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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Gag-Pol polyprotein: Mediates, with Gag polyrotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi). Gag-Pol polyprotein may regulate its own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, the polyprotein would promote translation, whereas at high concentration, the polyprotein would encapsidate genomic RNA and then shutt off translation.By similarity
Matrix protein p17: Targets the polyprotein to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. Matrix protein is part of the pre-integration complex. Implicated in the release from host cell mediated by Vpu. Binds to RNA.By similarity
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 disassembled soon after virion entry (By similarity). Host restriction factors such as TRIM5-alpha or TRIMCyp bind retroviral capsids and cause premature capsid disassembly, leading to blocks in reverse transcription. Capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species. Host PIN1 apparently facilitates the virion uncoating. On the other hand, interactions with PDZD8 or CYPA stabilize the capsid.By similarity
Nucleocapsid protein p7: Encapsulates and protects viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc fingers. Acts as a nucleic acid chaperone which is involved in rearangement of nucleic acid secondary structure during gRNA retrotranscription. Also facilitates template switch leading to recombination. As part of the polyprotein, participates in gRNA dimerization, packaging, tRNA incorporation and virion assembly.By similarity
Protease: Aspartyl protease that 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. Hydrolyzes host EIF4GI and PABP1 in order to shut off the capped cellular mRNA translation. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (By similarity).PROSITE-ProRule annotationBy similarity
Reverse transcriptase/ribonuclease H: 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.By similarity
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 allows 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.By similarity

Catalytic activityi

Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.PROSITE-ProRule annotation
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.By similarity
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.By similarity
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarityNote: Binds 2 magnesium ions for reverse transcriptase polymerase activity.By similarity
  • Mg2+By similarityNote: Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.By similarity
  • Mg2+By similarityNote: Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.By similarity

Enzyme regulationi

Protease: The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir. Use of protease inhibitors in tritherapy regimens permit more ambitious therapeutic strategies. Reverse transcriptase/ribonuclease H: RT can be inhibited either by nucleoside RT inhibitors (NRTIs) or by non nucleoside RT inhibitors (NNRTIs). NRTIs act as chain terminators, whereas NNRTIs inhibit DNA polymerization by binding a small hydrophobic pocket near the RT active site and inducing an allosteric change in this region. Classical NRTIs are abacavir, adefovir (PMEA), didanosine (ddI), lamivudine (3TC), stavudine (d4T), tenofovir (PMPA), zalcitabine (ddC), and zidovudine (AZT). Classical NNRTIs are atevirdine (BHAP U-87201E), delavirdine, efavirenz (DMP-266), emivirine (I-EBU), and nevirapine (BI-RG-587). The tritherapies used as a basic effective treatment of AIDS associate two NRTIs and one NNRTI.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei221 – 222Cis/trans isomerization of proline peptide bond; by human PPIA/CYPABy similarity2
Active sitei525For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1 Publication1
Metal bindingi709Magnesium; catalytic; for reverse transcriptase activity1
Metal bindingi784Magnesium; catalytic; for reverse transcriptase activity1
Metal bindingi785Magnesium; catalytic; for reverse transcriptase activity1
Sitei1000Essential for RT p66/p51 heterodimerization1
Sitei1013Essential for RT p66/p51 heterodimerization1
Metal bindingi1042Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1077Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1097Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1148Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1223Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1275Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1311Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri390 – 407CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri411 – 428CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1162 – 1203Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1382 – 1429Integrase-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

Activation of host caspases by virus, DNA integration, DNA recombination, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Modulation of host cell apoptosis by virus, Viral genome integration, Viral penetration into host nucleus, Virion maturation, Virus entry into host cell, Virus exit from host cell

Keywords - Ligandi

DNA-binding, Lipid-binding, Magnesium, Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

Enzyme and pathway databases

BRENDAi2.7.7.49. 2676.
3.1.13.2. 2676.
SABIO-RKP03366.

