#ID(s) interactor A	ID(s) interactor B	Alt. ID(s) interactor A	Alt. ID(s) interactor B	Alias(es) interactor A	Alias(es) interactor B	Interaction detection method(s)	Publication 1st author(s)	Publication Identifier(s)	Taxid interactor A	Taxid interactor B	Interaction type(s)	Source database(s)	Interaction identifier(s)	Confidence value(s)	Expansion method(s)	Biological role(s) interactor A	Biological role(s) interactor B	Experimental role(s) interactor A	Experimental role(s) interactor B	Type(s) interactor A	Type(s) interactor B	Xref(s) interactor A	Xref(s) interactor B	Interaction Xref(s)	Annotation(s) interactor A	Annotation(s) interactor B	Interaction annotation(s)	Host organism(s)	Interaction parameter(s)	Creation date	Update date	Checksum(s) interactor A	Checksum(s) interactor B	Interaction Checksum(s)	Negative	Feature(s) interactor A	Feature(s) interactor B	Stoichiometry(s) interactor A	Stoichiometry(s) interactor B	Identification method participant A	Identification method participant B
uniprotkb:P03367	uniprotkb:P03367	intact:EBI-8578100|intact:MINT-1506499	intact:EBI-8578100|intact:MINT-1506499	psi-mi:pol_hv1br(display_long)|uniprotkb:gag-pol(gene name)|psi-mi:gag-pol(display_short)|uniprotkb:Pr160Gag-Pol(gene name synonym)	psi-mi:pol_hv1br(display_long)|uniprotkb:gag-pol(gene name)|psi-mi:gag-pol(display_short)|uniprotkb:Pr160Gag-Pol(gene name synonym)	psi-mi:"MI:0114"(x-ray crystallography)	Kožíšek et al. (2014)	imex:IM-22544|pubmed:24785545	taxid:11686(hv1br)|taxid:11686("Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)")	taxid:11686(hv1br)|taxid:11686("Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)")	psi-mi:"MI:0407"(direct interaction)	psi-mi:"MI:0471"(MINT)	intact:EBI-9120069|imex:IM-22544-1	-	-	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0499"(unspecified role)	psi-mi:"MI:0497"(neutral component)	psi-mi:"MI:0497"(neutral component)	psi-mi:"MI:0326"(protein)	psi-mi:"MI:0326"(protein)	rcsb pdb:2HND|rcsb pdb:2HNY|rcsb pdb:5E5K|rcsb pdb:6VLM|rcsb pdb:6VOD|rcsb pdb:6VOE|go:"GO:0020002"(host cell plasma membrane)|go:"GO:0039651"(induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process)|go:"GO:0039657"(suppression by virus of host gene expression)|go:"GO:0042025"(host cell nucleus)|go:"GO:0044826"(viral genome integration into host DNA)|go:"GO:0046718"(viral entry into host cell)|go:"GO:0055036"(virion membrane)|go:"GO:0072494"(host multivesicular body)|go:"GO:0075713"(establishment of integrated proviral latency)|go:"GO:0075732"(viral penetration into host nucleus)|go:"GO:0019013"(viral nucleocapsid)|go:"GO:0003677"(DNA binding)|go:"GO:0003723"(RNA binding)|go:"GO:0003887"(DNA-directed DNA polymerase activity)|go:"GO:0003964"(RNA-directed DNA polymerase activity)|go:"GO:0004190"(aspartic-type endopeptidase activity)|go:"GO:0004523"(RNA-DNA hybrid ribonuclease activity)|go:"GO:0004533"(exoribonuclease