HIV Life Cycle (Homo sapiens)

From WikiPathways

Revision as of 10:34, 18 November 2015 by ReactomeTeam (Talk | contribs)
Jump to: navigation, search
41, 1566413920, 33, 105, 1586913, 7726, 45, 59, 86, 87, 103...911334, 39, 59, 66, 78...64, 9114826, 30, 49, 92, 111...6497, 98, 12515916, 194, 21, 47, 48, 69...821338, 1436469, 14031, 11299, 1306440121564136433, 6960466435, 9710, 56, 1376, 11, 124, 146, 151...1086417, 59, 80, 944015718, 26, 36, 42-44, 65...3, 12, 15, 63, 73...1112370, 13653, 55, 1337, 139104, 147, 1531350, 51, 75, 11564150976432975462, 12723, 31, 89, 1122, 136951, 75, 13422, 10969, 1406, 1129, 33, 69, 1072537, 67, 83, 11715014111822521, 22, 11014, 68, 79, 85, 951481276027, 31, 71, 1126415014, 68, 8179, 84, 971526, 118, 2279, 95, 9764113, 13810024, 2864976, 11150694011383972232, 57, 131117, 139Golgi membranecytosolendoplasmic reticulum membranenucleoplasmearly endosome membraneGTF2F1 NUP210 GTF2H2 GTF2F2 NUP88 MNAT1 CTDP1 TAF13 TAF3 GTP PDCD6IPGTF2H5 TFIIDATP POLR2D TAF1 POLR2F PPip-S2,S5-POLR2A minus strand DNA (extending) ATP tRNA-Lysine3 HMGA1 NUPL2 POLR2B UBC(381-456) CCNH GTF2E1 Trimeric ENVprecursorRAN viral plus strand DNA with sticky 3' end CTDP1 Ran:GTPVPU (P05919) protein POLR2L UTP VPR CD4 GTF2H1 TCEA1 GTF2F1 minus strand DNA (extending) CHMP2B CCR5 POLR2A p6 (P04585) protein GTF2H4 GTF2E1 P-TEFb(CyclinT1:Cdk9) complexMultimeric matrix layer NELFCD tRNA-Lysine3 TAF10 POLR2F GTF2F2 capped HIV-1 pre-mRNA TAF12 capped HIV-1 pre-mRNA tRNA-Lysine3 RNGTT PR (Protease) (P04585) protein VPU (P05919) protein GTF2F1 p51 (RT) TFIIAREV (P04618) protein CCNT1 p6 (P04591) protein TAF5 POLR2K Surface protein gp120 GTF2F2 myristoylated Nef Protein (UniProt:P04601) GTP viral minus strand DNA (full-length) TBP POLR2D POLR2L POLR2G POLR2I GTF2H4 ERCC3 POLR2I POLR2C TAF3 POLR2I ERCC2 NCBP2 CTDP1 POLR2E GTF2H5 SSRP1 GAG-POL Polyprotein(P04585)UBC(609-684) CXCR4 BANF1 REV (P04618) protein POM121 HMGA1 POLR2H MNAT1 CCR5 GAG-POL Polyprotein(P04585)ADPTCEA1 ATP GTF2F1 UBB(77-152) NCBP1 ATP RTIN (Integrase) (P04585) protein TCEB3 GTF2F2 REV (P04618) proteinIN (Integrase) (P04585) protein Rev-multimer Transmembrane protein gp41 (P04578) p6 (P04591) protein Tat (P04608) GTF2F1 NELFE SSRP1 POLR2C p-S5-POLR2A GTF2A1(275-376) Tat (P04608) MNAT1 GTF2H5 tRNA-Lysine3 UBC(229-304) PR (Protease) (P04585) protein MA (P04591) protein POLR2G NUP35 GTF2E2 ERCC3 POLR2I POLR2D GTF2H5 GTP VPR Reverse transcriptase/ribonuclease H Reverse transcriptase/ribonuclease H SSRP1 XRCC6 GTF2H5 Host genomic DNA viral plus strand DNA with sticky 3' end POLR2J CCNH CTDP1 TAF1L POLR2K Multimeric capsid coat TAF2 TAF2 POLR2H ERCC3 POLR2E NUP98-3 CCNH GTF2F2 GTF2H2 GTF2H1 RTC with minussssDNA transferredto 3'-end of viralRNA templatePOLR2F MA (P04585) protein POLR2E TAF3 VIF (P69723) protein POLR2I MA (P04591) protein PPIA HIV-1 mRNA p6 (P04591) NELFCD MNAT1 GTF2H1 GTF2A2 GTF2F1 POLR2K POLR2J VPU (P05919) protein MA (P04585) protein TAF9B TAF6 XPO1POLR2C POLR2L POLR2I GTF2E1 Ran-GTPTCEB2 HIV-1 cappedpre-mRNA:CBC:RNAPol II(phosphorylated)complexGTF2H2 POLR2I AAAS p6 (P04591) protein PPIA ESCRT-IGTF2A1(1-274) viral minus strand DNA with sticky 3' end NELFCD HIV-1 transcriptioncomplex containing4-9 nucleotide longtranscriptPOLR2A GTF2A2 MA (P04585) protein NELFA POLR2J RTC with integrationcompetent viral DNAVPU (P05919) protein tRNA-Lysine3 MYS-CoAPOLR2G PPIA Multimeric matrix layer viral minus strand DNA with sticky 3' end POLR2D POLR2K UBB(1-76) VIF (P69723) protein PPIA p-S5-POLR2A POLR2I HIV-1 RNA template POLR2B NUP85 TAF4 POLR2L POLR2I UBC(609-684) MA (P04585) protein Multimeric capsidcoatp-SUPT5H RAN REV (P04618) protein NC (P04585) protein p6 (P04585) protein tRNA-Lysine3 Surface protein gp120 NUPL1-2 CDK9 p6 (P04591) protein POLR2L HIV-1 transcriptioncomplex containing9 nucleotide longtranscriptXPO1 CDK7 POLR2L TCEB3 UBC(609-684) CHMP7 PPIA MNAT1 p-SUPT5H GTF2F2 HIV-1 template:capped HIV-1 transcript hybrid VIF (P69723) protein NELFE VPR (P69726) protein RPS27A(1-76) RNGTT TBP GTF2H2 CCNH CDK9 POLR2I GTF2H5 NUP107 RTC with tRNAprimer:RNA templateELL GTF2B CCNH POLR2B TAF9B SUPT4H1 UBC(77-152) GTF2F1 UBC(1-76) POLR2L GTF2B Surface protein gp120 POLR2B viral plus strand DNA (full-length) POLR2I p51 (RT) UBC(609-684) Early elongationcomplex withseparated abortedtranscriptVPU (P05919) protein POLR2J REV (P04618) protein POLR2F CCNT1 MNAT1 TAF10 LIG1POLR2D POLR2L PSIP1 POLR2L TAF11 CTP HIV-1 RNA POLR2E TAF9B NC (P04585) protein CCNT1 PPIA CDK7 POLR2L SUPT4H1 POLR2G CDK9 ERCC3 NC (P04591) protein HIV-1 transcriptioncomplex containingextruded transcriptto +30p51 (RT) Tat (P04608) CTDP1 GTF2H3 POLR2L NTPPOLR2F CDK7 p6 (P04585) protein p51 (RT) SEH1L-2 CCNT2 UBB(153-228) p-SUPT5H NUP54 PPIA REV (P04618) protein GTF2H3 POLR2C CDK7 NELFB VPR TAF9 NELFE POLR2A HIV-1 abortedelongation complexafter arrestElongating HIV-1 transcript in processive Pol II mediated elongation GTF2H2 NUP214 GTF2F2 NUP98-5 ERCC3 REV (P04618) protein TCEB2 GTF2A2 POLR2F VPR TBP viral minus strand DNA (ful-length) POLR2F VPR (P69726) protein POLR2F UBB(77-152) p6 (P04591) protein TAF11 TBP POLR2C SUPT4H1 CHMP4C UBC(229-304) Ku proteins bound toviral DNACHMP7 POLR2L TCEB1 CCR5 HIV-1 mRNA GTF2A1(275-376) POLR2H PPIA MA (P04585) protein UBC(1-76) XRCC5 GTF2E1 POLR2K VIF (P69723) protein NELFCD POLR2D Tat:P-TEFb(CyclinT1:Cdk9) complexPOLR2I p6 (P04585) protein POLR2H POLR2D TAF9 POLR2L HIV-1 template DNAcontaining promoterwith transcript of 2 or 3 nucleotidesReverse transcriptase/ribonuclease H POLR2J GTF2F1 GTF2A2 CXCR4 POLR2D REV (P04618) protein Ku proteins bound toviral DNAPOLR2H GTF2H5 POLR2J p6 (P04585) protein CHMP4A GTF2B tRNA-Lysine3 HIV-1 template DNA:4-9 nucleotide transcript hybrid MA (P04591) protein IN (Integrase) (P04585) protein VPR (P69726) protein POLR2B p6 (P04585) protein p6 (P04591) protein p51 (RT) POLR2K capped HIV-1 pre-mRNA Multimeric matrix layer POLR2B POLR2E POLR2F POLR2H GTF2H2 POLR2K ADPGTF2F1 CHMP5 POLR2F NUP155 TCEA1 Surface protein gp120 (P04578) SUPT4H1 CDK9 POLR2J TFIIHSUPT4H1 NC (P04585) protein TAF11 TAF6 NELFCD PPIA RNGTT POLR2H BANF1 GTF2F2 TFIIDPOLR2A POLR2G POLR2G capped HIV-1 pre-mRNA POLR2F VPU (P05919) protein p-SUPT5H GTF2A1(275-376) DSIF:NELF:earlyelongation complexPOLR2K CTDP1 POLR2L POLR2I POLR2K MA (P04585) protein UBB(77-152) POLR2J POLR2C viral minus strand DNA (full-length) POLR2C Virion with gp41fusion peptide ininsertion complexXRCC6 GTF2H4 TAF1 POLR2K Multimeric capsid coat NELFCD GTF2F1 Reverse transcriptase/ribonuclease H p-SUPT5H Elongating HIV-1 transcript in processive Pol II mediated elongation GTF2H1 RPS27A(1-76) TAF13 GTF2F1 TAF3 POLR2K VIF (P69723) protein NUPL2 TCEB2 VPR (P69726) protein ERCC2 UTP TPR GTF2H5 GTF2F1 GTF2H4 ATP tRNA-Lysine3 TAF1L Reverse transcriptase/ribonuclease H VPR (P69726) protein Glycosylated Envelope glycoprotein gp160 p-S2,S5-POLR2A UBC(77-152) POLR2G POLR2L LIG4 Reverse transcriptase/ribonuclease H TAF1 TAF4 p51 (RT) GTF2F1 POLR2B CDK7 MA (P04591) protein NELFA VPU (P05919) protein POLR2C CTDP1 NELFCD POLR2L MA (P04591) protein NELF complexNCBP2 ERCC3 p6 (P04591) GTF2H1 POLR2G POLR2B p6 (P04585) protein POLR2K UBC(77-152) POLR2I Transmembrane protein gp41 TAF4B CDK7 ERCC3 GTF2H1 BANF1 capped HIV-1 pre-mRNA TAF11 myristoylated Nef Protein (UniProt:P04601) REV (P04618) protein POLR2A RAN POLR2F ERCC3 CTP POLR2K Surface protein gp120 (P04578) VPU (P05919) protein UBC(609-684) Multimeric capsid coat TAF9 POLR2E UTP GTF2H3 ATP Vps/Vta1tRNA-Lysine3 viral minus strand DNA (ful-length) VPR (P69726) protein TAF3 POLR2L SSRP1 BANF1minus sssDNA PR (Protease) (P04585) protein BANF1 POLR2E p6 (P04591) protein POLR2C CTP NUP35 POLR2J GTF2H2 TAF5 NELFB NC (P04585) protein IN (Integrase) (P04585) protein HIV-1 initiationcomplex withphosphodiester-PPiintermediateVIF (P69723) protein TAF6 POLR2J GTF2B POLR2F TFIIHPOLR2E XPO1 p6 (P04591) protein UBB(153-228) NELFA NELFB VIF (P69723) protein p6 (P04585) protein UTP CCNT1 GTF2H4 POLR2F Rev multimer-boundHIV-1 mRNAMA (P04591) protein CDK9 TCEB1 p51 (RT) ATP GTF2F1 viral minus strand DNA (initial) ELLHIV-1 elongationcomplexGTF2F2 TCEB1 TBP POLR2H VIF (P69723) protein POLR2A IN (Integrase)(P04585) proteinCap Binding Complex(CBC)GTF2E2 UTP POLR2C GTF2F2 CDK7 POLR2G ERCC2 TCEA1 NUP153 POLR2G GTF2H5 Multimeric matrix layer p51 (RT) SSRP1 ERCC3 MNAT1 CCNT1 PSIP1 POLR2I Virion withfusogenicallyactivated gp41capped HIV-1 pre-mRNA Transmembrane protein gp41 MA (P04585) protein POLR2D XPO1TCEB3 CCNT2 p-S5-POLR2A VPU (P05919) protein TCEB1 GTP CTDP1POLR2H POLR2H minus sssDNA TAF4 TAF9B MNAT1 Reverse transcriptase/ribonuclease H MA (P04591) protein