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Alternative name(s):
Pr160Gag-Pol
Cleaved into the following 11 chains:
Matrix protein p17
Short name:
MA
Capsid protein p24
Short name:
CA
Spacer peptide 1By similarity
Short name:
SP1
Alternative name(s):
p2
Transframe peptide
Short name:
TF
p6-pol
Short name:
p6*
Alternative name(s):
PR
Retropepsin
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
p66 RT
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiHuman immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1)
Taxonomic identifieri11678 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007690 Componenti: Genome

Subcellular locationi

Gag-Pol polyprotein :
  • Host cell membrane; Lipid-anchor
  • Host endosomehost multivesicular body

  • Note: These locations are linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly.By similarity
Integrase :

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host endosome, Host membrane, Host nucleus, Membrane, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi440F → I: Complete loss of cleavage between NC and TF. 1 Publication1
Mutagenesisi500F → I: Complete loss of cleavage between TF and p15. 1 Publication1
Mutagenesisi651P → G: 74% loss of polymerase activity. 86% loss of RNase H activity. 1 Publication1
Mutagenesisi654P → G: 64% loss of polymerase activity. 57% loss of RNase H activity. 1 Publication1
Mutagenesisi664K → A: Strong decrease in RT binding affinity for all dNTP substrates and in catalytic efficiency. 100-fold decreased sensitivity to ddNTP inhibitors. 1 Publication1
Mutagenesisi664K → E: Strong decrease in RT binding affinity for all dNTP substrates and in catalytic efficiency. 100-fold decreased sensitivity to ddNTP inhibitors. 1 Publication1
Mutagenesisi664K → Q: Strong decrease in RT binding affinity for all dNTP substrates and in catalytic efficiency. 100-fold decreased sensitivity to ddNTP inhibitors. 1 Publication1
Mutagenesisi664K → R: 10-fold decreased sensitivity to ddATP and ddCTP inhibitors. 1 Publication1
Mutagenesisi673L → V: No loss of polymerase activity. No loss of RNase H activity. 1 Publication1
Mutagenesisi709D → A: 5- to 12-fold decrease in affinity for dTTP substrates. Strongly decreased RNA-directed and DNA-directed DNA polymerase activities. No effect on RNase H activity. Loss of pyrophosphorolysis (reverse of the polymerase reaction). 1 Publication1
Mutagenesisi709D → S: 5- to 12-fold decrease in affinity for dTTP substrates. Strongly decreased RNA-directed DNA polymerase activity. Slightly decreased DNA-directed DNA polymerase activity. No effect on RNase H activity. Loss of pyrophosphorolysis (reverse of the polymerase reaction). 1 Publication1
Mutagenesisi752W → A: 73% loss of DNA-directed DNA polymerase activity. 70% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi752W → F: 10% loss of DNA-directed DNA polymerase activity. 22% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi752W → Y: 58% loss of DNA-directed DNA polymerase activity. 42% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi755S → A: 74% loss of polymerase activity. 56% loss of RNase H activity. 1 Publication1
Mutagenesisi755S → G: Complete loss of polymerase activity. No loss of RNase H activity. 1 Publication1
Mutagenesisi755S → T: Complete loss of polymerase activity. No loss of RNase H activity. 1 Publication1
Mutagenesisi756P → G: 34% loss of polymerase activity. No loss of RNase H activity. 1 Publication1
Mutagenesisi766I → A: 71% loss of DNA-directed DNA polymerase activity. 61% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi766I → D: 16% loss of DNA-directed DNA polymerase activity. 24% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi766I → L: 80% loss of DNA-directed DNA polymerase activity. 23% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi766I → T: 34% increase of DNA-directed DNA polymerase activity. 18% increase of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi766I → V: 70% loss of DNA-directed DNA polymerase activity. 64% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi782Y → A: Almost complete loss of polymerase activity. 1 Publication1