H activity)|go:"GO:0005198"(structural molecule activity)|go:"GO:0006310"(DNA recombination)|go:"GO:0008270"(zinc ion binding)|go:"GO:0008289"(lipid binding)|go:"GO:0015074"(DNA integration)|go:"GO:0016020"(membrane)|rcsb pdb:4LL3|rcsb pdb:1HPO|rcsb pdb:1ZJ7|rcsb pdb:3TOF|rcsb pdb:3NDW|rcsb pdb:2UPJ|rcsb pdb:2QNQ|rcsb pdb:1AAQ|rcsb pdb:4J54|rcsb pdb:2Z4O|rcsb pdb:3QN8|rcsb pdb:4DFG|rcsb pdb:3ST5|rcsb pdb:4FM6|rcsb pdb:1SP5|rcsb pdb:2Q64|rcsb pdb:1SDT|rcsb pdb:3PWR|rcsb pdb:3TOH|rcsb pdb:2R43|rcsb pdb:1XL2|rcsb pdb:3H5B|rcsb pdb:1HNI|rcsb pdb:3NLS|rcsb pdb:2PWC|rcsb pdb:1ZTZ|rcsb pdb:3JVW|rcsb pdb:1HVL|rcsb pdb:1Z8C|rcsb pdb:1XL5|rcsb pdb:1A94|rcsb pdb:4FAF|rcsb pdb:2BB9|rcsb pdb:1ZPK|rcsb pdb:1ZLF|rcsb pdb:3QRS|rcsb pdb:2QNP|rcsb pdb:2ZYE|rcsb pdb:2HB2|rcsb pdb:2FND|rcsb pdb:3VF5|rcsb pdb:3VFB|rcsb pdb:3UHL|rcsb pdb:1D4S|rcsb pdb:4FL8|rcsb pdb:3A2O|rcsb pdb:7UPJ|rcsb pdb:3PWM|rcsb pdb:1SDU|rcsb pdb:1HSG|rcsb pdb:2AZB|rcsb pdb:2O4N|rcsb pdb:3KDC|rcsb pdb:3QIH|rcsb pdb:3BVB|rcsb pdb:2FDE|rcsb pdb:3JVY|rcsb pdb:2AZ8|rcsb pdb:3KDD|rcsb pdb:3NDU|rcsb pdb:2PK6|rcsb pdb:4FLG|rcsb pdb:1HPX|rcsb pdb:1A8G|rcsb pdb:3UF3|rcsb pdb:3QPJ|rcsb pdb:3GGU|rcsb pdb:1DIF|rcsb pdb:2PYN|rcsb pdb:1ZBG|rcsb pdb:2O4L|rcsb pdb:2IEN|rcsb pdb:2B7Z|rcsb pdb:1U8G|rcsb pdb:2QD6|rcsb pdb:3NDX|rcsb pdb:1LZQ|interpro:IPR021109|rcsb pdb:1D4Y|rcsb pdb:3KDB|rcsb pdb:3DJK|rcsb pdb:2A1E|rcsb pdb:1MRW|rcsb pdb:3QBF|rcsb pdb:1DAZ|rcsb pdb:3BVA|rcsb pdb:1HHP|rcsb pdb:3UFN|rcsb pdb:1MRX|rcsb pdb:3BHE|rcsb pdb:1MSN|rcsb pdb:2HB4|rcsb pdb:1M0B|rcsb pdb:4J55|rcsb pdb:3UCB|rcsb pdb:2QD8|rcsb pdb:4J5J|rcsb pdb:1SGU|rcsb pdb:1SDV|rcsb pdb:3QRO|rcsb pdb:2P3B|rcsb pdb:2PK5|rcsb pdb:1IIQ|rcsb pdb:3TOG|rcsb pdb:2AZC|rcsb pdb:1UPJ|rcsb pdb:1SH9|rcsb pdb:3QRM|interpro:IPR012337(Polynucleotidyl transferase, Ribonuclease H fold)|rcsb pdb:3QP0|rcsb pdb:2Q63|rcsb pdb:1NH0|rcsb pdb:1FQX|rcsb pdb:2AZ9|rcsb pdb:2PYM|rcsb pdb:3CKT|rcsb pdb:3I6O|rcsb pdb:2PQZ|rcsb pdb:3U7S|interpro:IPR017856(Integrase, N-terminal zinc-binding domain-like)|rcsb pdb:1IZI|rcsb pdb:1RL8|rcsb pdb:3T11|rcsb pdb:2QD7|rcsb pdb:2PWR|rcsb pdb:1A8K|rcsb pdb:4FE6|rcsb pdb:2QNN|rcsb pdb:2O4K|rcsb pdb:3FX5|rcsb pdb:2QCI|interpro:IPR010999(Retroviral matrix, N-terminal)|rcsb pdb:3T3C|rcsb pdb:2HC0|rcsb pdb:2ZGA|rcsb pdb:1MSM|rcsb pdb:3DK1|rcsb pdb:2O4S|rcsb pdb:3TTP|rcsb pdb:3I8W|rcsb pdb:3VF7|rcsb pdb:2O4P|rcsb pdb:2QAK|interpro:IPR018061|rcsb pdb:3JW2|rcsb pdb:2QHC|rcsb pdb:4GB2|rcsb pdb:4HDB|rcsb pdb:4HDF|rcsb pdb:4HDP|rcsb pdb:4HE9|rcsb pdb:4HEG|rcsb pdb:4HLA|rcsb pdb:4JEC|interpro:IPR034170|rcsb pdb:6VCE|rcsb pdb:5YOK|interpro:IPR012344(Lentiviral and alpha-retroviral matrix protein, N-terminal)|rcsb pdb:6BSH|interpro:IPR036397|interpro:IPR036862|interpro:IPR036875|interpro:IPR043128|interpro:IPR043502|rcsb pdb:6P9A|rcsb pdb:6P9B|interpro:IPR000071(Immunodeficiency lentiviral matrix, N-terminal)|interpro:IPR000477("RNA-directed