HIV Life Cycle (Homo sapiens)

From WikiPathways

Description

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...

Compare	Revision	Action	Time	User	Comment
	112577	view	15:54, 9 October 2020	ReactomeTeam	Reactome version 73
	101491	view	11:36, 1 November 2018	ReactomeTeam	reactome version 66
	101028	view	21:16, 31 October 2018	ReactomeTeam	reactome version 65
	100562	view	19:50, 31 October 2018	ReactomeTeam	reactome version 64
	100110	view	16:35, 31 October 2018	ReactomeTeam	reactome version 63
	99660	view	15:06, 31 October 2018	ReactomeTeam	reactome version 62 (2nd attempt)
	99260	view	12:45, 31 October 2018	ReactomeTeam	reactome version 62
	93960	view	13:48, 16 August 2017	ReactomeTeam	reactome version 61
	93556	view	11:27, 9 August 2017	ReactomeTeam	reactome version 61
	87467	view	14:14, 22 July 2016	Mkutmon	Ontology Term : 'infectious disease pathway' added !
	86659	view	09:23, 11 July 2016	ReactomeTeam	reactome version 56
	83257	view	10:34, 18 November 2015	ReactomeTeam	Version54
	81368	view	12:53, 21 August 2015	ReactomeTeam	Version53
	76836	view	08:06, 17 July 2014	ReactomeTeam	Fixed remaining interactions
	76540	view	11:52, 16 July 2014	ReactomeTeam	Fixed remaining interactions
	75873	view	09:52, 11 June 2014	ReactomeTeam	Re-fixing comment source
	75573	view	10:39, 10 June 2014	ReactomeTeam	Reactome 48 Update
	74928	view	13:45, 8 May 2014	Anwesha	Fixing comment source for displaying WikiPathways description
	74572	view	08:37, 30 April 2014	ReactomeTeam	New pathway

External references

DataNodes

View all...

Name	Type	Database reference	Comment
1-LTR form of circular viral DNA	Complex	R-HIV-175558 (Reactome)
2-LTR form of circular viral DNA	Complex	R-HIV-175242 (Reactome)
AAAS	Protein	Q9NRG9 (Uniprot-TrEMBL)
ADP	Metabolite	CHEBI:16761 (ChEBI)
ATP	Metabolite	CHEBI:15422 (ChEBI)
ATP	Metabolite	CHEBI:15422 (ChEBI)
Aborted HIV-1 early elongation complex	Complex	R-HSA-167467 (Reactome)
Assembling HIV virion	Complex	R-HIV-3149451 (Reactome)
Autointegrated viral DNA as smaller circles	Complex	R-HIV-175037 (Reactome)
Autointegrated viral DNA as an inverted circle	Complex	R-HIV-175415 (Reactome)
BANF1	Protein	O75531 (Uniprot-TrEMBL)
BANF1	Protein	O75531 (Uniprot-TrEMBL)
CCNH	Protein	P51946 (Uniprot-TrEMBL)
CCNT1	Protein	O60563 (Uniprot-TrEMBL)
CCNT2	Protein	O60583 (Uniprot-TrEMBL)
CCR5	Protein	P51681 (Uniprot-TrEMBL)
CCR5, CXCR4		R-HSA-175536 (Reactome)
CD4	Protein	P01730 (Uniprot-TrEMBL)
CD4:Env gp120/gp41 hairpin complex:CCR5/CXCR4	Complex	R-HSA-171297 (Reactome)
CD4	Protein	P01730 (Uniprot-TrEMBL)
CDK7	Protein	P50613 (Uniprot-TrEMBL)
CDK9	Protein	P50750 (Uniprot-TrEMBL)
CE:Pol II CTD:Spt5 complex	Complex	R-HSA-167139 (Reactome)	Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CHMP2A	Protein	O43633 (Uniprot-TrEMBL)
CHMP2B	Protein	Q9UQN3 (Uniprot-TrEMBL)
CHMP3	Protein	Q9Y3E7 (Uniprot-TrEMBL)
CHMP4A	Protein	Q9BY43 (Uniprot-TrEMBL)
CHMP4B	Protein	Q9H444 (Uniprot-TrEMBL)
CHMP4C	Protein	Q96CF2 (Uniprot-TrEMBL)
CHMP5	Protein	Q9NZZ3 (Uniprot-TrEMBL)
CHMP6	Protein	Q96FZ7 (Uniprot-TrEMBL)
CHMP7	Protein	Q8WUX9 (Uniprot-TrEMBL)
CTDP1	Protein	Q9Y5B0 (Uniprot-TrEMBL)
CTDP1	Protein	Q9Y5B0 (Uniprot-TrEMBL)
CTP	Metabolite	CHEBI:17677 (ChEBI)
CXCR4	Protein	P61073 (Uniprot-TrEMBL)
Cap Binding Complex (CBC)	Complex	R-HSA-77088 (Reactome)
CoA-SH	Metabolite	CHEBI:15346 (ChEBI)
DSIF complex	Complex	R-HSA-112420 (Reactome)
DSIF:NELF:early elongation complex after limited nucleotide addition	Complex	R-HSA-170726 (Reactome)
DSIF:NELF:early elongation complex	Complex	R-HSA-167078 (Reactome)
ELL	Protein	P55199 (Uniprot-TrEMBL)
ELL	Protein	P55199 (Uniprot-TrEMBL)
ERCC2	Protein	P18074 (Uniprot-TrEMBL)
ERCC3	Protein	P19447 (Uniprot-TrEMBL)
ESCRT-III	Complex	R-HSA-917723 (Reactome)
ESCRT-I	Complex	R-HSA-184398 (Reactome)
Early elongation complex with separated aborted transcript	Complex	R-HSA-170736 (Reactome)
Elongin Complex	Complex	R-HSA-112425 (Reactome)
Encapsidated viral core	Complex	R-HIV-188943 (Reactome)
Envelope glycoprotein gp160	Protein	P04578 (Uniprot-TrEMBL)
Envelope glycoprotein gp160	Protein	P04578 (Uniprot-TrEMBL)
FACT complex	Complex	R-HSA-112417 (Reactome)
FEN1	Protein	P39748 (Uniprot-TrEMBL)
FURIN	Protein	P09958 (Uniprot-TrEMBL)
GAG Polyprotein (P04591)	Protein	P04591 (Uniprot-TrEMBL)
GAG-POL Polyprotein (P04585)	Protein	P04585 (Uniprot-TrEMBL)
GAG-POL Polyprotein (P04585)	Protein	P04585 (Uniprot-TrEMBL)
GDP	Metabolite	CHEBI:17552 (ChEBI)
GDP	Metabolite	CHEBI:17552 (ChEBI)
GTF2A1(1-274)	Protein	P52655 (Uniprot-TrEMBL)
GTF2A1(275-376)	Protein	P52655 (Uniprot-TrEMBL)
GTF2A2	Protein	P52657 (Uniprot-TrEMBL)
GTF2B	Protein	Q00403 (Uniprot-TrEMBL)
GTF2B	Protein	Q00403 (Uniprot-TrEMBL)
GTF2E1	Protein	P29083 (Uniprot-TrEMBL)
GTF2E2	Protein	P29084 (Uniprot-TrEMBL)
GTF2F1	Protein	P35269 (Uniprot-TrEMBL)
GTF2F2	Protein	P13984 (Uniprot-TrEMBL)
GTF2H1	Protein	P32780 (Uniprot-TrEMBL)
GTF2H2	Protein	Q13888 (Uniprot-TrEMBL)
GTF2H3	Protein	Q13889 (Uniprot-TrEMBL)
GTF2H4	Protein	Q92759 (Uniprot-TrEMBL)
GTF2H5	Protein	Q6ZYL4 (Uniprot-TrEMBL)
GTP	Metabolite	CHEBI:15996 (ChEBI)
GTP	Metabolite	CHEBI:15996 (ChEBI)
Glycosylated Envelope glycoprotein gp160	Protein	P04578 (Uniprot-TrEMBL)
HIV-1 Polymerase II (phosphorylated):TFIIF:capped pre-mRNA	Complex	R-HSA-167088 (Reactome)