TAF2 NUP62 Elongating HIV-1 transcript in processive Pol II mediated elongation UBC(381-456) POLR2J NUP98-3 TFIIEGTF2H2 CDK7 GTF2H4 GDP POLR2I POLR2K NCBP1 TAF10 UBC(533-608) tRNA-Lysine3 TCEA1 tRNA-Lysine3 NC (P04591) protein NCBP1 SUPT16H POLR2K TAF1L REV (P04618) protein REV (P04618) protein POLR2I POLR2D GTF2H1 NC (P04591) protein viral plus strand DNA (full-length) HIV-1 template DNA:30 nt transcript hybrid Surface protein gp120 (P04578) POLR2B POLR2E SUPT16H PiUBB(77-152) myristoylated Nef Protein (UniProt:P04601) TCEB2 REV (P04618) protein Tat (P04608) Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD andphospho-NELFTransmembrane protein gp41 (P04578) viral minus strand DNA (ful-length) GTF2F2 MA (P04591) protein ERCC2 POLR2K GTF2H2 POLR2B TAF11 GTF2H4 POLR2E NELFA p51 (RT) IN (Integrase) (P04585) protein POLR2C Elongating HIV-1 transcript prior to cleavage VPS37B POLR2A CTP POLR2B POLR2A NUP210 PPIA POLR2G p51 (RT) CD4POLR2C p-SUPT5H TAF2 NELFB POLR2J GTF2H4 TAF6 MA (P04585) protein TAF13 POLR2H VIF (P69723) protein POLR2I Tat (P04608) p-S2,S5-POLR2A tRNA-Lysine3 VIF (P69723) protein myristoylated NefProtein(UniProt:P04601)ERCC3 POLR2E viral minus strand DNA after ligation POLR2L POLR2D GTP POLR2K p-S2,S5-POLR2A GTF2E2 REV (P04618) protein POLR2G RTC without viralRNA templateTAF6 CD4 TCEB3 UBA52(1-76) VPU (P05919) protein p-SUPT5HPOLR2J tRNA-Lysine3 UBB(153-228) TAF10 IN bound to sticky3' ends of viralDNA in PICERCC2 NC (P04591) protein ATP POLR2C POLR2G POLR2F TCEA1 p-S5-POLR2A N-myristoyl GAG (P04591) protein GTF2F2 POLR2B POLR2I VPU (P05919) protein minus strand DNA (extending) VPU (P05919) protein POLR2B Trimeric gp120:gp41oligomerGTF2H3 POLR2F GTF2H3 POLR2G minus sssDNA VPS4B TAF9 POLR2C GTF2H3 BANF1 UTP p-S2,S5-POLR2A CCNT1 GTF2H4 RNAPolymeraseII(unphosphorylated):TFIIF complexVPU (P05919) protein NC (P04585) protein TAF4 CCNH UBC(77-152) Rev-multimer HMGA1 IN (Integrase) (P04585) protein GTF2B GTF2F1 ERCC3 minus sssDNA TAF13 GTF2F2 GTF2B TAF5 POLR2E UBC(305-380) GTP GTF2F1 POLR2F CDK9 REV (P04618) protein NELFCD p-SUPT5H POLR2B Transmembrane protein gp41 POLR2I PR (Protease) (P04585) protein GTF2H3 POLR2K GTF2A1(1-274) RAE1 p-S2,S5-POLR2A ATP dGTP p6 (P04585) protein POLR2C VPR viral plus strand DNA (full-length) UBC(381-456) REV (P04618) protein PSIP1 POLR2B POLR2L PR (Protease) (P04585) protein HIV-1 Tat-containingprocessiveelongation complexVPU (P05919) protein MA (P04585) protein POLR2L RNGTTVIF (P69723) protein Reverse transcriptase/ribonuclease H NELFB myristoylated NefProtein(UniProt:P04601)VPS28 POLR2B TCEB1 GTF2F1 POLR2C CD4 PPIA HIV-1 template DNA:3 nucleotide transcript hybrid p6 (P04591) protein TAF2 VPU (P05919) protein RNAPolymeraseII(unphosphorylated):TFIIF complexNMT2POLR2J CTDP1 other viral genomicRNACCR5, CXCR4LIG4 NCBP1 POLR2F SUPT16H GTF2H1 POLR2C TAF3 UBB(1-76) myristoylated Nef Protein (UniProt:P04601) CHMP2A HIV-1 RNA template p6 (P04585) SUPT16H POLR2H PR (Protease) (P04585) protein GTP GTF2H2 GTF2F1 POLR2I POLR2F GTF2H5 GTP NUP43 NUP160 POLR2K viral minus strand DNA (initial) SUPT16H XRCC5 TAF13 SUPT16H POLR2H GTF2E2 SSRP1 p-S2,S5-POLR2A CD4 REV (P04618) protein POLR2G POLR2H GTF2H5 NELFB GTP GTF2H3 POLR2E POLR2J minus strand DNA (extending) HIV-1 Tat-containingaborted elongationcomplex afterarrestHIV-1 elongationcomplex containingTatCDK9 ERCC2 POLR2I MA (P04591) protein SUPT4H1 CTP POLR2E POLR2A VPR POM121 GAG-POL Polyprotein (P04585) POLR2G POLR2J POLR2B GTF2F1 Reverse transcriptase/ribonuclease H ELL CCNH RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complexHMGA1 MA (P04591) protein GTF2F1 POLR2I XRCC6 GTP VPU (P05919) protein CCNT1 genomic DNA with staggered 5' ends TAF5 POLR2G p6 (P04585) NUP153 TAF1 PIC (PreIntegrationComplex)GTF2H5 POLR2K p6 (P04591) protein TAF11 POLR2L POLR2B CDK9 GTF2H2 POLR2C POLR2E NUP62 POLR2D TAF10 IN:viral DNA boundto host genomic DNAwith staggered endsCTDP1 N-myristoyl GAG CXCR4 tRNA-Lysine3 PPIASUPT16H myristoylated Nef Protein (UniProt:P04601) SUPT4H1 HIV-1 mRNA TAF12 p6 (P04591) TAF4B GTF2A1(275-376) HIV-1 RNA template TAF5 POLR2B PSIP1 REV (P04618) protein POLR2H GTF2A1(1-274) NEDD4L Rev-multimer NCBP2 HIV-1 transcriptioncomplex containingtranscript to +30POLR2I POLR2E GTF2H4 Viral coresurrounded byMatrix layerTAF4B minus sssDNA Multimeric capsid coat POLR2C TCEB2 Ran GTPase:GDPTCEB3 POLR2E MA (P04591) protein GTF2H1 POLR2E viral second strand DNA with plus sssDNA (extending) POLR2E N-myristoyl GAG(P04591) proteinNELFA POLR2D VPR (P69726) protein NELFE Spliced Env mRNAUBC(153-228) p6 (P04585) protein NC (P04591) protein Tat (P04608) VPR ERCC2 POLR2K viral PIC proteinsPOLR2I HIV-1 template DNA:4 nucleotide transcript hybrid Assembling HIVvirionGTF2F1 TAF10 RANBP2 MA (P04585) protein p-S2,S5-POLR2A NTPCCNH myristoylated Nef Protein (UniProt:P04601) MNAT1 Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTDUBC(1-76) POLR2E TCEB2 CHMP3 CCNH NUP214 NC (P04585) protein POLR2I REV (P04618) protein NELFB ELL TAF1L NUP85 TCEB2 p-SUPT5H GTF2F1 viral PIC proteinsGTF2F2 CoA-SHNCBP2 NELFA Host genomic DNASSRP1 GTF2H3 GTF2H3 p6 (P04591) protein POLR2J MA (P04585) protein NUP155 UBB(1-76) POLR2K POLR2G TAF11 VIF (P69723) protein GTF2H5 NELFA POLR2H TCEB2 HIV-1 transcriptioncomplex containing11 nucleotide longtranscriptGTF2F1 UBC(381-456) GTF2E2 REV (P04618) protein VPR viral minus strand DNA (ful-length) CDK7 POLR2I POLR2I CCNH POLR2B HIV-1 transcriptioncomplexTAF4 UBB(153-228) IN (Integrase) (P04585) protein GTF2H3 UTP Reverse transcriptase/ribonuclease H ERCC3 tRNA-Lysine3 POLR2A REV (P04618) protein viral plus strand DNA (full-length) GTF2H1 CTDP1 NCBP2 VPU (P05919) protein Elongating HIV-1 transcript in processive Pol II mediated elongation POLR2D TAF3 IN (Integrase) (P04585) protein tRNA-Lysine3 CTDP1 REV (P04618) protein CD4 GTP POLR2D TCEB1 UBA52(1-76) GTF2H1 p6 (P04591) protein ELL MA (P04585) protein GTF2E1 UBC(305-380) POLR2E PPiGTF2F2 GTF2F2 POLR2A viral plus strand DNA with sticky 3' end NELFE POLR2E p6 (P04591) NELFE TAF1 NELFB UBC(229-304) NCBP1 CHMP4B TAF12 HIV-1 template:capped HIV-1 transcript hybrid NUP188 NELFB ESCRT-IIIReverse transcriptase/ribonuclease H UTP Elongating HIV-1 transcript prior to separation N-myristoyl GAG (P04591) protein Trimeric gp120:gp41oligomerPOLR2L p6 (P04585) protein PR (Protease) (P04585) protein p6 (P04585) protein p6 (P04591) protein p6 (P04591) NC (P04585) protein CCR5 TAF9B Tat-containing earlyelongation complexwithhyperphosphorylatedPol II CTD (phospho-NELFphospho DSIF)TAF13 POLR2B TAF2 VIF (P69723) protein POLR2C GTF2A1(275-376) GTF2A1(275-376) POLR2K Virion with CD4bound to gp120TAF9 TAF9B tRNA-Lysine3Rev multimer-boundHIV-1 mRNA:CRM1complexRANBP1UBC(533-608) p6 (P04591) protein POLR2G GTF2H1 TAF11 POLR2L POLR2I TAF2 PPIA MA (P04591) protein CDK7 ERCC2 POLR2H TCEB3 1-LTR form ofcircular viral DNATFIIATCEA1 POLR2D GTP TCEA1 CDK9 CCNH GTF2A1(1-274) monoubiquitinatedN-myristoyl GAG(P04591) proteinmyristoylated Nef Protein (UniProt:P04601) p6 (P04591) protein POLR2H GTF2F2 SUPT4H1 viral plus strand DNA with sticky 3' end CTDP1 POLR2E RNAPolII(hypophosphorylated) complex bound to DSIF proteinPOLR2I p-SUPT5H TBP PSIP1 POLR2K Virion with gp41exposedPOLR2I NELFE PPiREV (P04618) protein CDK9 TFIIHp6 (P04591) protein p-S5-POLR2A GTF2A2 CDK9 MA (P04591) protein POLR2I p6 (P04585) protein IN (Integrase) (P04585) protein GTF2H2 p6 (P04585) protein HIV-1 template DNA:30 nt transcript hybrid NTPBANF1 CTP POLR2D POLR2J POLR2B GTF2E2 NEDD4LPOLR2K POLR2A p-NELFE MA (P04591) protein POLR2F ERCC3 NELFA POLR2K Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPUBC(533-608) ELL POLR2G POLR2K POLR2J TAF2 GTF2H3 GTF2H2 GTF2F2 TAF2 p-SUPT5H POLR2K GTF2E1 KPNA1 capped HIV-1 pre-mRNA p6 (P04585) protein TAF6 GTF2A2 GTF2A1(275-376) POLR2D POLR2J CCNH GTF2H3 p-S2,S5-POLR2A CHMP2B NUP50 TSG101 POLR2F Nucleocapsidminus sssDNA Vpr:importin-alphacomplexAutointegrated viralDNA as an invertedcircleCDK7 RNAPolymeraseII(unphosphorylated):TFIIF complexGTF2F2 POLR2D POLR2K tRNA-Lysine3 VPR (P69726) protein POLR2B GTF2F1 Rev-multimer p-SUPT5H MA (P04591) protein TAF4B POLR2A CD4 POLR2C MA (P04585) protein POLR2L P-TEFb complexImmature HIV virionRTC with extendingminus strand DNATAF10 viral second strand DNA (plus sss) POLR2F GTF2H4 CCNH POLR2L p6 (P04591) protein RNAPolymeraseII(unphosphorylated):TFIIF complexp-SUPT5H ERCC2 GTF2F1 VIF (P69723) protein Tat (P04608) RANBP2 CCNT1 PDCD6IP POLR2H CCNH Reverse transcriptase/ribonuclease H ERCC2 POLR2H POLR2L ERCC3 POLR2J Nuclear Pore Complex(NPC)GTP RNA Pol II withphosphorylated CTD:CE complex withactivated GTp-S5-POLR2A Rev-multimerPOLR2J