DNA polymerase (reverse transcriptase)")|interpro:IPR000721(Retroviral nucleocapsid protein Gag)|interpro:IPR001037(Integrase, C-terminal, retroviral)|interpro:IPR001584(Integrase, catalytic core)|interpro:IPR001878(Zinc finger, CCHC-type)|interpro:IPR001969(Peptidase aspartic, active site)|interpro:IPR001995(Peptidase A2A, retrovirus, catalytic)|interpro:IPR002156(Ribonuclease H)|interpro:IPR003308(Integrase, N-terminal zinc-binding domain)|interpro:IPR008916(Retrovirus capsid, C-terminal)|interpro:IPR008919(Retrovirus capsid, N-terminal core)|interpro:IPR010659(Reverse transcriptase connection)|interpro:IPR010661(Reverse transcriptase thumb)	rcsb pdb:2HND|rcsb pdb:2HNY|rcsb pdb:5E5K|rcsb pdb:6VLM|rcsb pdb:6VOD|rcsb pdb:6VOE|go:"GO:0020002"(host cell plasma membrane)|go:"GO:0039651"(induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process)|go:"GO:0039657"(suppression by virus of host gene expression)|go:"GO:0042025"(host cell nucleus)|go:"GO:0044826"(viral genome integration into host DNA)|go:"GO:0046718"(viral entry into host cell)|go:"GO:0055036"(virion membrane)|go:"GO:0072494"(host multivesicular body)|go:"GO:0075713"(establishment of integrated proviral latency)|go:"GO:0075732"(viral penetration into host nucleus)|go:"GO:0019013"(viral nucleocapsid)|go:"GO:0003677"(DNA binding)|go:"GO:0003723"(RNA binding)|go:"GO:0003887"(DNA-directed DNA polymerase activity)|go:"GO:0003964"(RNA-directed DNA polymerase activity)|go:"GO:0004190"(aspartic-type endopeptidase activity)|go:"GO:0004523"(RNA-DNA hybrid ribonuclease activity)|go:"GO:0004533"(exoribonuclease H activity)|go:"GO:0005198"(structural molecule activity)|go:"GO:0006310"(DNA recombination)|go:"GO:0008270"(zinc ion binding)|go:"GO:0008289"(lipid binding)|go:"GO:0015074"(DNA integration)|go:"GO:0016020"(membrane)|rcsb pdb:4LL3|rcsb pdb:1HPO|rcsb pdb:1ZJ7|rcsb pdb:3TOF|rcsb pdb:3NDW|rcsb pdb:2UPJ|rcsb pdb:2QNQ|rcsb pdb:1AAQ|rcsb pdb:4J54|rcsb pdb:2Z4O|rcsb pdb:3QN8|rcsb pdb:4DFG|rcsb pdb:3ST5|rcsb pdb:4FM6|rcsb pdb:1SP5|rcsb pdb:2Q64|rcsb pdb:1SDT|rcsb pdb:3PWR|rcsb pdb:3TOH|rcsb pdb:2R43|rcsb pdb:1XL2|rcsb pdb:3H5B|rcsb pdb:1HNI|rcsb pdb:3NLS|rcsb pdb:2PWC|rcsb pdb:1ZTZ|rcsb pdb:3JVW|rcsb pdb:1HVL|rcsb pdb:1Z8C|rcsb pdb:1XL5|rcsb pdb:1A94|rcsb pdb:4FAF|rcsb pdb:2BB9|rcsb pdb:1ZPK|rcsb pdb:1ZLF|rcsb pdb:3QRS|rcsb pdb:2QNP|rcsb pdb:2ZYE|rcsb pdb:2HB2|rcsb pdb:2FND|rcsb pdb:3VF5|rcsb pdb:3VFB|rcsb pdb:3UHL|rcsb pdb:1D4S|rcsb pdb:4FL8|rcsb pdb:3A2O|rcsb pdb:7UPJ|rcsb pdb:3PWM|rcsb pdb:1SDU|rcsb pdb:1HSG|rcsb pdb:2AZB|rcsb pdb:2O4N|rcsb pdb:3KDC|rcsb pdb:3QIH|rcsb pdb:3BVB|rcsb pdb:2FDE|rcsb pdb:3JVY|rcsb pdb:2AZ8|rcsb pdb:3KDD|rcsb pdb:3NDU|rcsb pdb:2PK6|rcsb pdb:4FLG|rcsb pdb:1HPX|rcsb pdb:1A8G|rcsb pdb:3UF3|rcsb pdb:3QPJ|rcsb pdb:3GGU|rcsb pdb:1DIF|rcsb pdb:2PYN|rcsb pdb:1ZBG|rcsb pdb:2O4L|rcsb pdb:2IEN|rcsb pdb:2B7Z|rcsb pdb:1U8G|rcsb