HIV-1 Promoter Escape Complex	Complex	R-HSA-167472 (Reactome)
HIV-1 RNA	Protein	AF033819 (EMBL)
HIV-1 RNA homodimer	Complex	R-HIV-174985 (Reactome)
HIV-1 RNA template	Protein	AF033819 (EMBL)
HIV-1 Tat-containing aborted elongation complex after arrest	Complex	R-HSA-167460 (Reactome)
HIV-1 Tat-containing arrested processive elongation complex	Complex	R-HSA-167091 (Reactome)
HIV-1 Tat-containing paused processive elongation complex	Complex	R-HSA-167071 (Reactome)
HIV-1 Tat-containing processive elongation complex	Complex	R-HSA-167184 (Reactome)
HIV-1 aborted elongation complex after arrest	Complex	R-HSA-167482 (Reactome)
HIV-1 arrested processive elongation complex	Complex	R-HSA-167286 (Reactome)
HIV-1 capped pre-mRNA:CBC:RNA Pol II (phosphorylated) complex	Complex	R-HSA-167080 (Reactome)
HIV-1 closed pre-initiation complex	Complex	R-HSA-167125 (Reactome)
HIV-1 early elongation complex with hyperphosphorylated Pol II CTD	Complex	R-HSA-167075 (Reactome)
HIV-1 elongation complex containing Tat	Complex	R-HSA-167185 (Reactome)
HIV-1 elongation complex	Complex	R-HSA-167082 (Reactome)
HIV-1 initiation complex with phosphodiester-PPi intermediate	Complex	R-HSA-167106 (Reactome)
HIV-1 initiation complex	Complex	R-HSA-167129 (Reactome)
HIV-1 mRNA	Protein	AF033819 (EMBL)
HIV-1 mRNA	Rna	AF033819 (EMBL)
HIV-1 open pre-initiation complex	Complex	R-HSA-167137 (Reactome)
HIV-1 paused processive elongation complex	Complex	R-HSA-167283 (Reactome)
HIV-1 processive elongation complex	Complex	R-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 transcription complex containing 11 nucleotide long transcript	Complex	R-HSA-167132 (Reactome)
HIV-1 transcription complex containing 3 nucleotide long transcript	Complex	R-HSA-167119 (Reactome)
HIV-1 transcription complex containing 4 nucleotide long transcript	Complex	R-HSA-167124 (Reactome)
HIV-1 transcription complex containing 4-9 nucleotide long transcript	Complex	R-HSA-167471 (Reactome)
HIV-1 transcription complex containing 9 nucleotide long transcript	Complex	R-HSA-167100 (Reactome)
HIV-1 transcription complex containing extruded transcript to +30	Complex	R-HSA-167102 (Reactome)
HIV-1 transcription complex containing transcript to +30	Complex	R-HSA-167120 (Reactome)
HIV-1 transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30	Complex	R-HSA-167127 (Reactome)
HIV-1 transcription complex	Complex	R-HSA-167101 (Reactome)
HIV-1 unspliced RNA	Rna	AF033819 (EMBL)
HMGA1	Protein	P17096 (Uniprot-TrEMBL)
HMGA1	Protein	P17096 (Uniprot-TrEMBL)
Host genomic DNA		R-HSA-175158 (Reactome)
IN (Integrase) (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
IN (Integrase) (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
IN bound to sticky 3' ends of viral DNA in PIC	Complex	R-HIV-175416 (Reactome)
IN bound to sticky 3' ends of viral DNA in PIC	Complex	R-HIV-177526 (Reactome)
IN:viral DNA bound to host genomic DNA with staggered ends	Complex	R-HSA-175224 (Reactome)
Immature HIV virion	Complex	R-HIV-3139025 (Reactome)
Integrated provirus	Complex	R-HSA-175486 (Reactome)
Integration intermediate	Complex	R-HSA-175148 (Reactome)
KPNA1	Protein	P52294 (Uniprot-TrEMBL)
Ku proteins bound to viral DNA	Complex	R-HSA-175247 (Reactome)
LIG1	Protein	P18858 (Uniprot-TrEMBL)
LIG4	Protein	P49917 (Uniprot-TrEMBL)
MA (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
MA (P04591) protein	Protein	P04591 (Uniprot-TrEMBL)
MNAT1	Protein	P51948 (Uniprot-TrEMBL)
MYS-CoA	Metabolite	CHEBI:15532 (ChEBI)
Matrix		R-HIV-173120 (Reactome)
Mature HIV virion	Complex	R-HIV-175514 (Reactome)
Multimeric capsid coat		R-HIV-175314 (Reactome)
N-myristoyl GAG (P04591) protein	Protein	P04591 (Uniprot-TrEMBL)
N-myristoyl GAG (P04591) protein	Protein	P04591 (Uniprot-TrEMBL)
N-myristoyl GAG	Protein	P04591 (Uniprot-TrEMBL)
NC (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
NC (P04591) protein	Protein	P04591 (Uniprot-TrEMBL)
NCBP1	Protein	Q09161 (Uniprot-TrEMBL)
NCBP2	Protein	P52298 (Uniprot-TrEMBL)
NEDD4L	Protein	Q96PU5 (Uniprot-TrEMBL)
NEDD4L	Protein	Q96PU5 (Uniprot-TrEMBL)
NELF complex	Complex	R-HSA-112432 (Reactome)
NELFA	Protein	Q9H3P2 (Uniprot-TrEMBL)
NELFB	Protein	Q8WX92 (Uniprot-TrEMBL)
NELFCD	Protein	Q8IXH7 (Uniprot-TrEMBL)
NELFE	Protein	P18615 (Uniprot-TrEMBL)
NMT 1	Protein	P30419 (Uniprot-TrEMBL)
NMT2	Protein	O60551 (Uniprot-TrEMBL)
NTP		R-ALL-30595 (Reactome)
NUP107	Protein	P57740 (Uniprot-TrEMBL)
NUP133	Protein	Q8WUM0 (Uniprot-TrEMBL)
NUP153	Protein	P49790 (Uniprot-TrEMBL)
NUP155	Protein	O75694 (Uniprot-TrEMBL)
NUP160	Protein	Q12769 (Uniprot-TrEMBL)
NUP188	Protein	Q5SRE5 (Uniprot-TrEMBL)
NUP205	Protein	Q92621 (Uniprot-TrEMBL)
NUP210	Protein	Q8TEM1 (Uniprot-TrEMBL)
NUP214	Protein	P35658 (Uniprot-TrEMBL)
NUP35	Protein	Q8NFH5 (Uniprot-TrEMBL)
NUP37	Protein	Q8NFH4 (Uniprot-TrEMBL)
NUP43	Protein	Q8NFH3 (Uniprot-TrEMBL)
NUP50	Protein	Q9UKX7 (Uniprot-TrEMBL)
NUP54	Protein	Q7Z3B4 (Uniprot-TrEMBL)
NUP62	Protein	P37198 (Uniprot-TrEMBL)
NUP85	Protein	Q9BW27 (Uniprot-TrEMBL)
NUP88	Protein	Q99567 (Uniprot-TrEMBL)
NUP93	Protein	Q8N1F7 (Uniprot-TrEMBL)
NUP98-5	Protein	P52948-5 (Uniprot-TrEMBL)
NUPL1-2	Protein	Q9BVL2-1 (Uniprot-TrEMBL)
NUPL2	Protein	O15504 (Uniprot-TrEMBL)
Nef Protein (UniProt:P04601)	Protein	P04601 (Uniprot-TrEMBL)
Nuclear Pore Complex (NPC)	Complex	R-HSA-157689 (Reactome)