minus sssDNA GTF2H3 RPS27A(1-76) VPR TTP GTP p-NELFE POLR2G VPU (P05919) protein POLR2G REV (P04618) protein NELFCD UBB(1-76) NUP205 IN (Integrase) (P04585) protein POLR2H POLR2K NC (P04585) protein GTF2F1 POLR2H POLR2L GTF2B GTF2H1 UBC(305-380) NELFCD CCNH GTF2F1 TCEB1 ERCC3 Tat (P04608) UBC(229-304) UBC(305-380) p-SUPT5H REV (P04618) protein HMGA1 CTP POLR2B SSRP1 POLR2I TAF13 VPU (P05919) protein POLR2E VPS37D RPS27A(1-76) TAF6 GTF2A2 p51 (RT) POLR2K GTF2H5 GTF2A2 NC (P04585) protein HIV-1 earlyelongation complexwithhyperphosphorylatedPol II CTDVPR (P69726) protein GTF2H2 SUPT4H1 IN (Integrase) (P04585) protein RCC1POLR2F TAF4 ERCC3 UBA52(1-76) HIV-1 template:capped HIV-1 transcript hybrid PPiPOLR2B ERCC3 TCEB3 POLR2I POLR2E VIF (P69723) protein POLR2L VPR (P69726) protein GTF2H5 UBC(153-228) NELFE ERCC2 Transmembrane protein gp41 (P04578) viral RNA template extensively digested except in PPT region PSIP1 ERCC2 NELFA NUP98-4 POLR2B POLR2D CDK9 p6 (P04585) TBP POLR2B viral RNA template degraded by RNase-H (initial) POLR2I tRNA-Lysine3 viral minus strand DNA (ful-length) POLR2L POLR2C GTF2F1 GTF2H5 Virion with exposedcoreceptor bindingsitesUBC(457-532) NUP50 TCEA1 GTF2F1 POLR2E GTF2H2 p6 (P04585) SUPT4H1 CTP MNAT1 HIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end POLR2F POLR2H SUPT16H Surface protein gp120 IN (Integrase) (P04585) protein NUP205 POLR2J REV (P04618) protein POLR2F p-S2,S5-POLR2A VIF (P69723) protein HIV-1 template DNA:30 nt transcript hybrid CTP POLR2H GTF2H1 GTF2A1(1-274) CCNT1 NELFA POLR2B p-SUPT5H CD4 CTDP1 TFIIHREV (P04618) proteinPPIA UBC(533-608) POLR2G IN (Integrase) (P04585) protein TAF1L CDK7 POLR2E POLR2F GTP GTF2A1(275-376) POLR2K Virion BuddingComplexIN (Integrase) (P04585) protein GTF2F2 VIF (P69723) protein GTF2H4 IN (Integrase) (P04585) protein POLR2J MA (P04591) protein p51 (RT) NUP98-4 NELFA NELFCD POLR2F Multimeric capsid coat NELFE MA (P04591) protein GTF2F1 POLR2C REV (P04618) protein TBP GTF2H4 POLR2L POLR2I POLR2L PR (Protease) (P04585) protein GTF2A2 MNAT1 GTF2H4 GTF2F1 GTF2E2 p6 (P04591) protein NC (P04591) protein VIF (P69723) protein MA (P04591) protein Reverse transcriptase/ribonuclease H p51 (RT) REV (P04618) protein TAF1 Reverse transcriptase/ribonuclease H GTF2H3 POLR2E CCNT1 VPU (P05919)TSG101 NUP43 p51 (RT) viral PIC proteinsNELFB UTP Reverse transcriptase/ribonuclease H TAF12 POLR2H p-SUPT5H GTF2F2 VPRATP POLR2F ERCC2 HIV-1 pausedprocessiveelongation complexVPU (P05919) protein TAF4 p-S5-POLR2A VPU (P05919) protein POLR2C CTP Multimeric matrix layer p-SUPT5H GTF2F1 VPR p6 (P04585) protein NCBP1 TAF12 HIV-1 template:capped HIV-1 transcript hybrid TAF9 RNAPolymeraseII(unphosphorylated):TFIIF complexHMGA1 HIV-1 template DNA:30 nt transcript hybrid p6 (P04591) protein GTF2H2 TAF1 PPIATCEB3 CHMP6 REV (P04618) protein GTF2H5 VIF (P69723) protein NELFCD POLR2K p-S5-POLR2A UBC(77-152) POLR2C ELL UBC(153-228) N-myristoyl GAG POLR2D p-S5-POLR2A p51 (RT) POLR2G POLR2D POLR2H MNAT1 NC (P04591) protein TAF1L CDK7 SSRP1 VPU (P05919) protein TAF6 TAF6 RAE1 POLR2J POLR2K POLR2B GTF2A1(1-274) IN (Integrase) (P04585) protein POLR2F POLR2L POLR2G FEN1PSIP1 HIV-1 mRNATransmembrane protein gp41 POLR2H NELFA POLR2J ERCC2 UBC(457-532) TAF3 CCNH BANF1 VPU (P05919) protein IN (Integrase) (P04585) protein GTF2F2 ERCC2 PPIA POLR2C HIV-1 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end GTF2H3 p-S2,S5-POLR2A AAAS p51 (RT) Elongating HIV-1 transcript in processive Pol II mediated elongation CHMP5 NELFE CDK9 VPU (P05919) protein VPR (P69726) protein VPU (P05919) protein viral second strand DNA with plus sssDNA (discontinuous) Reverse transcriptase/ribonuclease H POLR2K SUPT4H1 POLR2E IN (Integrase) (P04585) protein SUPT4H1 VPU (P05919) protein GTF2H3 PSIP1POLR2G RTC with extensiveRNase-H digestionIN (Integrase) (P04585) protein HIV-1 RNA Transmembrane protein gp41 POLR2G NELFB ERCC3 CTDP1 viral plus strand DNA after ligation POLR2F POLR2G GTF2H1 viral minus strand DNA (full-length) ERCC3 NELFCD HIV-1 RNA GTPSUPT4H1 p-SUPT5H NELFB viral minus strand DNA (ful-length) Reverse transcriptase/ribonuclease H RTC with duplex DNAcontainingdiscontinuous plusstrand flapUBC(457-532) Integrated provirusMA (P04591) protein ATP VPS37A UBB(153-228) MNAT1 POLR2J UBC(305-380) CHMP2A UBC(229-304) p51 (RT) NC (P04591) protein POLR2J VPR (P69726) protein SUPT4H1 CDK9 GTF2H1 GTF2H2 POLR2A IN (Integrase) (P04585) protein MNAT1 TAF4 p-S2,S5-POLR2A CDK7 p51 (RT) VPS37A GTF2H4 POLR2D VIF (P69723) protein POLR2B VPR (P69726) protein POLR2F MA (P04585) protein TAF12 UBA52(1-76) GTF2F2 RTTAF9 NUP133 CXCR4 POLR2A viral minus strand DNA with sticky 3' end UTP PPIA GTF2F2 ATP UBC(1-76) POLR2C RAN POLR2A Transmembrane protein gp41 GTF2F2 VPR (P69726) protein Rev-multimer NELFE VPS28 POLR2C Reverse transcriptase/ribonuclease H TCEB2 REV (P04618) protein REV (P04618) protein POLR2G POLR2L p6 (P04585) protein POLR2K UBC(457-532) TAF3 CDK7 TCEA1 UTP HIV-1 template:capped HIV-1 transcript hybrid viral plus strand DNA (full-length) minus sssDNA ATPviral plus strand DNA (full-length) POLR2F MNAT1 TCEB2 VPS37D GTP N-myristoyl GAG (P04591) protein VPS4A POLR2J NELFA IN (Integrase)(P04585) proteinCCNH TCEA1 IN (Integrase) (P04585) protein HIV-1 arrestedprocessiveelongation complexMultimeric capsid coat SUPT4H1 POLR2I HIV-1 closedpre-initiationcomplexHIV-1 template DNA hybrid with phosphodiester-PPi intermediate Tat (P04608)NCBP1 REV (P04618) protein XRCC5 p51 (RT) POLR2J CHMP4A POLR2G POLR2G GTF2H5 Reverse transcriptase/ribonuclease H ERCC3 NELFB NELFCD FURINPOLR2C SEH1L-2 SUPT16H NCBP2 CTDP1 viral DNA bound withIntegrase in PICp51 (RT) p6 (P04585) protein POLR2C TCEB3 TAF6 p6 (P04585) protein UBC(381-456) GTF2F2 RTC with minusstrand DNAsynthesis initiatedfrom 3'-endGTF2F2 GTF2H3 CCNT1 Envelope glycoprotein gp160 TCEB3 GTF2H2 POLR2C CCNT1 GTF2H1 NELFA Cap Binding Complex(CBC)MatrixPOLR2F minus sssDNA TAF4B POLR2I MA (P04591) protein TBP CTDP1 Surface protein gp120 TFIIHVPR GTF2H2 MA (P04585) protein Multimeric matrix layer TCEB3 UBC(457-532) UBC(153-228) p-SUPT5H REV (P04618) protein viral RNA template degraded by RNase-H (initial) GTF2H4 HIV-1 template DNAwith firsttranscriptdinucleotide,opened to +8positionHMGA1POLR2K Transmembrane protein gp41 POLR2F RNMT p-NELFE GTF2E1 POLR2F PPiMNAT1 TAF5 VIF (P69723) protein Nef Protein(UniProt:P04601)GTF2H4 GTF2H3 viral minus strand DNA (ful-length) CDK7 Elongin ComplexGTF2E1 CTDP1 p6 (P04591) protein tRNA-Lysine3 POLR2G RPS27A(1-76) Reverse transcriptase/ribonuclease H HIV-1 RNA Elongating HIV-1 transcript in processive Pol II mediated elongation p6 (P04585) protein MA (P04591) protein VIF (P69723) protein ELL TAF5 Multimeric capsid coat GTF2F1 GTF2F2 VPR ERCC2 HIV-1 processiveelongation complexNELFB viral plus strand DNA with sticky 3' end p6 (P04585) protein XPO1 POLR2C VPU (P05919)NELFCD CCNH ELL UBB(153-228) CCNH POLR2F POLR2A p6 (P04585) protein DSIF:NELF:earlyelongation complexafter limitednucleotide additionGTF2A2 POLR2D POLR2L p6 (P04591) protein VPR RNAPolII(hypophosphorylated):capped pre-mRNA complexCDK7 GTF2F1 XRCC5 VPU (P05919) protein Multimeric matrix layer POLR2E GTF2A1(1-274) POLR2D POLR2C GTF2H4 GAG-POL Polyprotein (P04585) POLR2D POLR2D POLR2D TCEB3 NCBP1 POLR2G Reverse transcriptase/ribonuclease H PPIA GTF2H4 POLR2J MA (P04585) protein Ran-GDPPOLR2H CCNH GTF2BUBC(153-228) Reverse transcriptase/ribonuclease H GAG Polyprotein(P04591)POLR2D RTC with extendingsecond-strand DNAGTF2A1(1-274) SUPT4H1 CTP MNAT1 XRCC4:LIG4POLR2K UbIN (Integrase) (P04585) protein myristoylated Nef Protein (UniProt:P04601) TAF9B HIV-1 openpre-initiationcomplexCCNT2 HMGA1 Autointegrated viralDNA as smallercirclesPOLR2H dCTP FACT complexPOLR2L POLR2F SSRP1 CCR5 p6 (P04591) protein REV (P04618) protein IN bound to sticky3' ends of viralDNA in PICUBA52(1-76) VIF (P69723) proteinGTF2H3 HIV-1 RNA template BANF1 IN (Integrase) (P04585) protein p6 (P04591) protein VIF (P69723) protein NELFCD VIF (P69723) protein Host genomic DNA REV (P04618) protein VPR GTF2E1 CCNT1 POLR2C UBB(1-76) MA (P04585) protein GTF2H5 POLR2B viral minus strand DNA with sticky 3' end GTF2F1 POLR2J POLR2I Rev-multimerPOLR2H POLR2K Reverse transcriptase/ribonuclease H POLR2F VTA1 MA (P04585) protein GTF2F1 GTF2F2 Multimeric capsid coat POLR2L p-SUPT5H p6 (P04591) protein Transmembrane protein gp41 UBC(457-532) TCEA1HIV-1 template DNA:11 nucleotide transcript hybrid p51 (RT) viral plus strand DNA (full-length) RAN REV (P04618) protein UBC(533-608) POLR2C CCNH PPIA POLR2C ERCC2 RAN NUP37 GTP POLR2C TCEB1 GTF2F2 ATP HIV-1 template DNA:9 nucleotide transcript hybrid GTF2H2 p-SUPT5H Rev