pdb:2QD6|rcsb pdb:3NDX|rcsb pdb:1LZQ|interpro:IPR021109|rcsb pdb:1D4Y|rcsb pdb:3KDB|rcsb pdb:3DJK|rcsb pdb:2A1E|rcsb pdb:1MRW|rcsb pdb:3QBF|rcsb pdb:1DAZ|rcsb pdb:3BVA|rcsb pdb:1HHP|rcsb pdb:3UFN|rcsb pdb:1MRX|rcsb pdb:3BHE|rcsb pdb:1MSN|rcsb pdb:2HB4|rcsb pdb:1M0B|rcsb pdb:4J55|rcsb pdb:3UCB|rcsb pdb:2QD8|rcsb pdb:4J5J|rcsb pdb:1SGU|rcsb pdb:1SDV|rcsb pdb:3QRO|rcsb pdb:2P3B|rcsb pdb:2PK5|rcsb pdb:1IIQ|rcsb pdb:3TOG|rcsb pdb:2AZC|rcsb pdb:1UPJ|rcsb pdb:1SH9|rcsb pdb:3QRM|interpro:IPR012337(Polynucleotidyl transferase, Ribonuclease H fold)|rcsb pdb:3QP0|rcsb pdb:2Q63|rcsb pdb:1NH0|rcsb pdb:1FQX|rcsb pdb:2AZ9|rcsb pdb:2PYM|rcsb pdb:3CKT|rcsb pdb:3I6O|rcsb pdb:2PQZ|rcsb pdb:3U7S|interpro:IPR017856(Integrase, N-terminal zinc-binding domain-like)|rcsb pdb:1IZI|rcsb pdb:1RL8|rcsb pdb:3T11|rcsb pdb:2QD7|rcsb pdb:2PWR|rcsb pdb:1A8K|rcsb pdb:4FE6|rcsb pdb:2QNN|rcsb pdb:2O4K|rcsb pdb:3FX5|rcsb pdb:2QCI|interpro:IPR010999(Retroviral matrix, N-terminal)|rcsb pdb:3T3C|rcsb pdb:2HC0|rcsb pdb:2ZGA|rcsb pdb:1MSM|rcsb pdb:3DK1|rcsb pdb:2O4S|rcsb pdb:3TTP|rcsb pdb:3I8W|rcsb pdb:3VF7|rcsb pdb:2O4P|rcsb pdb:2QAK|interpro:IPR018061|rcsb pdb:3JW2|rcsb pdb:2QHC|rcsb pdb:4GB2|rcsb pdb:4HDB|rcsb pdb:4HDF|rcsb pdb:4HDP|rcsb pdb:4HE9|rcsb pdb:4HEG|rcsb pdb:4HLA|rcsb pdb:4JEC|interpro:IPR034170|rcsb pdb:6VCE|rcsb pdb:5YOK|interpro:IPR012344(Lentiviral and alpha-retroviral matrix protein, N-terminal)|rcsb pdb:6BSH|interpro:IPR036397|interpro:IPR036862|interpro:IPR036875|interpro:IPR043128|interpro:IPR043502|rcsb pdb:6P9A|rcsb pdb:6P9B|interpro:IPR000071(Immunodeficiency lentiviral matrix, N-terminal)|interpro:IPR000477("RNA-directed DNA polymerase (reverse transcriptase)")|interpro:IPR000721(Retroviral nucleocapsid protein Gag)|interpro:IPR001037(Integrase, C-terminal, retroviral)|interpro:IPR001584(Integrase, catalytic core)|interpro:IPR001878(Zinc finger, CCHC-type)|interpro:IPR001969(Peptidase aspartic, active site)|interpro:IPR001995(Peptidase A2A, retrovirus, catalytic)|interpro:IPR002156(Ribonuclease H)|interpro:IPR003308(Integrase, N-terminal zinc-binding domain)|interpro:IPR008916(Retrovirus capsid, C-terminal)|interpro:IPR008919(Retrovirus capsid, N-terminal core)|interpro:IPR010659(Reverse transcriptase connection)|interpro:IPR010661(Reverse transcriptase thumb)	rcsb pdb:4ll3|rcsb pdb:3ttp	function:"Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity"|comment:mint|function:"Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for two polypurine tracts (PPTs) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPTs that have not been removed by RNase H as primers. PPTs and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends"|function:"Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allow the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration"|function:"Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to plays a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu"|function:Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation|function:The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles|function:Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is dissassembled soon after virion entry. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species	function:"Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity"|comment:mint|function:"Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for two polypurine tracts (PPTs) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPTs that have not been removed by RNase H as primers. PPTs and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends"|function:"Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allow the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration"|function:"Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to plays a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu"|function:Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation|function:The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles|function:Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is dissassembled soon after virion entry. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species	figure legend:t4 f1c f5c f5a sf1|comment:"The crystal structure of PRDRV2 in complex with DRV was determined at 2.2 Å  resolution. Although there are four crystal structures of the wild-type PR-DRV complex  available (PDB codes 2IEN, 1T3R, 4DQB and 4HLA [12-15]) we also determined the  structure of the wild-type enzyme in complex with DRV at 1.9 Å resolution to have a  reference structure from crystals produced under similar experimental conditions using  enzymes with amino acid sequences corresponding to those used for ITC analysis. Both  crystals exhibited hexagonal symmetry with identical space group (P61) containing one  protease dimer in the asymmetric unit. Structures were refined with two inhibitor molecules  bound in alternative orientations related by 180º rotation with 50% relative occupancy  (Supplementary Figure S1).  The two crystal structures presented here (PRwt and PRDRV2) were isostructural with  crystal structures of resistant variants PRDRV1 and PRDRV5, which we determined previously  (PDB codes 3U7S and 3GGU, respectively [10]) and used in structural comparisons and  analyses in this work."|full coverage:Only protein-protein interactions|curation depth:imex curation	taxid:-1(in vitro)|taxid:-1(In vitro)	-	2014/02/07	2014/10/16	rogid:Schh9TbTILiQf/iM1hcy42uotgI11686	rogid:Schh9TbTILiQf/iM1hcy42uotgI11686	intact-crc:44DF1252FC6FFDB8|rigid:LYkaXFBb8RCzo3NW9W34n5dX8IA	false	polyprotein fragment:501-599|polyprotein fragment:501-599	polyprotein fragment:501-599|polyprotein fragment:501-599	2	0	psi-mi:"MI:0396"(predetermined participant)	psi-mi:"MI:0396"(predetermined participant)