Nucleocapsid		R-HIV-175167 (Reactome)
Nup45	Protein	Q9BVL2-2 (Uniprot-TrEMBL)
P-TEFb complex	Complex	R-HSA-112431 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complex	Complex	R-HSA-167183 (Reactome)
P-TEFb(Cyclin T1:Cdk9)-containing elongation complex with separated and uncleaved transcript	Complex	R-HSA-167199 (Reactome)
PDCD6IP	Protein	Q8WUM4 (Uniprot-TrEMBL)
PDCD6IP	Protein	Q8WUM4 (Uniprot-TrEMBL)
PIC (PreIntegration Complex)	Complex	R-HIV-175143 (Reactome)
POLR2A	Protein	P24928 (Uniprot-TrEMBL)
POLR2B	Protein	P30876 (Uniprot-TrEMBL)
POLR2C	Protein	P19387 (Uniprot-TrEMBL)
POLR2D	Protein	O15514 (Uniprot-TrEMBL)
POLR2E	Protein	P19388 (Uniprot-TrEMBL)
POLR2F	Protein	P61218 (Uniprot-TrEMBL)
POLR2G	Protein	P62487 (Uniprot-TrEMBL)
POLR2H	Protein	P52434 (Uniprot-TrEMBL)
POLR2I	Protein	P36954 (Uniprot-TrEMBL)
POLR2J	Protein	P52435 (Uniprot-TrEMBL)
POLR2K	Protein	P53803 (Uniprot-TrEMBL)
POLR2L	Protein	P62875 (Uniprot-TrEMBL)
POM121	Protein	Q96HA1 (Uniprot-TrEMBL)
PPIA	Protein	P62937 (Uniprot-TrEMBL)
PPIA	Protein	P62937 (Uniprot-TrEMBL)
PPi	Metabolite	CHEBI:29888 (ChEBI)
PR (Protease) (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
PR (Protease) (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
PSIP1	Protein	O75475 (Uniprot-TrEMBL)
PSIP1	Protein	O75475 (Uniprot-TrEMBL)
Pi	Metabolite	CHEBI:18367 (ChEBI)
RAE1	Protein	P78406 (Uniprot-TrEMBL)
RAN	Protein	P62826 (Uniprot-TrEMBL)
RANBP1	Protein	P43487 (Uniprot-TrEMBL)
RANBP1	Protein	P43487 (Uniprot-TrEMBL)
RANBP2	Protein	P49792 (Uniprot-TrEMBL)
RANGAP1	Protein	P46060 (Uniprot-TrEMBL)
RCC1	Protein	P18754 (Uniprot-TrEMBL)
REV (P04618) protein	Protein	P04618 (Uniprot-TrEMBL)
REV (P04618) protein	Protein	P04618 (Uniprot-TrEMBL)
RNA Pol II (hypophosphorylated) complex bound to DSIF protein	Complex	R-HSA-167070 (Reactome)
RNA Pol II (hypophosphorylated):capped pre-mRNA complex	Complex	R-HSA-167086 (Reactome)
RNA Polymerase II (unphosphorylated):TFIIF complex	Complex	R-HSA-71307 (Reactome)
RNA Pol II with phosphorylated CTD: CE complex with activated GT	Complex	R-HSA-167123 (Reactome)
RNA Pol II with phosphorylated CTD: CE complex	Complex	R-HSA-167107 (Reactome)
RNGTT	Protein	O60942 (Uniprot-TrEMBL)
RNGTT	Protein	O60942 (Uniprot-TrEMBL)
RNMT	Protein	O43148 (Uniprot-TrEMBL)
RNMT	Protein	O43148 (Uniprot-TrEMBL)
RPS27A(1-76)	Protein	P62979 (Uniprot-TrEMBL)
RTC (Reverse Transcription Complex) with RNA template	Complex	R-HIV-173814 (Reactome)
RTC with annealed complementary PBS seqments in +sssDNA and -strand DNA	Complex	R-HIV-173792 (Reactome)
RTC with degraded RNA template and minus sssDNA	Complex	R-HIV-173773 (Reactome)
RTC with duplex DNA containing discontinuous plus strand flap	Complex	R-HIV-188560 (Reactome)
RTC with extending minus strand DNA	Complex	R-HIV-173764 (Reactome)
RTC with extending second-strand DNA	Complex	R-HIV-182880 (Reactome)
RTC with extensive RNase-H digestion	Complex	R-HIV-173789 (Reactome)
RTC with integration competent viral DNA	Complex	R-HIV-175254 (Reactome)
RTC with minus sssDNA transferred to 3'-end of viral RNA template	Complex	R-HIV-173779 (Reactome)
RTC with minus sssDNA:tRNA primer:RNA template	Complex	R-HIV-173774 (Reactome)
RTC with minus strand DNA synthesis initiated from 3'-end	Complex	R-HIV-173786 (Reactome)
RTC with nicked minus sssDNA:tRNA primer:RNA template	Complex	R-HIV-182804 (Reactome)
RTC with tRNA primer:RNA template	Complex	R-HIV-173801 (Reactome)
RTC without viral RNA template	Complex	R-HIV-173824 (Reactome)
RT	Complex	R-HIV-173772 (Reactome)
Ran GTPase:GDP	Complex	R-HSA-165549 (Reactome)
Ran-GDP	Complex	R-HSA-180701 (Reactome)
Ran-GTP	Complex	R-HSA-180738 (Reactome)
Ran:GTP	Complex	R-HSA-180686 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complex	Complex	R-HSA-180718 (Reactome)
Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP:NPC	Complex	R-HSA-165531 (Reactome)
Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP	Complex	R-HSA-165537 (Reactome)
Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP	Complex	R-HSA-165552 (Reactome)
Rev multimer-bound HIV-1 mRNA:CRM1 complex	Complex	R-HSA-180873 (Reactome)
Rev multimer-bound HIV-1 mRNA	Complex	R-HIV-165532 (Reactome)
Rev-bound HIV-1 mRNA	Complex	R-HIV-165535 (Reactome)
Rev-multimer		R-HIV-165542 (Reactome)
Rev-multimer		R-HIV-165543 (Reactome)
Reverse transcriptase/ribonuclease H	Protein	P04585 (Uniprot-TrEMBL)
SEH1L-2	Protein	Q96EE3-2 (Uniprot-TrEMBL)
SSRP1	Protein	Q08945 (Uniprot-TrEMBL)
SUPT16H	Protein	Q9Y5B9 (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	Protein	P63272 (Uniprot-TrEMBL)
Spliced Env mRNA	Rna	AF033819 (EMBL)
Surface protein gp120 (P04578)	Protein	P04578 (Uniprot-TrEMBL)
Surface protein gp120	Protein	P04578 (Uniprot-TrEMBL)
TAF1	Protein	P21675 (Uniprot-TrEMBL)
TAF10	Protein	Q12962 (Uniprot-TrEMBL)
TAF11	Protein	Q15544 (Uniprot-TrEMBL)
TAF12	Protein	Q16514 (Uniprot-TrEMBL)
TAF13	Protein	Q15543 (Uniprot-TrEMBL)
TAF1L	Protein	Q8IZX4 (Uniprot-TrEMBL)
TAF2	Protein	Q6P1X5 (Uniprot-TrEMBL)
TAF3	Protein	Q5VWG9 (Uniprot-TrEMBL)
TAF4	Protein	O00268 (Uniprot-TrEMBL)
TAF4B	Protein	Q92750 (Uniprot-TrEMBL)
TAF5	Protein	Q15542 (Uniprot-TrEMBL)
TAF6	Protein	P49848 (Uniprot-TrEMBL)
TAF9	Protein	Q16594 (Uniprot-TrEMBL)
TAF9B	Protein	Q9HBM6 (Uniprot-TrEMBL)