multimer-boundHIV-1mRNA:Crm1:Ran:GTPGTF2H4 POLR2F POLR2E DSIF complexELL NUP88 POLR2D NC (P04591) protein POLR2H REV (P04618) protein HIV-1 template:capped HIV-1 transcript hybrid Tat (P04608) POLR2D HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotides POLR2J ERCC2 HIV-1 RNA template RAN GTF2H5 NC (P04585) protein ERCC3 POLR2J POLR2E HIV-1PolymeraseII(phosphorylated):TFIIF:capped pre-mRNANUP93 CCR5 POLR2H UTP POLR2B GTF2F2 TAF10 TAF9B TCEB2 HIV-1 initiationcomplexPOLR2F POLR2J CTP Reverse transcriptase/ribonuclease H POLR2D RNAPolymeraseII(unphosphorylated):TFIIF complexPOLR2B HIV-1 PromoterEscape Complexuncoated viralcomplexPOLR2E GTF2E2 GTF2F1 GTF2H3 GTF2H3 HIV-1 mRNA PPIA HIV-1 RNA Virion withCD4:gp120 bound toCCR5/CXCR4NELFE SUPT16H NCBP2 NUP37 POLR2E GTF2F1 p6 (P04591) protein HIV-1 RNA template GTF2H1 MA (P04585) protein Nup45 POLR2G TBP viral plus strand DNA (full-length) POLR2F PPimonoubiquitinatedN-myristoyl GAG(P04591) proteinp6 (P04585) protein PPIA NELFCD NELFE tRNA-Lysine3 Envelopeglycoprotein gp160POLR2I TAF13 HIV-1 unspliced RNARTC with minussssDNA:tRNAprimer:RNA templateGTF2H4 ERCC2 POLR2C TAF12 XRCC4 HIV-1 mRNA VPU (P05919) protein GTF2H4 p6 (P04585) protein POLR2L CD4:Env gp120/gp41hairpincomplex:CCR5/CXCR4TAF5 NTPTAF12 tRNA-Lysine3 MA (P04585) protein POLR2C POLR2G POLR2E TAF12 MNAT1 POLR2J IN (Integrase) (P04585) protein CTDP1 GTF2H1 TCEB2 HIV-1 RNA POLR2D RANGAP1GTF2A1(1-274) POLR2G VPS37C POLR2D REV (P04618) protein POLR2H CHMP4B VPU (P05919) protein UBC(381-456) GTF2H5 POLR2J Encapsidated viralcoreVIF (P69723) protein TAF4 POLR2J POLR2E Trimeric ENVprecursorNUP107 UBC(1-76) GTF2H2 VIF (P69723) protein POLR2K tRNA-Lysine3 GTF2F2 POLR2E ERCC2 VIF (P69723) protein HIV-1 RNA template POLR2H POLR2G POLR2D XPO1 minus sssDNA POLR2G MA (P04591) protein TAF4B POLR2F XRCC5:XRCC6viral RNA template being digested by RNase-H (extensive) POLR2D NMT 1VPU (P05919) protein PR (Protease) (P04585) protein GTF2A1(1-274) HIV-1 RNA template VPR VTA1 MNAT1 NELFCD PPIA VPS4A CDK9 Reverse transcriptase/ribonuclease H NC (P04591) protein Multimeric matrix layer p-S5-POLR2A MA (P04585) protein HIV-1 transcriptioncomplex containing3 nucleotide longtranscriptPPIA RANBP1VPS37C REV (P04618) protein TCEB1 POLR2D POLR2E POLR2D IN (Integrase) (P04585) protein p-S2,S5-POLR2A VPR (P69726) protein TAF1 TAF9 SUPT4H1 CXCR4 POLR2E HIV-1 mRNA PR (Protease)(P04585) proteinPOLR2E TAF4B RTC with degradedRNA template andminus sssDNAHMGA1 p6 (P04585) protein IntegrationintermediateCTDP1 POLR2B NELFA HIV-1 template DNA:30 nt transcript hybrid VPR p-S2,S5-POLR2A ERCC2 NELFE ADPPOLR2B SUPT4H1 myristoylated Nef Protein (UniProt:P04601) TCEB3 CDK9 CXCR4 TAF5 CCNT2 CCR5 CCNT1 p-SUPT5H Surface protein gp120 TAF1 NUP98-5 CDK7 MNAT1 ELL p-S5-POLR2A POLR2B TAF1 MA (P04585) protein POLR2B NELFCD POLR2I POLR2L NELFA TCEB1 2-LTR form ofcircular viral DNAElongating HIV-1 transcript in processive Pol II mediated elongation POLR2I POLR2J CCNT1 MNAT1 CCNH POLR2F tRNA-Lysine3GTF2H3 ELL TCEA1 POLR2G IN (Integrase) (P04585) protein GTF2H2 POLR2J PiPOLR2H POLR2I p-S2,S5-POLR2A NC (P04591) protein POLR2C VPR HIV-1 Tat-containingarrested processiveelongation complexTat (P04608) POLR2B TCEB2 TAF9 ERCC3 MNAT1 GTF2F2 TAF1L p51 (RT) POLR2H ATP Tat (P04608) GTF2H1 POLR2L CHMP4C Tat-containingelongation complexprior to separationPOLR2G NELFE RNMTP-TEFb(CyclinT1:Cdk9)-containingelongation complexwith separated anduncleavedtranscriptPOLR2F VIF (P69723) protein CDK7 GTF2F2 UBC(533-608) POLR2D SUPT16H NELFB GTF2BVPU (P05919) protein POLR2C POLR2E GTF2H5 TAF10 GTF2H2 POLR2E viral RNA template extensively digested except in PPT region ELL HIV-1 templateDNA:4-9 nucleotidetranscript hybridMA (P04591) protein CTP IN (Integrase) (P04585) protein POLR2H NCBP2 RPS27A(1-76) POLR2G POLR2K VIF (P69723) protein TCEB1 NELFCD POLR2K HIV-1 template DNA with first transcript dinucleotide, opened to +8 position CCNH HIV-1 template DNA:30 nt transcript hybrid POLR2K CCNT2 NCBP1 Multimeric capsid coat POLR2I PPIA GTF2E1 RTC with nickedminus sssDNA:tRNAprimer:RNA templateTAF3 REV (P04618) protein GTF2A1(275-376) viral plus strand DNA (full-length) NELFA GTF2H1 SSRP1 p51 (RT) VPU (P05919) protein ERCC2 Reverse transcriptase/ribonuclease H REV (P04618) protein VIF (P69723) protein ERCC2 POLR2B XPO1 GTF2H4 viral minus strand DNA (ful-length) CCNH Surface protein gp120 p6 (P04585) protein NELFB VIF (P69723) protein PPIA GTF2F2 viral plus strand DNA (full-length) Transmembrane protein gp41 RTC with annealedcomplementary PBSseqments in +sssDNAand -strand DNACDK7 POLR2L ERCC2 CDK7 Nup45 POLR2H VPR POLR2E POLR2F POLR2L UBC(305-380) p-SUPT5H POLR2G MA (P04585) protein GTF2H5 TFIIHNCBP2 TAF5 p51 (RT) VPU (P05919)IN (Integrase) (P04585) protein MNAT1 POLR2J POLR2E GTF2E2 POLR2L TAF12 POLR2D HMGA1 GTF2F1 VIF (P69723) protein GTP HIV-1 transcriptioncomplex containing4 nucleotide longtranscriptVPU (P05919) protein CTP NC (P04585) protein GTF2F2 CHMP6 p6 (P04585) protein UBC(153-228) p-S2,S5-POLR2A myristoylated Nef Protein (UniProt:P04601) GTF2F1 POLR2H CDK9 GTF2F1 GTF2F2 TCEB1 MNAT1 TAF9 PR (Protease) (P04585) protein MNAT1 REV (P04618) protein BANF1 CCNT2 POLR2B TAF9B TAF4 MA (P04585) protein CDK7 POLR2G CCNH POLR2D GTF2F2 POLR2B GTP POLR2B tRNA-Lysine3 GTF2E1 POLR2H VPS4B POLR2C POLR2I VPR CDK7 p6 (P04591) protein Multimeric matrix layer POLR2L NELFA Revmultimer-boundHIV-1mRNA:Crm1:Ran:GTP:NPCPOLR2B PPIA NELFB TAF9B UBC(609-684) POLR2K POLR2K SUPT16H minus sssDNA POLR2K IN (Integrase) (P04585) protein ATPTFIIEGTF2H5 GTF2H4 TAF4B VIF (P69723) protein RTC (ReverseTranscriptionComplex) with RNAtemplateMA (P04591) protein IN (Integrase) (P04585) protein POLR2E POLR2K TAF11 POLR2L GTF2F1 p6 (P04591) protein IN (Integrase) (P04585) protein POLR2B PPIA NUPL1-2 NTPTAF10 GTF2F2 CTDP1 GTF2H3 GTF2H1 POLR2H POLR2C MA (P04585) protein HIV-1 RNA POLR2J POLR2A POLR2D IN (Integrase) (P04585) protein NELFA POLR2F PSIP1 NC (P04591) protein p6 (P04585) protein POLR2H ERCC2 CCNH HIV-1 RNA POLR2I UBC(229-304) POLR2L PPIA NELFB GTP SUPT4H1 REV (P04618) protein p-S5-POLR2A Surface protein gp120 NUP133 POLR2J p6 (P04585) CDK7 GTF2H1 viral plus strand DNA (full-length) TAF13 GTF2H5 ERCC3 minus strand DNA (extending) POLR2C UBC(77-152) POLR2C NUP93 GTF2H2 TAF4B GTF2H3 VPR (P69726) protein Surface protein gp120 VPS37B CDK9 UTP POLR2J tRNA-Lysine3 TAF1L POLR2G GTF2H2 UTP HIV-1 RNA MA (P04591) protein TAF1L RAN POLR2H GTF2F2 POLR2J POLR2L ERCC3 NELFE GTF2F2 NELFCD ERCC2 POLR2D CTP POLR2C IN (Integrase) (P04585) protein VIF (P69723) protein SUPT16H viral minus strand DNA with sticky 3' end GTF2H2 ATP POLR2G UBC(1-76) NELFB GTF2H3 HIV-1 RNA template GDPSurface protein gp120 NELFE NC (P04585) protein Aborted HIV-1 earlyelongation complexmyristoylated Nef Protein (UniProt:P04601) viral second strand DNA with plus sssDNA (extending) CXCR4 POLR2F POLR2J GTF2F2 GTF2F2 NELFA HIV-1 mRNA POLR2B VIF (P69723) protein NTPPOLR2B UBB(1-76) GTF2F1 GTF2F2 XRCC6 HIV-1 transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30GTF2F2 SUPT4H1 TFIIHNUP188 CE:Pol II CTD:Spt5complexPOLR2D ATPGTF2H4 CCNT1 POLR2E genomic DNA with staggered 5' ends Rev-multimer RANBP1 CDK7 PR (Protease) (P04585) protein dATP Reverse transcriptase/ribonuclease H MNAT1 p6 (P04591) protein GTF2H5 GTF2E2 POLR2D GTF2A1(275-376) p51 (RT) p6 (P04591) protein IN (Integrase) (P04585) protein TAF1L NELFB UTP GDP GTF2F1 ERCC3 NELFB CCNT1 p51 (RT) HIV-1 Tat-containingpaused processiveelongation complexREV (P04618) protein VPU (P05919) protein CDK7 dNTPRNA Pol II withphosphorylated CTD:CE complexPOLR2G GTF2F1 POLR2L p51 (RT) NUP54 TPR NELFA GTF2H4 Transmembrane protein gp41 GTF2E2 GTP CTDP1 CDK9 POLR2A UBB(77-152) POLR2J PSIP1 POLR2H VPU (P05919) protein Virion with gp41forming hairpinstructureCTDP1 SSRP1 POLR2B POLR2H Multimeric capsid coat UBB(77-152) POLR2E POLR2G NELFE GTF2F2 CHMP3 p-SUPT5H GTF2F1 VIF (P69723) protein VPR HIV-1 RNA homodimerPPiPPIA TCEB1 GTF2H1 VPU (P05919) protein SUPT4H1 CD4 POLR2I Rev-bound HIV-1 mRNAp6 (P04585) protein capped HIV-1 pre-mRNA UBA52(1-76) CCNT1 Mature HIV virionMA (P04585) protein XRCC4 monoubiquitinatedN-myristoyl GAG(P04591) proteinMA (P04591) protein TAF11 TAF4B viral PIC proteinsGTF2H1 TAF13 ERCC3 GTF2H1 GTF2F1 CCNT1 NUP160 REV (P04618) protein SSRP1 POLR2D CCNT2 POLR2H GTF2F2 Elongating HIV-1 transcript in processive Pol II mediated elongation SUPT4H1 POLR2C Host genomic DNA TAF2 POLR2D POLR2H IN (Integrase) (P04585) protein viral DNA:Kuproteins:XRCC4:DNAligase IV complex1175861, 93, 1459061, 93, 14561, 93, 14561, 93, 14511961, 93, 14561, 93, 1459061, 93, 14515974, 101, 129, 13274, 101, 129, 13272, 114, 142