Mutagenesisi782Y → F: 70% loss of polymerase activity. No loss of polymerase activity; when associated with V-783. 1 Publication1
Mutagenesisi783M → I: 54% loss of polymerase activity according to PubMed:9533880; increases polymerase activity according to PubMed:9657675. No loss of RNase H activity. 2 Publications1
Mutagenesisi783M → L: 90% loss of polymerase activity. No loss of RNase H activity. 2 Publications1
Mutagenesisi783M → V: 58% loss of polymerase activity. No loss of RNase H activity. 2 Publications1
Mutagenesisi784D → A: Strongly decreased RNA-directed and DNA-directed DNA polymerase activities. No effect on RNase H activity. 2 Publications1
Mutagenesisi784D → E: Strongly decreased RNA-directed and DNA-directed DNA polymerase activities. No effect on RNase H activity. 2 Publications1
Mutagenesisi784D → N: Strongly decreased RNA-directed and DNA-directed DNA polymerase activities. No effect on RNase H activity. 2 Publications1
Mutagenesisi785D → A: Strongly decreased RNA-directed and DNA-directed DNA polymerase activities. Loss of pyrophosphorolysis (reverse of the polymerase reaction). No effect on RNase H activity. 2 Publications1
Mutagenesisi785D → E: Drastically reduced incorporation of phosphorothioate nucleotide. Loss of pyrophosphorolysis (reverse of the polymerase reaction). No effect on RNase H activity. 2 Publications1
Mutagenesisi785D → N: Loss of pyrophosphorolysis (reverse of the polymerase reaction). No effect on RNase H activity. 2 Publications1
Mutagenesisi786L → A: 76% loss of DNA-directed DNA polymerase activity. 60% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi786L → I: 29% loss of DNA-directed DNA polymerase activity. 46% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi786L → R: 20% loss of DNA-directed DNA polymerase activity. 21% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi786L → V: 22% loss of DNA-directed DNA polymerase activity. No loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi788V → A: 37% increase of DNA-directed DNA polymerase activity. No loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi788V → I: 25% increase of DNA-directed DNA polymerase activity. No loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi788V → M: 27% increase of DNA-directed DNA polymerase activity. 10% loss of RNA-directed DNA polymerase activity. 1 Publication1
Mutagenesisi823E → A: No effect on RNA-dependent DNA polymerase activity. No effect on RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi824P → A: No effect on RNA-dependent DNA polymerase activity. No effect on RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi825P → A: No effect on RNA-dependent DNA polymerase activity. Complete loss of RNA 5'-end cleavage. No effect on RNA 3'-end cleavage. 1 Publication1
Mutagenesisi826F → A: No effect on RNA-dependent DNA polymerase activity. Complete loss of RNA 5'-end cleavage. No effect on RNA 3'-end cleavage. 1 Publication1
Mutagenesisi827L → A: No effect on RNA-dependent DNA polymerase activity. No effect on RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi828W → A: Complete loss of RNA-dependent DNA polymerase activity. No effect on RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi829M → A: No effect on RNA-dependent DNA polymerase activity. No effect on RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi830G → A: Complete loss of RNA-dependent DNA polymerase activity. Complete loss of RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi831Y → A: Complete loss of RNA-dependent DNA polymerase activity. Complete loss of RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi832E → A: Complete loss of RNA-dependent DNA polymerase activity. Complete loss of RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi834H → A: Complete loss of RNA-dependent DNA polymerase activity. Complete loss of RNA 5'-end and 3'-end cleavages. 1 Publication1
Mutagenesisi856I → T: 96% loss of polymerase activity. 45% loss of RNase H activity. 1 Publication1