TBP	Protein	P20226 (Uniprot-TrEMBL)
TCEA1	Protein	P23193 (Uniprot-TrEMBL)
TCEA1	Protein	P23193 (Uniprot-TrEMBL)
TCEB1	Protein	Q15369 (Uniprot-TrEMBL)
TCEB2	Protein	Q15370 (Uniprot-TrEMBL)
TCEB3	Protein	Q14241 (Uniprot-TrEMBL)
TFIIA	Complex	R-HSA-109629 (Reactome)
TFIID	Complex	R-HSA-109626 (Reactome)
TFIIE	Complex	R-HSA-109633 (Reactome)
TFIIH	Complex	R-HSA-109634 (Reactome)
TPR	Protein	P12270 (Uniprot-TrEMBL)
TSG101	Protein	Q99816 (Uniprot-TrEMBL)
Tat (P04608)	Protein	P04608 (Uniprot-TrEMBL)
Tat (P04608)	Protein	P04608 (Uniprot-TrEMBL)
Tat-containing elongation complex prior to separation	Complex	R-HSA-167193 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD ( phospho-NELF phospho DSIF)	Complex	R-HSA-170710 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD and phospho-NELF	Complex	R-HSA-170707 (Reactome)
Tat-containing early elongation complex with hyperphosphorylated Pol II CTD	Complex	R-HSA-167182 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complex	Complex	R-NUL-167237 (Reactome)
Transmembrane protein gp41 (P04578)	Protein	P04578 (Uniprot-TrEMBL)
Transmembrane protein gp41	Protein	P04578 (Uniprot-TrEMBL)
Trimeric ENV precursor	Complex	R-HIV-189843 (Reactome)
Trimeric ENV precursor	Complex	R-HIV-3149446 (Reactome)
Trimeric gp120:gp41 oligomer	Complex	R-HIV-189281 (Reactome)
Trimeric gp120:gp41 oligomer	Complex	R-HIV-189840 (Reactome)
UBA52(1-76)	Protein	P62987 (Uniprot-TrEMBL)
UBB(1-76)	Protein	P0CG47 (Uniprot-TrEMBL)
UBB(153-228)	Protein	P0CG47 (Uniprot-TrEMBL)
UBB(77-152)	Protein	P0CG47 (Uniprot-TrEMBL)
UBC(1-76)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(153-228)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(229-304)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(305-380)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(381-456)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(457-532)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(533-608)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(609-684)	Protein	P0CG48 (Uniprot-TrEMBL)
UBC(77-152)	Protein	P0CG48 (Uniprot-TrEMBL)
UTP	Metabolite	CHEBI:15713 (ChEBI)
Ub		R-HSA-113595 (Reactome)
VIF (P69723) protein	Protein	P69723 (Uniprot-TrEMBL)
VIF (P69723) protein	Protein	P69723 (Uniprot-TrEMBL)
VPR (P69726) protein	Protein	P69726 (Uniprot-TrEMBL)
VPR	Protein	P69726 (Uniprot-TrEMBL)
VPR	Protein	P69726 (Uniprot-TrEMBL)
VPS28	Protein	Q9UK41 (Uniprot-TrEMBL)
VPS37A	Protein	Q8NEZ2 (Uniprot-TrEMBL)
VPS37B	Protein	Q9H9H4 (Uniprot-TrEMBL)
VPS37C	Protein	A5D8V6 (Uniprot-TrEMBL)
VPS37D	Protein	Q86XT2 (Uniprot-TrEMBL)
VPS4A	Protein	Q9UN37 (Uniprot-TrEMBL)
VPS4B	Protein	O75351 (Uniprot-TrEMBL)
VPU (P05919) protein	Protein	P05919 (Uniprot-TrEMBL)
VPU (P05919)	Protein	P05919 (Uniprot-TrEMBL)
VTA1	Protein	Q9NP79 (Uniprot-TrEMBL)
Viral core surrounded by Matrix layer	Complex	R-HIV-173664 (Reactome)
Virion Budding Complex	Complex	R-HSA-3211408 (Reactome)
Virion with CD4:gp120 bound to CCR5/CXCR4	Complex	R-HIV-173663 (Reactome)
Virion with fusogenically activated gp41	Complex	R-HIV-173639 (Reactome)
Virion with CD4 bound to gp120	Complex	R-HIV-173650 (Reactome)
Virion with exposed coreceptor binding sites	Complex	R-HIV-173648 (Reactome)
Virion with gp41 exposed	Complex	R-HIV-173665 (Reactome)
Virion with gp41 forming hairpin structure	Complex	R-HIV-173649 (Reactome)
Virion with gp41 fusion peptide in insertion complex	Complex	R-HIV-173656 (Reactome)
Vpr:importin-alpha complex	Complex	R-HSA-180623 (Reactome)
Vps/Vta1	Complex	R-HSA-917724 (Reactome)
XPO1	Protein	O14980 (Uniprot-TrEMBL)
XPO1	Protein	O14980 (Uniprot-TrEMBL)
XRCC4	Protein	Q13426 (Uniprot-TrEMBL)
XRCC4:LIG4	Complex	R-HSA-75912 (Reactome)
XRCC5	Protein	P13010 (Uniprot-TrEMBL)
XRCC5:XRCC6	Complex	R-HSA-75905 (Reactome)
XRCC6	Protein	P12956 (Uniprot-TrEMBL)
dNTP		R-ALL-173818 (Reactome)
monoubiquitinated N-myristoyl GAG (P04591) protein	Complex	R-HSA-184369 (Reactome)
monoubiquitinated N-myristoyl GAG (P04591) protein	Complex	R-HSA-184475 (Reactome)
monoubiquitinated N-myristoyl GAG (P04591) protein	Complex	R-HSA-3149449 (Reactome)
myristoylated Nef Protein (UniProt:P04601)	Protein	P04601 (Uniprot-TrEMBL)
myristoylated Nef Protein (UniProt:P04601)	Protein	P04601 (Uniprot-TrEMBL)
other viral genomic RNA	Rna	AF033819 (EMBL)
p-NELFE	Protein	P18615 (Uniprot-TrEMBL)
p-S2,S5-POLR2A	Protein	P24928 (Uniprot-TrEMBL)
p-S5-POLR2A	Protein	P24928 (Uniprot-TrEMBL)
p-SUPT5H	Protein	O00267 (Uniprot-TrEMBL)
p-SUPT5H	Protein	O00267 (Uniprot-TrEMBL)
p51 (RT)	Protein	P04585 (Uniprot-TrEMBL)
p6 (P04585)	Protein	P04585 (Uniprot-TrEMBL)
p6 (P04585) protein	Protein	P04585 (Uniprot-TrEMBL)
p6 (P04591)	Protein	P04591 (Uniprot-TrEMBL)
p6 (P04591) protein	Protein	P04591 (Uniprot-TrEMBL)
tRNA-Lysine3		R-HSA-173782 (Reactome)
uncoated viral complex	Complex	R-HIV-173653 (Reactome)
viral DNA bound with Integrase in PIC	Complex	R-HIV-177532 (Reactome)
viral DNA:Ku proteins:XRCC4:DNA ligase IV complex	Complex	R-HSA-175440 (Reactome)
viral PIC proteins	Complex	R-HSA-177527 (Reactome)
viral RNA template being digested by RNase-H (extensive)	Protein	AF033819 (EMBL)
viral RNA template degraded by RNase-H (initial)	Protein	AF033819 (EMBL)
viral RNA template extensively digested except in PPT region	Protein	AF033819 (EMBL)

Annotated Interactions

View all...