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.

Try the New WikiPathways

View approved pathways at the new wikipathways.org.

Quality Tags

Ontology Terms

 

Bibliography

View all...
  1. Kim DK, Inukai N, Yamada T, Furuya A, Sato H, Yamaguchi Y, Wada T, Handa H.; ''Structure-function analysis of human Spt4: evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex.''; PubMed Europe PMC Scholia
  2. Daugherty MD, Liu B, Frankel AD.; ''Structural basis for cooperative RNA binding and export complex assembly by HIV Rev.''; PubMed Europe PMC Scholia
  3. Wisniewski M, Balakrishnan M, Palaniappan C, Fay PJ, Bambara RA.; ''The sequential mechanism of HIV reverse transcriptase RNase H.''; PubMed Europe PMC Scholia
  4. Malim MH, Tiley LS, McCarn DF, Rusche JR, Hauber J, Cullen BR.; ''HIV-1 structural gene expression requires binding of the Rev trans-activator to its RNA target sequence.''; PubMed Europe PMC Scholia
  5. Kanaseki T, Kawasaki K, Murata M, Ikeuchi Y, Ohnishi S.; ''Structural features of membrane fusion between influenza virus and liposome as revealed by quick-freezing electron microscopy.''; PubMed Europe PMC Scholia
  6. Ott DE, Coren LV, Chertova EN, Gagliardi TD, Schubert U.; ''Ubiquitination of HIV-1 and MuLV Gag.''; PubMed Europe PMC Scholia
  7. Furuta RA, Wild CT, Weng Y, Weiss CD.; ''Capture of an early fusion-active conformation of HIV-1 gp41.''; PubMed Europe PMC Scholia
  8. Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, Berger EA.; ''CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1.''; PubMed Europe PMC Scholia
  9. Furfine ES, Reardon JE.; ''Reverse transcriptase.RNase H from the human immunodeficiency virus. Relationship of the DNA polymerase and RNA hydrolysis activities.''; PubMed Europe PMC Scholia
  10. Morita E, Sundquist WI.; ''Retrovirus budding.''; PubMed Europe PMC Scholia
  11. Suntharalingam M, Wente SR.; ''Peering through the pore: nuclear pore complex structure, assembly, and function.''; PubMed Europe PMC Scholia
  12. Shilatifard A, Conaway RC, Conaway JW.; ''The RNA polymerase II elongation complex.''; PubMed Europe PMC Scholia
  13. Askjaer P, Jensen TH, Nilsson J, Englmeier L, Kjems J.; ''The specificity of the CRM1-Rev nuclear export signal interaction is mediated by RanGTP.''; PubMed Europe PMC Scholia
  14. Morris DP, Michelotti GA, Schwinn DA.; ''Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans.''; PubMed Europe PMC Scholia
  15. Sundquist WI, Kräusslich HG.; ''HIV-1 assembly, budding, and maturation.''; PubMed Europe PMC Scholia
  16. Martinez E, Ge H, Tao Y, Yuan CX, Palhan V, Roeder RG.; ''Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex.''; PubMed Europe PMC Scholia
  17. Gangloff YG, Pointud JC, Thuault S, Carré L, Romier C, Muratoglu S, Brand M, Tora L, Couderc JL, Davidson I.; ''The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger.''; PubMed Europe PMC Scholia
  18. Trkola A, Dragic T, Arthos J, Binley JM, Olson WC, Allaway GP, Cheng-Mayer C, Robinson J, Maddon PJ, Moore JP.; ''CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5.''; PubMed Europe PMC Scholia
  19. Yamashita M, Emerman M.; ''The cell cycle independence of HIV infections is not determined by known karyophilic viral elements.''; PubMed Europe PMC Scholia
  20. Conaway JW, Shilatifard A, Dvir A, Conaway RC.; ''Control of elongation by RNA polymerase II.''; PubMed Europe PMC Scholia
  21. Helseth E, Olshevsky U, Furman C, Sodroski J.; ''Human immunodeficiency virus type 1 gp120 envelope glycoprotein regions important for association with the gp41 transmembrane glycoprotein.''; PubMed Europe PMC Scholia
  22. Kowalski M, Potz J, Basiripour L, Dorfman T, Goh WC, Terwilliger E, Dayton A, Rosen C, Haseltine W, Sodroski J.; ''Functional regions of the envelope glycoprotein of human immunodeficiency virus type 1.''; PubMed Europe PMC Scholia
  23. Sinangil F, Loyter A, Volsky DJ.; ''Quantitative measurement of fusion between human immunodeficiency virus and cultured cells using membrane fluorescence dequenching.''; PubMed Europe PMC Scholia
  24. Gottwein E, Jäger S, Habermann A, Kräusslich HG.; ''Cumulative mutations of ubiquitin acceptor sites in human immunodeficiency virus type 1 gag cause a late budding defect.''; PubMed Europe PMC Scholia
  25. Stuchell MD, Garrus JE, Müller B, Stray KM, Ghaffarian S, McKinnon R, Kräusslich HG, Morham SG, Sundquist WI.; ''The human endosomal sorting complex required for transport (ESCRT-I) and its role in HIV-1 budding.''; PubMed Europe PMC Scholia
  26. Herrmann CH, Rice AP.; ''Lentivirus Tat proteins specifically associate with a cellular protein kinase, TAK, that hyperphosphorylates the carboxyl-terminal domain of the large subunit of RNA polymerase II: candidate for a Tat cofactor.''; PubMed Europe PMC Scholia
  27. Chackerian B, Long EM, Luciw PA, Overbaugh J.; ''Human immunodeficiency virus type 1 coreceptors participate in postentry stages in the virus replication cycle and function in simian immunodeficiency virus infection.''; PubMed Europe PMC Scholia
  28. Fontoura BM, Blobel G, Matunis MJ.; ''A conserved biogenesis pathway for nucleoporins: proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96.''; PubMed Europe PMC Scholia
  29. Jiang S, Lin K, Strick N, Neurath AR.; ''Inhibition of HIV-1 infection by a fusion domain binding peptide from the HIV-1 envelope glycoprotein GP41.''; PubMed Europe PMC Scholia
  30. Schaeffer L, Roy R, Humbert S, Moncollin V, Vermeulen W, Hoeijmakers JH, Chambon P, Egly JM.; ''DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor.''; PubMed Europe PMC Scholia
  31. Leduc R, Molloy SS, Thorne BA, Thomas G.; ''Activation of human furin precursor processing endoprotease occurs by an intramolecular autoproteolytic cleavage.''; PubMed Europe PMC Scholia
  32. Bandres JC, Wang QF, O'Leary J, Baleaux F, Amara A, Hoxie JA, Zolla-Pazner S, Gorny MK.; ''Human immunodeficiency virus (HIV) envelope binds to CXCR4 independently of CD4, and binding can be enhanced by interaction with soluble CD4 or by HIV envelope deglycosylation.''; PubMed Europe PMC Scholia
  33. Jiang S, Lu H, Liu S, Zhao Q, He Y, Debnath AK.; ''N-substituted pyrrole derivatives as novel human immunodeficiency virus type 1 entry inhibitors that interfere with the gp41 six-helix bundle formation and block virus fusion.''; PubMed Europe PMC Scholia
  34. Mondor I, Moulard M, Ugolini S, Klasse PJ, Hoxie J, Amara A, Delaunay T, Wyatt R, Sodroski J, Sattentau QJ.; ''Interactions among HIV gp120, CD4, and CXCR4: dependence on CD4 expression level, gp120 viral origin, conservation of the gp120 COOH- and NH2-termini and V1/V2 and V3 loops, and sensitivity to neutralizing antibodies.''; PubMed Europe PMC Scholia
  35. Zhu P, Liu J, Bess J, Chertova E, Lifson JD, Grisé H, Ofek GA, Taylor KA, Roux KH.; ''Distribution and three-dimensional structure of AIDS virus envelope spikes.''; PubMed Europe PMC Scholia
  36. Mandal SS, Cho H, Kim S, Cabane K, Reinberg D.; ''FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongation.''; PubMed Europe PMC Scholia
  37. Giglia-Mari G, Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ, Botta E, Stefanini M, Egly JM, Aebersold R, Hoeijmakers JH, Vermeulen W.; ''A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A.''; PubMed Europe PMC Scholia
  38. McKeating JA, Shotton C, Cordell J, Graham S, Balfe P, Sullivan N, Charles M, Page M, Bolmstedt A, Olofsson S.; ''Characterization of neutralizing monoclonal antibodies to linear and conformation-dependent epitopes within the first and second variable domains of human immunodeficiency virus type 1 gp120.''; PubMed Europe PMC Scholia
  39. Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L.; ''EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes.''; PubMed Europe PMC Scholia
  40. Lewinski MK, Bushman FD.; ''Retroviral DNA integration--mechanism and consequences.''; PubMed Europe PMC Scholia
  41. Hill CP, Sundquist WI.; ''Building a super elongation complex for HIV.''; PubMed Europe PMC Scholia
  42. Wang Z, Lee B, Murray JL, Bonneau F, Sun Y, Schweickart V, Zhang T, Peiper SC.; ''CCR5 HIV-1 coreceptor activity. Role of cooperativity between residues in N-terminal extracellular and intracellular domains.''; PubMed Europe PMC Scholia
  43. Fassati A, Goff SP.; ''Characterization of intracellular reverse transcription complexes of human immunodeficiency virus type 1.''; PubMed Europe PMC Scholia
  44. Stefani F, Zhang L, Taylor S, Donovan J, Rollinson S, Doyotte A, Brownhill K, Bennion J, Pickering-Brown S, Woodman P.; ''UBAP1 is a component of an endosome-specific ESCRT-I complex that is essential for MVB sorting.''; PubMed Europe PMC Scholia
  45. McDougal JS, Kennedy MS, Sligh JM, Cort SP, Mawle A, Nicholson JK.; ''Binding of HTLV-III/LAV to T4+ T cells by a complex of the 110K viral protein and the T4 molecule.''; PubMed Europe PMC Scholia
  46. Agromayor M, Soler N, Caballe A, Kueck T, Freund SM, Allen MD, Bycroft M, Perisic O, Ye Y, McDonald B, Scheel H, Hofmann K, Neil SJ, Martin-Serrano J, Williams RL.; ''The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain.''; PubMed Europe PMC Scholia
  47. Ott DE, Coren LV, Copeland TD, Kane BP, Johnson DG, Sowder RC, Yoshinaka Y, Oroszlan S, Arthur LO, Henderson LE.; ''Ubiquitin is covalently attached to the p6Gag proteins of human immunodeficiency virus type 1 and simian immunodeficiency virus and to the p12Gag protein of Moloney murine leukemia virus.''; PubMed Europe PMC Scholia
  48. Pullen KA, Rattray AJ, Champoux JJ.; ''The sequence features important for plus strand priming by human immunodeficiency virus type 1 reverse transcriptase.''; PubMed Europe PMC Scholia
  49. Orphanides G, Lagrange T, Reinberg D.; ''The general transcription factors of RNA polymerase II.''; PubMed Europe PMC Scholia
  50. Welman M, Lemay G, Cohen EA.; ''Role of envelope processing and gp41 membrane spanning domain in the formation of human immunodeficiency virus type 1 (HIV-1) fusion-competent envelope glycoprotein complex.''; PubMed Europe PMC Scholia
  51. Ghosh M, Howard KJ, Cameron CE, Benkovic SJ, Hughes SH, Le Grice SF.; ''Truncating alpha-helix E' of p66 human immunodeficiency virus reverse transcriptase modulates RNase H function and impairs DNA strand transfer.''; PubMed Europe PMC Scholia
