA-Lysine3 HMGA1 POLR2E IN (Integrase) (P04585) protein GTF2H2 POLR2A POLR2I POLR2C VPR NUP133 RANBP2 SUPT16H CCNH Virion with CD4bound to gp120TAF3 GTF2H5 POLR2D ATP GTF2H3 MYS-CoASUPT4H1 viral plus strand DNA with sticky 3' end POLR2I IN (Integrase) (P04585) protein REV (P04618) protein POLR2J CCNK CCNT1 POLR2J p6 (P04591) protein Tat (P04608)POLR2D POLR2F SSRP1 POLR2H ERCC3 POLR2H NELFB PPIA MA (P04585) protein N-myristoyl GAG MNAT1 minus sssDNA Tat (P04608) MNAT1 PPIA UTP VPU (P05919) protein GTF2H4 GDP NC (P04591) protein p-S5-POLR2A Vps/Vta1POLR2E REV (P04618) protein Reverse transcriptase/ribonuclease H viral minus strand DNA (ful-length) NEDD4LVPR TAF5 GTF2F2 NUP88 MNAT1 GTF2A1(275-376) GTF2F1 ERCC2 TCEB1 POLR2D PiMA (P04585) protein Elongating HIV-1 transcript in processive Pol II mediated elongation P-TEFb complexATP POLR2I POLR2K TCEB3 SUPT16H GTF2H2 IntegrationintermediateTAF11 RNAPolymeraseII(unphosphorylated):TFIIF complexGTF2F1 p6 (P04591) protein IN:viral DNA boundto host genomic DNAwith staggered ends7315961737316, 29, 12711, 95, 110, 12573737316, 29, 12714627738, 47, 117, 12216, 29, 12716, 29, 1277311, 95, 110, 12573737315916, 29, 12716, 29, 1271357366737316, 29, 1277373


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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  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-HIV-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-NUL-167142 (Reactome)
Elongating HIV-1 transcript prior to separation R-NUL-167145 (Reactome)
Elongin ComplexComplexR-HSA-112425 (Reactome)
Encapsidated viral coreComplexR-HIV-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-HIV-175416 (Reactome)
IN bound to sticky

3' ends of viral

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

to host genomic DNA

with staggered ends
ComplexR-HSA-175224 (Reactome)
Immature HIV virionComplexR-HIV-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)
MYS-CoAMetaboliteCHEBI:15532 (ChEBI)
MatrixComplexR-HIV-173120 (Reactome)
Mature HIV virionComplexR-HIV-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)
Nef Protein (UniProt:P04601)ProteinP04601 (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-HIV-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)
RAE1 ProteinP78406 (Uniprot-TrEMBL)
RAN ProteinP62826 (Uniprot-TrEMBL)
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 (Reverse

Transcription Complex) with RNA

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

complementary PBS seqments in +sssDNA

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

RNA template and

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

containing discontinuous plus

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

sssDNA transferred to 3'-end of viral

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

sssDNA:tRNA

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

strand DNA synthesis initiated

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

minus sssDNA:tRNA

primer:RNA template
ComplexR-HIV-182804 (Reactome)
RTC with tRNA primer:RNA templateComplexR-HIV-173801 (Reactome)
RTC without viral RNA templateComplexR-HIV-173824 (Reactome)
RTComplexR-HIV-173772 (Reactome)
Ran GTPase:GDPComplexR-HSA-165549 (Reactome)
Ran-GDPComplexR-HSA-180701 (Reactome)
Ran-GTPComplexR-HSA-180738 (Reactome)
Ran:GTPComplexR-HSA-180686 (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)
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)
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)
TFIIAComplexR-HSA-109629 (Reactome)
TFIIDComplexR-HSA-109626 (Reactome)
TFIIEComplexR-HSA-109633 (Reactome)
TFIIHComplexR-HSA-109634 (Reactome)
TPR ProteinP12270 (Uniprot-TrEMBL)
TSG101 ProteinQ99816 (Uniprot-TrEMBL)
TTP MetaboliteCHEBI:18077 (ChEBI)
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-NUL-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)
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-HIV-173664 (Reactome)
Virion Budding ComplexComplexR-HSA-3211408 (Reactome)
Virion with

CD4:gp120 bound to

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

fusogenically

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

coreceptor binding

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

forming hairpin

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

fusion peptide in

insertion complex
ComplexR-HIV-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)
dATP MetaboliteCHEBI:16284 (ChEBI)
dCTP MetaboliteCHEBI:16311 (ChEBI)
dGTP MetaboliteCHEBI:16497 (ChEBI)
dNTPComplexR-ALL-173818 (Reactome)
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 Protein (UniProt:P04601) ProteinP04601 (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)
uncoated viral complexComplexR-HIV-173653 (Reactome)
viral DNA bound with Integrase in PICComplexR-HIV-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-167097 (Reactome)
ADPArrowR-HSA-170704 (Reactome)
ADPArrowR-HSA-170706 (Reactome)
ATPR-HSA-167097 (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-173115 (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
R-HSA-167113 (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 complexR-HSA-167121 (Reactome)
HIV-1 transcription complexR-HSA-167477 (Reactome)
HIV-1 unspliced RNAArrowR-HSA-165028 (Reactome)
HIV-1 unspliced RNAR-HSA-187213 (Reactome)
HMGA1R-HSA-173115 (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)
Nef Protein (UniProt:P04601)R-HSA-162914 (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)
PR (Protease) (P04585) proteinArrowR-HSA-173771 (Reactome)
PSIP1R-HSA-173115 (Reactome)
PiArrowR-HSA-165055 (Reactome)
PiArrowR-HSA-167097 (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) At the beginning of this reaction, 1 molecule of 'FACT complex', 1 molecule of 'HIV-1 early elongation complex with hyperphosphorylated Pol II CTD', 1 molecule of 'Elongin Complex', 1 molecule of 'TFIIH', 1 molecule of 'RNA polymerase II elongation factor ELL', and 1 molecule of 'TFIIS protein' are present. At the end of this reaction, 1 molecule of 'HIV-1 elongation complex' is present.

This reaction takes place in the nucleus (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.
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) The VPU protein is produced
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.
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 (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-173115 (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)
Ran-GTPArrowR-HSA-180687 (Reactome)
Ran-GTPR-HSA-165034 (Reactome)
Ran:GTPArrowR-HSA-165028 (Reactome)
Ran:GTPR-HSA-165055 (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-167098 (Reactome)
TFIIHmim-catalysisR-HSA-167113 (Reactome)
TFIIHmim-catalysisR-HSA-167121 (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 Nef

Protein

(UniProt:P04601)
ArrowR-HSA-162914 (Reactome)
myristoylated Nef

Protein

(UniProt:P04601)
ArrowR-HSA-173642 (Reactome)
myristoylated Nef

Protein

(UniProt:P04601)
R-HSA-3149454 (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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