Source	Target	Type	Database reference	Comment
	1-LTR form of circular viral DNA	Arrow	R-HSA-175117 (Reactome)
	2-LTR form of circular viral DNA	Arrow	R-HSA-175258 (Reactome)
	ADP	Arrow	R-HSA-167097 (Reactome)
	ADP	Arrow	R-HSA-170704 (Reactome)
	ADP	Arrow	R-HSA-170706 (Reactome)
ATP			R-HSA-167097 (Reactome)
ATP			R-HSA-170704 (Reactome)
ATP			R-HSA-170706 (Reactome)
	Aborted HIV-1 early elongation complex	Arrow	R-HSA-167478 (Reactome)
	Assembling HIV virion	Arrow	R-HSA-3149454 (Reactome)
Assembling HIV virion			R-HSA-3159227 (Reactome)
	Autointegrated viral DNA as smaller circles	Arrow	R-HSA-175250 (Reactome)
	Autointegrated viral DNA as an inverted circle	Arrow	R-HSA-164845 (Reactome)
BANF1			R-HSA-173115 (Reactome)
CCR5, CXCR4			R-HSA-164507 (Reactome)
	CD4:Env gp120/gp41 hairpin complex:CCR5/CXCR4	Arrow	R-HSA-164524 (Reactome)
CD4			R-HSA-164509 (Reactome)
	CE:Pol II CTD:Spt5 complex	Arrow	R-HSA-167153 (Reactome)
CTDP1			R-HSA-167072 (Reactome)
CTDP1		mim-catalysis	R-HSA-167072 (Reactome)
	Cap Binding Complex (CBC)	Arrow	R-HSA-167084 (Reactome)
	Cap Binding Complex (CBC)	Arrow	R-HSA-167191 (Reactome)
Cap Binding Complex (CBC)			R-HSA-167089 (Reactome)
	CoA-SH	Arrow	R-HSA-162914 (Reactome)
	CoA-SH	Arrow	R-HSA-184392 (Reactome)
DSIF complex			R-HSA-167083 (Reactome)
	DSIF:NELF:early elongation complex after limited nucleotide addition	Arrow	R-HSA-167087 (Reactome)
DSIF:NELF:early elongation complex after limited nucleotide addition			R-HSA-167147 (Reactome)
	DSIF:NELF:early elongation complex	Arrow	R-HSA-167085 (Reactome)
DSIF:NELF:early elongation complex			R-HSA-167084 (Reactome)
DSIF:NELF:early elongation complex			R-HSA-167087 (Reactome)
DSIF:NELF:early elongation complex			R-HSA-167191 (Reactome)
DSIF:NELF:early elongation complex			R-HSA-167478 (Reactome)
ELL			R-HSA-167077 (Reactome)
ELL			R-HSA-167196 (Reactome)
ESCRT-III			R-HSA-3159232 (Reactome)
ESCRT-I			R-HSA-3159232 (Reactome)
ESCRT-I		mim-catalysis	R-HSA-184269 (Reactome)
ESCRT-I		mim-catalysis	R-HSA-3149434 (Reactome)
	Early elongation complex with separated aborted transcript	Arrow	R-HSA-167147 (Reactome)
Elongin Complex			R-HSA-167077 (Reactome)
Elongin Complex			R-HSA-167196 (Reactome)
	Encapsidated viral core	Arrow	R-HSA-173642 (Reactome)
Encapsidated viral core			R-HSA-173111 (Reactome)
	Envelope glycoprotein gp160	Arrow	R-HSA-174493 (Reactome)
	Envelope glycoprotein gp160	Arrow	R-HSA-174494 (Reactome)
Envelope glycoprotein gp160			R-HSA-171291 (Reactome)
Envelope glycoprotein gp160			R-HSA-174493 (Reactome)
FACT complex			R-HSA-167077 (Reactome)
FACT complex			R-HSA-167196 (Reactome)
FEN1		Arrow	R-HSA-182876 (Reactome)
FURIN		mim-catalysis	R-HSA-171288 (Reactome)
	GAG Polyprotein (P04591)	Arrow	R-HSA-187213 (Reactome)
GAG Polyprotein (P04591)			R-HSA-184392 (Reactome)
GAG-POL Polyprotein (P04585)			R-HSA-3149454 (Reactome)
GAG-POL Polyprotein (P04585)		mim-catalysis	R-HSA-3139027 (Reactome)
	GDP	Arrow	R-HSA-180687 (Reactome)
	GTF2B	Arrow	R-HSA-167113 (Reactome)
	GTF2B	Arrow	R-HSA-167474 (Reactome)
	GTF2B	Arrow	R-HSA-167477 (Reactome)
GTP			R-HSA-180687 (Reactome)
HIV-1 Polymerase II (phosphorylated):TFIIF:capped pre-mRNA			R-HSA-167089 (Reactome)
HIV-1 Promoter Escape Complex			R-HSA-167474 (Reactome)
HIV-1 RNA homodimer			R-HSA-3149454 (Reactome)
	HIV-1 Tat-containing aborted elongation complex after arrest	Arrow	R-HSA-167459 (Reactome)
	HIV-1 Tat-containing arrested processive elongation complex	Arrow	R-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	Arrow	R-HSA-167076 (Reactome)
HIV-1 Tat-containing paused processive elongation complex			R-HSA-167150 (Reactome)
	HIV-1 Tat-containing processive elongation complex	Arrow	R-HSA-167148 (Reactome)
	HIV-1 Tat-containing processive elongation complex	Arrow	R-HSA-167150 (Reactome)
	HIV-1 Tat-containing processive elongation complex	Arrow	R-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	Arrow	R-HSA-167481 (Reactome)
	HIV-1 arrested processive elongation complex	Arrow	R-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	Arrow	R-HSA-167089 (Reactome)
HIV-1 capped pre-mRNA:CBC:RNA Pol II (phosphorylated) complex			R-HSA-167072 (Reactome)
	HIV-1 closed pre-initiation complex	Arrow	R-HSA-167484 (Reactome)
HIV-1 closed pre-initiation complex			R-HSA-167097 (Reactome)
	HIV-1 early elongation complex with hyperphosphorylated Pol II CTD	Arrow	R-HSA-167084 (Reactome)
HIV-1 early elongation complex with hyperphosphorylated Pol II CTD			R-HSA-167077 (Reactome)
	HIV-1 elongation complex containing Tat	Arrow	R-HSA-167196 (Reactome)
HIV-1 elongation complex containing Tat			R-HSA-167181 (Reactome)
	HIV-1 elongation complex	Arrow	R-HSA-167077 (Reactome)
	HIV-1 initiation complex with phosphodiester-PPi intermediate	Arrow	R-HSA-167130 (Reactome)
HIV-1 initiation complex with phosphodiester-PPi intermediate			R-HSA-167134 (Reactome)
	HIV-1 initiation complex	Arrow	R-HSA-167118 (Reactome)
HIV-1 initiation complex			R-HSA-167130 (Reactome)