  52. Fujinaga K, Irwin D, Huang Y, Taube R, Kurosu T, Peterlin BM.; ''Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element.''; PubMed Europe PMC Scholia
  53. Wang W, Carey M, Gralla JD.; ''Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.''; PubMed Europe PMC Scholia
  54. Klaver B, Berkhout B.; ''Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis.''; PubMed Europe PMC Scholia
  55. Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C.; ''Genome-wide analysis of retroviral DNA integration.''; PubMed Europe PMC Scholia
  56. Ohi Y, Clever JL.; ''Sequences in the 5' and 3' R elements of human immunodeficiency virus type 1 critical for efficient reverse transcription.''; PubMed Europe PMC Scholia
  57. Rossignol M, Kolb-Cheynel I, Egly JM.; ''Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH.''; PubMed Europe PMC Scholia
  58. Farnet CM, Bushman FD.; ''HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro.''; PubMed Europe PMC Scholia
  59. Chan DC, Fass D, Berger JM, Kim PS.; ''Core structure of gp41 from the HIV envelope glycoprotein.''; PubMed Europe PMC Scholia
  60. Decroly E, Vandenbranden M, Ruysschaert JM, Cogniaux J, Jacob GS, Howard SC, Marshall G, Kompelli A, Basak A, Jean F.; ''The convertases furin and PC1 can both cleave the human immunodeficiency virus (HIV)-1 envelope glycoprotein gp160 into gp120 (HIV-1 SU) and gp41 (HIV-I TM).''; PubMed Europe PMC Scholia
  61. Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.''; PubMed Europe PMC Scholia
  62. Lin DH, Stuwe T, Schilbach S, Rundlet EJ, Perriches T, Mobbs G, Fan Y, Thierbach K, Huber FM, Collins LN, Davenport AM, Jeon YE, Hoelz A.; ''Architecture of the symmetric core of the nuclear pore.''; PubMed Europe PMC Scholia
  63. Ferrer M, Kapoor TM, Strassmaier T, Weissenhorn W, Skehel JJ, Oprian D, Schreiber SL, Wiley DC, Harrison SC.; ''Selection of gp41-mediated HIV-1 cell entry inhibitors from biased combinatorial libraries of non-natural binding elements.''; PubMed Europe PMC Scholia
  64. Buratowski S.; ''Progression through the RNA polymerase II CTD cycle.''; PubMed Europe PMC Scholia
  65. Wisniewski M, Balakrishnan M, Palaniappan C, Fay PJ, Bambara RA.; ''Unique progressive cleavage mechanism of HIV reverse transcriptase RNase H.''; PubMed Europe PMC Scholia
  66. Huber HE, Richardson CC.; ''Processing of the primer for plus strand DNA synthesis by human immunodeficiency virus 1 reverse transcriptase.''; PubMed Europe PMC Scholia
  67. Wada T, Takagi T, Yamaguchi Y, Watanabe D, Handa H.; ''Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro.''; PubMed Europe PMC Scholia
  68. Lin X, Taube R, Fujinaga K, Peterlin BM.; ''P-TEFb containing cyclin K and Cdk9 can activate transcription via RNA.''; PubMed Europe PMC Scholia
  69. Bell NM, Lever AM.; ''HIV Gag polyprotein: processing and early viral particle assembly.''; PubMed Europe PMC Scholia
  70. Cronshaw JM, Krutchinsky AN, Zhang W, Chait BT, Matunis MJ.; ''Proteomic analysis of the mammalian nuclear pore complex.''; PubMed Europe PMC Scholia
  71. Bukrinsky MI, Sharova N, McDonald TL, Pushkarskaya T, Tarpley WG, Stevenson M.; ''Association of integrase, matrix, and reverse transcriptase antigens of human immunodeficiency virus type 1 with viral nucleic acids following acute infection.''; PubMed Europe PMC Scholia
  72. Zawel L, Kumar KP, Reinberg D.; ''Recycling of the general transcription factors during RNA polymerase II transcription.''; PubMed Europe PMC Scholia
  73. Kabachinski G, Schwartz TU.; ''The nuclear pore complex--structure and function at a glance.''; PubMed Europe PMC Scholia
  74. Tazi J, Bakkour N, Marchand V, Ayadi L, Aboufirassi A, Branlant C.; ''Alternative splicing: regulation of HIV-1 multiplication as a target for therapeutic action.''; PubMed Europe PMC Scholia
  75. Morita E, Sandrin V, Alam SL, Eckert DM, Gygi SP, Sundquist WI.; ''Identification of human MVB12 proteins as ESCRT-I subunits that function in HIV budding.''; PubMed Europe PMC Scholia
  76. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA.; ''Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.''; PubMed Europe PMC Scholia
  77. Bosch ML, Earl PL, Fargnoli K, Picciafuoco S, Giombini F, Wong-Staal F, Franchini G.; ''Identification of the fusion peptide of primate immunodeficiency viruses.''; PubMed Europe PMC Scholia
  78. Choe H, Farzan M, Sun Y, Sullivan N, Rollins B, Ponath PD, Wu L, Mackay CR, LaRosa G, Newman W, Gerard N, Gerard C, Sodroski J.; ''The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates.''; PubMed Europe PMC Scholia
  79. Miller MD, Wang B, Bushman FD.; ''Human immunodeficiency virus type 1 preintegration complexes containing discontinuous plus strands are competent to integrate in vitro.''; PubMed Europe PMC Scholia
  80. Rumbaugh JA, Fuentes GM, Bambara RA.; ''Processing of an HIV replication intermediate by the human DNA replication enzyme FEN1.''; PubMed Europe PMC Scholia
  81. Schultz P, Fribourg S, Poterszman A, Mallouh V, Moras D, Egly JM.; ''Molecular structure of human TFIIH.''; PubMed Europe PMC Scholia
  82. Kugel JF, Goodrich JA.; ''Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.''; PubMed Europe PMC Scholia
  83. Björndal A, Deng H, Jansson M, Fiore JR, Colognesi C, Karlsson A, Albert J, Scarlatti G, Littman DR, Fenyö EM.; ''Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype.''; PubMed Europe PMC Scholia
  84. Pal M, McKean D, Luse DS.; ''Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.''; PubMed Europe PMC Scholia
  85. Schaal H, Klein M, Gehrmann P, Adams O, Scheid A.; ''Requirement of N-terminal amino acid residues of gp41 for human immunodeficiency virus type 1-mediated cell fusion.''; PubMed Europe PMC Scholia
  86. Tirode F, Busso D, Coin F, Egly JM.; ''Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7.''; PubMed Europe PMC Scholia
  87. Ivanov D, Kwak YT, Guo J, Gaynor RB.; ''Domains in the SPT5 protein that modulate its transcriptional regulatory properties.''; PubMed Europe PMC Scholia
  88. Ryu SE, Kwong PD, Truneh A, Porter TG, Arthos J, Rosenberg M, Dai XP, Xuong NH, Axel R, Sweet RW.; ''Crystal structure of an HIV-binding recombinant fragment of human CD4.''; PubMed Europe PMC Scholia
  89. Lasky LA, Nakamura G, Smith DH, Fennie C, Shimasaki C, Patzer E, Berman P, Gregory T, Capon DJ.; ''Delineation of a region of the human immunodeficiency virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor.''; PubMed Europe PMC Scholia
  90. Chen CH, Matthews TJ, McDanal CB, Bolognesi DP, Greenberg ML.; ''A molecular clasp in the human immunodeficiency virus (HIV) type 1 TM protein determines the anti-HIV activity of gp41 derivatives: implication for viral fusion.''; PubMed Europe PMC Scholia
  91. Delwart EL, Mosialos G, Gilmore T.; ''Retroviral envelope glycoproteins contain a "leucine zipper"-like repeat.''; PubMed Europe PMC Scholia
  92. Meyer BE, Malim MH.; ''The HIV-1 Rev trans-activator shuttles between the nucleus and the cytoplasm.''; PubMed Europe PMC Scholia
  93. Giang DK, Cravatt BF.; ''A second mammalian N-myristoyltransferase.''; PubMed Europe PMC Scholia
  94. Fiedler U, Timmers HT.; ''Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.''; PubMed Europe PMC Scholia
  95. Farnet CM, Bushman FD.; ''HIV cDNA integration: molecular biology and inhibitor development.''; PubMed Europe PMC Scholia
  96. de Souza RF, Aravind L.; ''UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes.''; PubMed Europe PMC Scholia
  97. Sullivan N, Sun Y, Sattentau Q, Thali M, Wu D, Denisova G, Gershoni J, Robinson J, Moore J, Sodroski J.; ''CD4-Induced conformational changes in the human immunodeficiency virus type 1 gp120 glycoprotein: consequences for virus entry and neutralization.''; PubMed Europe PMC Scholia
  98. Cao J, Bergeron L, Helseth E, Thali M, Repke H, Sodroski J.; ''Effects of amino acid changes in the extracellular domain of the human immunodeficiency virus type 1 gp41 envelope glycoprotein.''; PubMed Europe PMC Scholia
  99. Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S, Yano K, Hartzog GA, Winston F, Buratowski S, Handa H.; ''DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.''; PubMed Europe PMC Scholia
  100. Sibanda BL, Critchlow SE, Begun J, Pei XY, Jackson SP, Blundell TL, Pellegrini L.; ''Crystal structure of an Xrcc4-DNA ligase IV complex.''; PubMed Europe PMC Scholia
  101. Inlora J, Chukkapalli V, Derse D, Ono A.; ''Gag localization and virus-like particle release mediated by the matrix domain of human T-lymphotropic virus type 1 Gag are less dependent on phosphatidylinositol-(4,5)-bisphosphate than those mediated by the matrix domain of HIV-1 Gag.''; PubMed Europe PMC Scholia
  102. Eastman SW, Martin-Serrano J, Chung W, Zang T, Bieniasz PD.; ''Identification of human VPS37C, a component of endosomal sorting complex required for transport-I important for viral budding.''; PubMed Europe PMC Scholia
  103. Bischoff FR, Ponstingl H.; ''Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1.''; PubMed Europe PMC Scholia
  104. Gallo SA, Puri A, Blumenthal R.; ''HIV-1 gp41 six-helix bundle formation occurs rapidly after the engagement of gp120 by CXCR4 in the HIV-1 Env-mediated fusion process.''; PubMed Europe PMC Scholia
  105. Mahboobi SH, Javanpour AA, Mofrad MR.; ''The interaction of RNA helicase DDX3 with HIV-1 Rev-CRM1-RanGTP complex during the HIV replication cycle.''; PubMed Europe PMC Scholia
  106. Huang CC, Tang M, Zhang MY, Majeed S, Montabana E, Stanfield RL, Dimitrov DS, Korber B, Sodroski J, Wilson IA, Wyatt R, Kwong PD.; ''Structure of a V3-containing HIV-1 gp120 core.''; PubMed Europe PMC Scholia
  107. Hoffmann A, Roeder RG.; ''Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation.''; PubMed Europe PMC Scholia
  108. Weissenhorn W, Wharton SA, Calder LJ, Earl PL, Moss B, Aliprandis E, Skehel JJ, Wiley DC.; ''The ectodomain of HIV-1 env subunit gp41 forms a soluble, alpha-helical, rod-like oligomer in the absence of gp120 and the N-terminal fusion peptide.''; PubMed Europe PMC Scholia
  109. Brown PO, Bowerman B, Varmus HE, Bishop JM.; ''Correct integration of retroviral DNA in vitro.''; PubMed Europe PMC Scholia