HIV-1 mRNA			R-HSA-165027 (Reactome)
HIV-1 mRNA			R-HSA-187211 (Reactome)
	HIV-1 open pre-initiation complex	Arrow	R-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	Arrow	R-HSA-167282 (Reactome)
HIV-1 paused processive elongation complex			R-HSA-167292 (Reactome)
	HIV-1 processive elongation complex	Arrow	R-HSA-167288 (Reactome)
	HIV-1 processive elongation complex	Arrow	R-HSA-167292 (Reactome)
HIV-1 processive elongation complex			R-HSA-167282 (Reactome)
HIV-1 processive elongation complex			R-HSA-167284 (Reactome)
	HIV-1 template DNA:4-9 nucleotide transcript hybrid	Arrow	R-HSA-167468 (Reactome)
	HIV-1 template DNA containing promoter with transcript of 2 or 3 nucleotides	Arrow	R-HSA-167474 (Reactome)
	HIV-1 template DNA with first transcript dinucleotide, opened to +8 position	Arrow	R-HSA-167477 (Reactome)
	HIV-1 transcription complex containing 11 nucleotide long transcript	Arrow	R-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	Arrow	R-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	Arrow	R-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	Arrow	R-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	Arrow	R-HSA-167111 (Reactome)
HIV-1 transcription complex containing extruded transcript to +30			R-HSA-167098 (Reactome)
	HIV-1 transcription complex containing transcript to +30	Arrow	R-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	Arrow	R-HSA-167098 (Reactome)
HIV-1 transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30			R-HSA-167128 (Reactome)
	HIV-1 transcription complex	Arrow	R-HSA-167134 (Reactome)
HIV-1 transcription complex			R-HSA-167121 (Reactome)
HIV-1 transcription complex			R-HSA-167477 (Reactome)
	HIV-1 unspliced RNA	Arrow	R-HSA-165028 (Reactome)
HIV-1 unspliced RNA			R-HSA-187213 (Reactome)
HMGA1			R-HSA-173115 (Reactome)
Host genomic DNA			R-HSA-175108 (Reactome)
	IN (Integrase) (P04585) protein	Arrow	R-HSA-164506 (Reactome)
	IN (Integrase) (P04585) protein	Arrow	R-HSA-164845 (Reactome)
	IN (Integrase) (P04585) protein	Arrow	R-HSA-175117 (Reactome)
	IN (Integrase) (P04585) protein	Arrow	R-HSA-175250 (Reactome)
	IN (Integrase) (P04585) protein	Arrow	R-HSA-175258 (Reactome)
	IN bound to sticky 3' ends of viral DNA in PIC	Arrow	R-HSA-162590 (Reactome)
	IN bound to sticky 3' ends of viral DNA in PIC	Arrow	R-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	Arrow	R-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-catalysis	R-HSA-164523 (Reactome)
	Immature HIV virion	Arrow	R-HSA-3159227 (Reactome)
Immature HIV virion			R-HSA-3139027 (Reactome)
	Integrated provirus	Arrow	R-HSA-164506 (Reactome)
	Integration intermediate	Arrow	R-HSA-164523 (Reactome)
Integration intermediate			R-HSA-164506 (Reactome)
	Ku proteins bound to viral DNA	Arrow	R-HSA-175174 (Reactome)
Ku proteins bound to viral DNA			R-HSA-175177 (Reactome)
LIG1		Arrow	R-HSA-182876 (Reactome)
MYS-CoA			R-HSA-162914 (Reactome)
MYS-CoA			R-HSA-184392 (Reactome)
	Matrix	Arrow	R-HSA-173642 (Reactome)
	Mature HIV virion	Arrow	R-HSA-3139027 (Reactome)
Mature HIV virion			R-HSA-164509 (Reactome)
	Multimeric capsid coat	Arrow	R-HSA-173111 (Reactome)
	N-myristoyl GAG (P04591) protein	Arrow	R-HSA-184392 (Reactome)
N-myristoyl GAG (P04591) protein			R-HSA-184323 (Reactome)
NEDD4L			R-HSA-3159232 (Reactome)
NELF complex			R-HSA-167085 (Reactome)
NMT 1		mim-catalysis	R-HSA-162914 (Reactome)
NMT2		mim-catalysis	R-HSA-184392 (Reactome)
	NTP	Arrow	R-HSA-167085 (Reactome)
	NTP	Arrow	R-HSA-167192 (Reactome)
NTP			R-HSA-167085 (Reactome)
NTP			R-HSA-167087 (Reactome)
NTP			R-HSA-167113 (Reactome)
NTP			R-HSA-167115 (Reactome)
NTP			R-HSA-167117 (Reactome)
NTP			R-HSA-167118 (Reactome)
NTP			R-HSA-167121 (Reactome)
NTP			R-HSA-167136 (Reactome)
NTP			R-HSA-167181 (Reactome)
NTP			R-HSA-167192 (Reactome)
Nef Protein (UniProt:P04601)			R-HSA-162914 (Reactome)
	Nuclear Pore Complex (NPC)	Arrow	R-HSA-165047 (Reactome)
Nuclear Pore Complex (NPC)			R-HSA-165043 (Reactome)
	Nucleocapsid	Arrow	R-HSA-173771 (Reactome)
P-TEFb complex			R-HSA-167084 (Reactome)
P-TEFb complex		mim-catalysis	R-HSA-167084 (Reactome)
P-TEFb(Cyclin T1:Cdk9) complex			R-HSA-167234 (Reactome)
	P-TEFb(Cyclin T1:Cdk9)-containing elongation complex with separated and uncleaved transcript	Arrow	R-HSA-167197 (Reactome)
PDCD6IP			R-HSA-3159232 (Reactome)
	PIC (PreIntegration Complex)	Arrow	R-HSA-173115 (Reactome)
PIC (PreIntegration Complex)			R-HSA-164514 (Reactome)
	PPIA	Arrow	R-HSA-173115 (Reactome)
PPIA			R-HSA-3149454 (Reactome)
	PPi	Arrow	R-HSA-164504 (Reactome)
	PPi	Arrow	R-HSA-167113 (Reactome)
	PPi	Arrow	R-HSA-167115 (Reactome)
	PPi	Arrow	R-HSA-167117 (Reactome)
	PPi	Arrow	R-HSA-167121 (Reactome)
	PPi	Arrow	R-HSA-167134 (Reactome)
	PPi	Arrow	R-HSA-167136 (Reactome)
	PR (Protease) (P04585) protein	Arrow	R-HSA-173771 (Reactome)
PSIP1			R-HSA-173115 (Reactome)
	Pi	Arrow	R-HSA-165055 (Reactome)
	Pi	Arrow	R-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.
			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.
			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'.
			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.
			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.
			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'.
			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.
	RANBP1	Arrow	R-HSA-165028 (Reactome)
RANBP1		Arrow	R-HSA-165055 (Reactome)
RANBP1			R-HSA-180739 (Reactome)
RANGAP1		Arrow	R-HSA-165055 (Reactome)
RCC1		mim-catalysis	R-HSA-180687 (Reactome)
	REV (P04618) protein	Arrow	R-HSA-165028 (Reactome)
REV (P04618) protein			R-HSA-165027 (Reactome)
REV (P04618) protein			R-HSA-3149454 (Reactome)
	RNA Pol II (hypophosphorylated) complex bound to DSIF protein	Arrow	R-HSA-167083 (Reactome)
RNA Pol II (hypophosphorylated) complex bound to DSIF protein			R-HSA-167085 (Reactome)
	RNA Pol II (hypophosphorylated):capped pre-mRNA complex	Arrow	R-HSA-167072 (Reactome)
RNA Pol II (hypophosphorylated):capped pre-mRNA complex			R-HSA-167083 (Reactome)
	RNA Polymerase II (unphosphorylated):TFIIF complex	Arrow	R-HSA-167468 (Reactome)
	RNA Polymerase II (unphosphorylated):TFIIF complex	Arrow	R-HSA-167474 (Reactome)
	RNA Polymerase II (unphosphorylated):TFIIF complex	Arrow	R-HSA-167477 (Reactome)
RNA Polymerase II (unphosphorylated):TFIIF complex		mim-catalysis	R-HSA-167113 (Reactome)
RNA Polymerase II (unphosphorylated):TFIIF complex		mim-catalysis	R-HSA-167115 (Reactome)
RNA Polymerase II (unphosphorylated):TFIIF complex		mim-catalysis	R-HSA-167117 (Reactome)
RNA Polymerase II (unphosphorylated):TFIIF complex		mim-catalysis	R-HSA-167121 (Reactome)
RNA Polymerase II (unphosphorylated):TFIIF complex		mim-catalysis	R-HSA-167136 (Reactome)
	RNA Pol II with phosphorylated CTD: CE complex with activated GT	Arrow	R-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	Arrow	R-HSA-167128 (Reactome)
RNA Pol II with phosphorylated CTD: CE complex			R-HSA-167133 (Reactome)
RNGTT			R-HSA-167128 (Reactome)
RNMT			R-HSA-167153 (Reactome)
	RT	Arrow	R-HSA-173115 (Reactome)
	RTC (Reverse Transcription Complex) with RNA template	Arrow	R-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	Arrow	R-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-catalysis	R-HSA-164505 (Reactome)
	RTC with degraded RNA template and minus sssDNA	Arrow	R-HSA-182859 (Reactome)
RTC with degraded RNA template and minus sssDNA			R-HSA-164503 (Reactome)
	RTC with duplex DNA containing discontinuous plus strand flap	Arrow	R-HSA-164505 (Reactome)
RTC with duplex DNA containing discontinuous plus strand flap			R-HSA-182876 (Reactome)
	RTC with extending minus strand DNA	Arrow	R-HSA-182795 (Reactome)
RTC with extending minus strand DNA			R-HSA-164513 (Reactome)
RTC with extending minus strand DNA		mim-catalysis	R-HSA-164513 (Reactome)
	RTC with extending second-strand DNA	Arrow	R-HSA-164513 (Reactome)
RTC with extending second-strand DNA			R-HSA-173769 (Reactome)
RTC with extending second-strand DNA		mim-catalysis	R-HSA-173769 (Reactome)
	RTC with extensive RNase-H digestion	Arrow	R-HSA-164528 (Reactome)
RTC with extensive RNase-H digestion			R-HSA-182795 (Reactome)
RTC with extensive RNase-H digestion		mim-catalysis	R-HSA-182795 (Reactome)
	RTC with integration competent viral DNA	Arrow	R-HSA-182876 (Reactome)
RTC with integration competent viral DNA			R-HSA-173115 (Reactome)
	RTC with minus sssDNA transferred to 3'-end of viral RNA template	Arrow	R-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-catalysis	R-HSA-164520 (Reactome)
	RTC with minus sssDNA:tRNA primer:RNA template	Arrow	R-HSA-164504 (Reactome)
RTC with minus sssDNA:tRNA primer:RNA template			R-HSA-164519 (Reactome)
RTC with minus sssDNA:tRNA primer:RNA template		mim-catalysis	R-HSA-164519 (Reactome)
	RTC with minus strand DNA synthesis initiated from 3'-end	Arrow	R-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-catalysis	R-HSA-164528 (Reactome)
	RTC with nicked minus sssDNA:tRNA primer:RNA template	Arrow	R-HSA-164519 (Reactome)
RTC with nicked minus sssDNA:tRNA primer:RNA template			R-HSA-182859 (Reactome)
	RTC with tRNA primer:RNA template	Arrow	R-HSA-164527 (Reactome)
RTC with tRNA primer:RNA template			R-HSA-164504 (Reactome)
RTC with tRNA primer:RNA template		mim-catalysis	R-HSA-164504 (Reactome)
	RTC without viral RNA template	Arrow	R-HSA-173769 (Reactome)
RTC without viral RNA template			R-HSA-164512 (Reactome)
RT		mim-catalysis	R-HSA-182859 (Reactome)
	Ran GTPase:GDP	Arrow	R-HSA-165055 (Reactome)
Ran-GDP			R-HSA-180687 (Reactome)
	Ran-GTP	Arrow	R-HSA-180687 (Reactome)
Ran-GTP			R-HSA-165034 (Reactome)
	Ran:GTP	Arrow	R-HSA-165028 (Reactome)
Ran:GTP			R-HSA-165055 (Reactome)
	RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complex	Arrow	R-HSA-180739 (Reactome)
RanBP1:Ran-GTP:CRM1:Rev-bound mRNA complex			R-HSA-165028 (Reactome)
	Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP:NPC	Arrow	R-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	Arrow	R-HSA-165034 (Reactome)
	Rev multimer-bound HIV-1 mRNA:Crm1:Ran:GTP	Arrow	R-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-catalysis	R-HSA-165055 (Reactome)
	Rev multimer-bound HIV-1 mRNA:CRM1 complex	Arrow	R-HSA-180885 (Reactome)
Rev multimer-bound HIV-1 mRNA:CRM1 complex			R-HSA-165034 (Reactome)
	Rev multimer-bound HIV-1 mRNA	Arrow	R-HSA-165033 (Reactome)
Rev multimer-bound HIV-1 mRNA			R-HSA-180885 (Reactome)
	Rev-bound HIV-1 mRNA	Arrow	R-HSA-165027 (Reactome)
Rev-bound HIV-1 mRNA			R-HSA-165033 (Reactome)