  110. Lee WR, Syu WJ, Du B, Matsuda M, Tan S, Wolf A, Essex M, Lee TH.; ''Nonrandom distribution of gp120 N-linked glycosylation sites important for infectivity of human immunodeficiency virus type 1.''; PubMed Europe PMC Scholia
  111. Malim MH, Cullen BR.; ''HIV-1 structural gene expression requires the binding of multiple Rev monomers to the viral RRE: implications for HIV-1 latency.''; PubMed Europe PMC Scholia
  112. Freed EO, Myers DJ, Risser R.; ''Characterization of the fusion domain of the human immunodeficiency virus type 1 envelope glycoprotein gp41.''; PubMed Europe PMC Scholia
  113. Jonckheere H, Anné J, De Clercq E.; ''The HIV-1 reverse transcription (RT) process as target for RT inhibitors.''; PubMed Europe PMC Scholia
  114. Bunick D, Zandomeni R, Ackerman S, Weinmann R.; ''Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts.''; PubMed Europe PMC Scholia
  115. Dvir A, Conaway RC, Conaway JW.; ''A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes.''; PubMed Europe PMC Scholia
  116. Klatzmann D, Champagne E, Chamaret S, Gruest J, Guetard D, Hercend T, Gluckman JC, Montagnier L.; ''T-lymphocyte T4 molecule behaves as the receptor for human retrovirus LAV.''; PubMed Europe PMC Scholia
  117. Bieniasz PD.; ''The cell biology of HIV-1 virion genesis.''; PubMed Europe PMC Scholia
  118. Mousson F, Kolkman A, Pijnappel WW, Timmers HT, Heck AJ.; ''Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes.''; PubMed Europe PMC Scholia
  119. Zhou M, Halanski MA, Radonovich MF, Kashanchi F, Peng J, Price DH, Brady JN.; ''Tat modifies the activity of CDK9 to phosphorylate serine 5 of the RNA polymerase II carboxyl-terminal domain during human immunodeficiency virus type 1 transcription.''; PubMed Europe PMC Scholia
  120. Gallaher WR, Ball JM, Garry RF, Griffin MC, Montelaro RC.; ''A general model for the transmembrane proteins of HIV and other retroviruses.''; PubMed Europe PMC Scholia
  121. Jiang M, Mak J, Ladha A, Cohen E, Klein M, Rovinski B, Kleiman L.; ''Identification of tRNAs incorporated into wild-type and mutant human immunodeficiency virus type 1.''; PubMed Europe PMC Scholia
  122. Malim MH, Bieniasz PD.; ''HIV Restriction Factors and Mechanisms of Evasion.''; PubMed Europe PMC Scholia
  123. Zapp ML, Green MR.; ''Sequence-specific RNA binding by the HIV-1 Rev protein.''; PubMed Europe PMC Scholia
  124. Fischer U, Meyer S, Teufel M, Heckel C, Lührmann R, Rautmann G.; ''Evidence that HIV-1 Rev directly promotes the nuclear export of unspliced RNA.''; PubMed Europe PMC Scholia
  125. Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L.; ''TAF9b (formerly TAF9L) is a bona fide TAF that has unique and overlapping roles with TAF9.''; PubMed Europe PMC Scholia
  126. Fritz CC, Green MR.; ''HIV Rev uses a conserved cellular protein export pathway for the nucleocytoplasmic transport of viral RNAs.''; PubMed Europe PMC Scholia
  127. Kao SY, Calman AF, Luciw PA, Peterlin BM.; ''Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product.''; PubMed Europe PMC Scholia
  128. Parvin JD, Sharp PA.; ''DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.''; PubMed Europe PMC Scholia
  129. Bischoff FR, Krebber H, Kempf T, Hermes I, Ponstingl H.; ''Human RanGTPase-activating protein RanGAP1 is a homologue of yeast Rna1p involved in mRNA processing and transport.''; PubMed Europe PMC Scholia
  130. Frankel AD, Young JA.; ''HIV-1: fifteen proteins and an RNA.''; PubMed Europe PMC Scholia
  131. Ori A, Banterle N, Iskar M, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M.; ''Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.''; PubMed Europe PMC Scholia
  132. Dvir A, Tan S, Conaway JW, Conaway RC.; ''Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.''; PubMed Europe PMC Scholia
  133. Yi R, Bogerd HP, Cullen BR.; ''Recruitment of the Crm1 nuclear export factor is sufficient to induce cytoplasmic expression of incompletely spliced human immunodeficiency virus mRNAs.''; PubMed Europe PMC Scholia
  134. Wild C, Oas T, McDanal C, Bolognesi D, Matthews T.; ''A synthetic peptide inhibitor of human immunodeficiency virus replication: correlation between solution structure and viral inhibition.''; PubMed Europe PMC Scholia
  135. Conaway RC, Conaway JW.; ''ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.''; PubMed Europe PMC Scholia
  136. Farazi TA, Waksman G, Gordon JI.; ''The biology and enzymology of protein N-myristoylation.''; PubMed Europe PMC Scholia
  137. Charneau P, Alizon M, Clavel F.; ''A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication.''; PubMed Europe PMC Scholia
  138. Ehrlich LS, Liu T, Scarlata S, Chu B, Carter CA.; ''HIV-1 capsid protein forms spherical (immature-like) and tubular (mature-like) particles in vitro: structure switching by pH-induced conformational changes.''; PubMed Europe PMC Scholia
  139. Rabut G, Doye V, Ellenberg J.; ''Mapping the dynamic organization of the nuclear pore complex inside single living cells.''; PubMed Europe PMC Scholia
  140. Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JA, Glavy JS, Hurt E, Beck M.; ''Molecular architecture of the inner ring scaffold of the human nuclear pore complex.''; PubMed Europe PMC Scholia
  141. Pal M, Luse DS.; ''Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA.''; PubMed Europe PMC Scholia
  142. Dubay JW, Roberts SJ, Brody B, Hunter E.; ''Mutations in the leucine zipper of the human immunodeficiency virus type 1 transmembrane glycoprotein affect fusion and infectivity.''; PubMed Europe PMC Scholia
  143. McDougal JS, Nicholson JK, Cross GD, Cort SP, Kennedy MS, Mawle AC.; ''Binding of the human retrovirus HTLV-III/LAV/ARV/HIV to the CD4 (T4) molecule: conformation dependence, epitope mapping, antibody inhibition, and potential for idiotypic mimicry.''; PubMed Europe PMC Scholia
  144. Kilby JM, Eron JJ.; ''Novel therapies based on mechanisms of HIV-1 cell entry.''; PubMed Europe PMC Scholia
  145. Rizzuto CD, Wyatt R, Hernández-Ramos N, Sun Y, Kwong PD, Hendrickson WA, Sodroski J.; ''A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding.''; PubMed Europe PMC Scholia
  146. Fiedler U, Marc Timmers HT.; ''Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.''; PubMed Europe PMC Scholia
  147. Goodrich JA, Tjian R.; ''Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.''; PubMed Europe PMC Scholia
  148. Melikyan GB, Markosyan RM, Hemmati H, Delmedico MK, Lambert DM, Cohen FS.; ''Evidence that the transition of HIV-1 gp41 into a six-helix bundle, not the bundle configuration, induces membrane fusion.''; PubMed Europe PMC Scholia
  149. Zhang W, Canziani G, Plugariu C, Wyatt R, Sodroski J, Sweet R, Kwong P, Hendrickson W, Chaiken I.; ''Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic.''; PubMed Europe PMC Scholia
  150. Brown PO, Bowerman B, Varmus HE, Bishop JM.; ''Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein.''; PubMed Europe PMC Scholia
  151. Miller MD, Farnet CM, Bushman FD.; ''Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition.''; PubMed Europe PMC Scholia
  152. Meng B, Lever AM.; ''Wrapping up the bad news: HIV assembly and release.''; PubMed Europe PMC Scholia
  153. Cramer P, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.''; PubMed Europe PMC Scholia
  154. Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H.; ''NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  155. Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR.; ''Identification of a major co-receptor for primary isolates of HIV-1.''; PubMed Europe PMC Scholia
  156. Chen H, Engelman A.; ''The barrier-to-autointegration protein is a host factor for HIV type 1 integration.''; PubMed Europe PMC Scholia
  157. Julias JG, McWilliams MJ, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.; ''Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage.''; PubMed Europe PMC Scholia
  158. Kati WM, Johnson KA, Jerva LF, Anderson KS.; ''Mechanism and fidelity of HIV reverse transcriptase.''; PubMed Europe PMC Scholia
  159. Sackett K, Shai Y.; ''The HIV-1 gp41 N-terminal heptad repeat plays an essential role in membrane fusion.''; PubMed Europe PMC Scholia
  160. Gonatopoulos-Pournatzis T, Cowling VH.; ''Cap-binding complex (CBC).''; PubMed Europe PMC Scholia
  161. Hill BT, Skowronski J.; ''Human N-myristoyltransferases form stable complexes with lentiviral nef and other viral and cellular substrate proteins.''; PubMed Europe PMC Scholia
  162. Rausch JW, Le Grice SF.; '''Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus.''; PubMed Europe PMC Scholia
  163. Dalgleish AG, Beverley PC, Clapham PR, Crawford DH, Greaves MF, Weiss RA.; ''The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus.''; PubMed Europe PMC Scholia
  164. Martin-Serrano J, Zang T, Bieniasz PD.; ''Role of ESCRT-I in retroviral budding.''; PubMed Europe PMC Scholia
  165. Iordanskiy S, Berro R, Altieri M, Kashanchi F, Bukrinsky M.; ''Intracytoplasmic maturation of the human immunodeficiency virus type 1 reverse transcription complexes determines their capacity to integrate into chromatin.''; PubMed Europe PMC Scholia
  166. Zhang H, Dornadula G, Orenstein J, Pomerantz RJ.; ''Morphologic changes in human immunodeficiency virus type 1 virions secondary to intravirion reverse transcription: evidence indicating that reverse transcription may not take place within the intact viral core.''; PubMed Europe PMC Scholia
  167. Bushman FD, Fujiwara T, Craigie R.; ''Retroviral DNA integration directed by HIV integration protein in vitro.''; PubMed Europe PMC Scholia
  168. Pullen KA, Ishimoto LK, Champoux JJ.; ''Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase.''; PubMed Europe PMC Scholia
  169. Holstege FC, Fiedler U, Timmers HT.; ''Three transitions in the RNA polymerase II transcription complex during initiation.''; PubMed Europe PMC Scholia
  170. Carr CM, Kim PS.; ''A spring-loaded mechanism for the conformational change of influenza hemagglutinin.''; PubMed Europe PMC Scholia
  171. Jacob GA, Luse SW, Luse DS.; ''Abortive initiation is increased only for the weakest members of a set of down mutants of the adenovirus 2 major late promoter.''; PubMed Europe PMC Scholia
  172. Mak J, Jiang M, Wainberg MA, Hammarskjöld ML, Rekosh D, Kleiman L.; ''Role of Pr160gag-pol in mediating the selective incorporation of tRNA(Lys) into human immunodeficiency virus type 1 particles.''; PubMed Europe PMC Scholia