	Rev-multimer	Arrow	R-HSA-165028 (Reactome)
Rev-multimer			R-HSA-165033 (Reactome)
	Spliced Env mRNA	Arrow	R-HSA-187211 (Reactome)
Spliced Env mRNA			R-HSA-174494 (Reactome)
Spliced Env mRNA			R-HSA-3149433 (Reactome)
TCEA1			R-HSA-167077 (Reactome)
TCEA1			R-HSA-167196 (Reactome)
	TFIIA	Arrow	R-HSA-167136 (Reactome)
	TFIIA	Arrow	R-HSA-167474 (Reactome)
	TFIIA	Arrow	R-HSA-167477 (Reactome)
	TFIID	Arrow	R-HSA-167136 (Reactome)
	TFIID	Arrow	R-HSA-167474 (Reactome)
	TFIID	Arrow	R-HSA-167477 (Reactome)
	TFIIE	Arrow	R-HSA-167136 (Reactome)
	TFIIE	Arrow	R-HSA-167468 (Reactome)
	TFIIE	Arrow	R-HSA-167474 (Reactome)
	TFIIE	Arrow	R-HSA-167477 (Reactome)
	TFIIH	Arrow	R-HSA-167072 (Reactome)
	TFIIH	Arrow	R-HSA-167181 (Reactome)
	TFIIH	Arrow	R-HSA-167468 (Reactome)
	TFIIH	Arrow	R-HSA-167474 (Reactome)
	TFIIH	Arrow	R-HSA-167477 (Reactome)
TFIIH			R-HSA-167072 (Reactome)
TFIIH			R-HSA-167077 (Reactome)
TFIIH			R-HSA-167196 (Reactome)
TFIIH		mim-catalysis	R-HSA-167097 (Reactome)
TFIIH		mim-catalysis	R-HSA-167098 (Reactome)
TFIIH		mim-catalysis	R-HSA-167113 (Reactome)
TFIIH		mim-catalysis	R-HSA-167121 (Reactome)
Tat (P04608)			R-HSA-167234 (Reactome)
	Tat-containing elongation complex prior to separation	Arrow	R-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)	Arrow	R-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	Arrow	R-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-catalysis	R-HSA-170704 (Reactome)
	Tat-containing early elongation complex with hyperphosphorylated Pol II CTD	Arrow	R-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-catalysis	R-HSA-170706 (Reactome)
	Tat:P-TEFb(Cyclin T1:Cdk9) complex	Arrow	R-HSA-167234 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complex			R-HSA-167191 (Reactome)
Tat:P-TEFb(Cyclin T1:Cdk9) complex		mim-catalysis	R-HSA-167191 (Reactome)
	Trimeric ENV precursor	Arrow	R-HSA-171291 (Reactome)
	Trimeric ENV precursor	Arrow	R-HSA-174491 (Reactome)
Trimeric ENV precursor			R-HSA-171288 (Reactome)
Trimeric ENV precursor			R-HSA-174491 (Reactome)
	Trimeric gp120:gp41 oligomer	Arrow	R-HSA-171288 (Reactome)
	Trimeric gp120:gp41 oligomer	Arrow	R-HSA-173647 (Reactome)
Trimeric gp120:gp41 oligomer			R-HSA-173647 (Reactome)
Trimeric gp120:gp41 oligomer			R-HSA-3149454 (Reactome)
Ub			R-HSA-184323 (Reactome)
VIF (P69723) protein			R-HSA-3149454 (Reactome)
VPR			R-HSA-3149454 (Reactome)
	VPU (P05919)	Arrow	R-HSA-3149432 (Reactome)
	VPU (P05919)	Arrow	R-HSA-3149433 (Reactome)
	VPU (P05919)	Arrow	R-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	Arrow	R-HSA-164524 (Reactome)
Viral core surrounded by Matrix layer			R-HSA-173642 (Reactome)
Virion Budding Complex		Arrow	R-HSA-3159227 (Reactome)
	Virion Budding Complex	Arrow	R-HSA-3159232 (Reactome)
	Virion with CD4:gp120 bound to CCR5/CXCR4	Arrow	R-HSA-164507 (Reactome)
Virion with CD4:gp120 bound to CCR5/CXCR4			R-HSA-164500 (Reactome)
	Virion with fusogenically activated gp41	Arrow	R-HSA-164515 (Reactome)
Virion with fusogenically activated gp41			R-HSA-164521 (Reactome)
	Virion with CD4 bound to gp120	Arrow	R-HSA-164509 (Reactome)
Virion with CD4 bound to gp120			R-HSA-164510 (Reactome)
	Virion with exposed coreceptor binding sites	Arrow	R-HSA-164510 (Reactome)
Virion with exposed coreceptor binding sites			R-HSA-164507 (Reactome)
	Virion with gp41 exposed	Arrow	R-HSA-164500 (Reactome)
Virion with gp41 exposed			R-HSA-164515 (Reactome)
	Virion with gp41 forming hairpin structure	Arrow	R-HSA-164508 (Reactome)
Virion with gp41 forming hairpin structure			R-HSA-164524 (Reactome)
	Virion with gp41 fusion peptide in insertion complex	Arrow	R-HSA-164521 (Reactome)
Virion with gp41 fusion peptide in insertion complex			R-HSA-164508 (Reactome)
Vpr:importin-alpha complex		Arrow	R-HSA-162590 (Reactome)
Vps/Vta1			R-HSA-3159232 (Reactome)
	XPO1	Arrow	R-HSA-165028 (Reactome)
XPO1			R-HSA-180885 (Reactome)
	XRCC4:LIG4	Arrow	R-HSA-175258 (Reactome)
XRCC4:LIG4			R-HSA-175177 (Reactome)
	XRCC5:XRCC6	Arrow	R-HSA-175258 (Reactome)
XRCC5:XRCC6			R-HSA-175174 (Reactome)
dNTP			R-HSA-164504 (Reactome)
	monoubiquitinated N-myristoyl GAG (P04591) protein	Arrow	R-HSA-184269 (Reactome)
	monoubiquitinated N-myristoyl GAG (P04591) protein	Arrow	R-HSA-184323 (Reactome)
	monoubiquitinated N-myristoyl GAG (P04591) protein	Arrow	R-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)	Arrow	R-HSA-162914 (Reactome)
	myristoylated Nef Protein (UniProt:P04601)	Arrow	R-HSA-173642 (Reactome)
myristoylated Nef Protein (UniProt:P04601)			R-HSA-3149454 (Reactome)
	other viral genomic RNA	Arrow	R-HSA-173771 (Reactome)
p-SUPT5H			R-HSA-167153 (Reactome)
tRNA-Lysine3			R-HSA-164527 (Reactome)
tRNA-Lysine3			R-HSA-3149454 (Reactome)
	uncoated viral complex	Arrow	R-HSA-173111 (Reactome)
uncoated viral complex			R-HSA-173771 (Reactome)
	viral DNA bound with Integrase in PIC	Arrow	R-HSA-164514 (Reactome)
viral DNA bound with Integrase in PIC			R-HSA-164522 (Reactome)
	viral DNA:Ku proteins:XRCC4:DNA ligase IV complex	Arrow	R-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-catalysis	R-HSA-175258 (Reactome)
	viral PIC proteins	Arrow	R-HSA-164506 (Reactome)
	viral PIC proteins	Arrow	R-HSA-164523 (Reactome)
	viral PIC proteins	Arrow	R-HSA-164845 (Reactome)
	viral PIC proteins	Arrow	R-HSA-175108 (Reactome)
	viral PIC proteins	Arrow	R-HSA-175117 (Reactome)
	viral PIC proteins	Arrow	R-HSA-175174 (Reactome)
	viral PIC proteins	Arrow	R-HSA-175250 (Reactome)
viral PIC proteins			R-HSA-164506 (Reactome)
viral PIC proteins			R-HSA-164523 (Reactome)