History

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

External references

DataNodes

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

DNA as smaller

circles
ComplexR-HSA-R-HIV-175037 (Reactome)
Autointegrated viral

DNA as an inverted

circle
ComplexR-HSA-R-HIV-175415 (Reactome)
BANF1 ProteinO75531 (Uniprot-TrEMBL)
BANF1ProteinO75531 (Uniprot-TrEMBL)
CCNH ProteinP51946 (Uniprot-TrEMBL)
CCNT1 ProteinO60563 (Uniprot-TrEMBL)
CCNT2 ProteinO60583 (Uniprot-TrEMBL)
CCR5 ProteinP51681 (Uniprot-TrEMBL)
CCR5, 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-HSA-R-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-HSA-R-HIV-174985 (Reactome)
HIV-1 RNA template ProteinAF033819 (EMBL)
HIV-1 Tat-containing

aborted elongation complex after

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

arrested processive

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

paused processive

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

processive

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

elongation complex

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

processive

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

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

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

pre-initiation

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

elongation complex with hyperphosphorylated

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

complex containing

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

complex with phosphodiester-PPi

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

pre-initiation

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

processive

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

DNA:4-9 nucleotide

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

containing promoter with transcript of

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

with first transcript dinucleotide, opened to +8

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

complex containing 11 nucleotide long

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

complex containing 3 nucleotide long

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

complex containing 4 nucleotide long

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

complex containing 4-9 nucleotide long

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

complex containing 9 nucleotide long

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

complex containing extruded transcript

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

complex containing

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

complex with (ser5) phosphorylated CTD containing extruded

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

3' ends of viral

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

3' ends of viral

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

to host genomic DNA

with staggered ends
ComplexR-HSA-175224 (Reactome)
Immature HIV virionComplexR-HSA-R-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-HSA-R-HIV-173120 (Reactome)
Mature HIV virionComplexR-HSA-R-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)
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-HSA-R-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-HSA-R-HIV-175167 (Reactome)
Nup45 ProteinQ9BVL2-2 (Uniprot-TrEMBL)
P-TEFb complexComplexR-HSA-112431 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complexComplexR-HSA-167183 (Reactome)
P-TEFb(Cyclin

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

transcript
ComplexR-HSA-167199 (Reactome)
PDCD6IP ProteinQ8WUM4 (Uniprot-TrEMBL)
PDCD6IPProteinQ8WUM4 (Uniprot-TrEMBL)
PIC (PreIntegration Complex)ComplexR-HSA-R-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)
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-HSA-R-HIV-173814 (Reactome)
RTC with annealed

complementary PBS seqments in +sssDNA

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

RNA template and

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

containing discontinuous plus

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

sssDNA transferred to 3'-end of viral

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

sssDNA:tRNA

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

strand DNA synthesis initiated

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

minus sssDNA:tRNA

primer:RNA template
ComplexR-HSA-R-HIV-182804 (Reactome)
RTC with tRNA primer:RNA templateComplexR-HSA-R-HIV-173801 (Reactome)
RTC without viral RNA templateComplexR-HSA-R-HIV-173824 (Reactome)
RTComplexR-HSA-R-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-HSA-R-HIV-165532 (Reactome)
Rev-bound HIV-1 mRNAComplexR-HSA-R-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-HSA-R-NUL-167237 (Reactome)
Transmembrane protein gp41 (P04578) ProteinP04578 (Uniprot-TrEMBL)
Transmembrane protein gp41 ProteinP04578 (Uniprot-TrEMBL)
Trimeric ENV precursorComplexR-HSA-R-HIV-189843 (Reactome)
Trimeric ENV precursorComplexR-HSA-R-HIV-3149446 (Reactome)
Trimeric gp120:gp41 oligomerComplexR-HSA-R-HIV-189281 (Reactome)
Trimeric gp120:gp41 oligomerComplexR-HSA-R-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-HSA-R-HIV-173664 (Reactome)
Virion Budding ComplexComplexR-HSA-3211408 (Reactome)
Virion with

CD4:gp120 bound to

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

fusogenically

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

coreceptor binding

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

forming hairpin

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

fusion peptide in

insertion complex
ComplexR-HSA-R-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-HSA-R-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)
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-HSA-R-HIV-173653 (Reactome)
viral DNA bound with Integrase in PICComplexR-HSA-R-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-164506 (Reactome)
viral PIC proteinsArrowR-HSA-164523 (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)
viral PIC proteinsR-HSA-164506 (Reactome)
viral PIC proteinsR-HSA-164523 (Reactome)
Personal tools