Mutagenesisi861G → A: Complete loss of polymerase activity. 25% loss of RNase H activity. 1 Publication1
Mutagenesisi863L → S: 17% loss of polymerase activity. 30% loss of RNase H activity. 1 Publication1
Mutagenesisi865W → T: Complete loss of polymerase activity. 87% loss of RNase H activity. 1 Publication1
Mutagenesisi878L → S: 21% loss of polymerase activity. 16% loss of RNase H activity. 1 Publication1
Mutagenesisi898A → L: 68% loss of polymerase activity. 10% loss of RNase H activity. 1 Publication1
Mutagenesisi902L → S: 59% loss of polymerase activity. 8% loss of RNase H activity. 1 Publication1
Mutagenesisi909L → S: 31% loss of polymerase activity. No loss of RNase H activity. 1 Publication1
Mutagenesisi997W → L: No effect on RT p66/p51 heterodimerization. 1 Publication1
Mutagenesisi1000W → A: Almost complete loss of RT p66/p51 heterodimerization. Complete loss of polymerase activity. 2 Publications1
Mutagenesisi1000W → F: No effect on RT p66/p51 heterodimerization. 2 Publications1
Mutagenesisi1000W → L: Almost complete loss of RT p66/p51 heterodimerization. Complete loss of polymerase activity. 2 Publications1
Mutagenesisi1001W → L: No effect on RT p66/p51 heterodimerization. 1 Publication1
Mutagenesisi1004Y → L: No effect on RT p66/p51 heterodimerization. 1 Publication1
Mutagenesisi1005W → L: Decreased RT p66/p51 heterodimerization. 1 Publication1
Mutagenesisi1009W → L: No effect on RT p66/p51 heterodimerization. 1 Publication1
Mutagenesisi1013W → L: Almost complete loss of RT p66/p51 heterodimerization. 1 Publication1
Mutagenesisi1036A → I: Replication slightly delayed. 1 Publication1
Mutagenesisi1037E → N: Virions contain primarily p51 RT. 1 Publication1
Mutagenesisi1038T → S: Almost complete loss of virion production; when associated with G-1041. 1 Publication1
Mutagenesisi1039F → A: Virions contain primarily p51 RT. 2 Publications1
Mutagenesisi1039F → I: Loss of cleavage between p51 RT and p15. 2 Publications1
Mutagenesisi1039F → L: No effect on cleavage between p51 RT and p15. 2 Publications1
Mutagenesisi1039F → V: Slight delays in replication. Virions contain primarily p51 RT. 2 Publications1
Mutagenesisi1039F → W: Slight delays in replication. Virions contain primarily p51 RT. 2 Publications1
Mutagenesisi1040Y → A: Virions contain primarily p51 RT; when associated with A-1039. 1 Publication1
Mutagenesisi1040Y → I: Almost complete loss of virion production; when associated with K-1041. 1 Publication1
Mutagenesisi1040Y → W: Virions contain primarily p51 RT; when associated with W-1039. 1 Publication1
Mutagenesisi1041V → G: Almost complete loss of virion production; when associated with S-1038. 1 Publication1
Mutagenesisi1041V → K: Almost complete loss of virion production; when associated with I-1038. 1 Publication1
Mutagenesisi1041V → S: Slight delays in replication. 1 Publication1
Mutagenesisi1077E → Q: No loss of polymerase activity. complete loss of RNase H activity. 1 Publication1
Mutagenesisi1100Y → A, G, H, L, S or Q: Complete loss of RNAase H activity. 1 Publication1
Mutagenesisi1100Y → E: Almost complete loss of RNAase H activity. 1 Publication1
Mutagenesisi1100Y → F: Almost no effect on RNAase H activity and replication. 1 Publication1
Mutagenesisi1100Y → R: Almost no effect on RNAase H activity. Unable to replicate. Completely resistant to inhibition by BBNH. 1 Publication1
Mutagenesisi1100Y → W: Almost no effect on RNAase H activity and replication. 6-fold resistance to inhibition by BBNH. 1 Publication1
Mutagenesisi1138H → D or N: Severely reduces exonuclease activity of RNase H. Probably also reduces substrate binding affinity. Modifies cleavage preferences of RNase H. No effect on the endonuclease activity. 1 Publication1
Mutagenesisi1138H → D: Severely reduced exonuclease activity of RNase H, but no effect on endonucleonuclease activity. 1 Publication1
Mutagenesisi1138H → N: Severely reduced exonuclease activity of RNase H, but no effect on endonucleonuclease activity. 1 Publication1
Mutagenesisi1159L → F: No effect on cleavage between reverse transcriptase/ribonuclease H and integrase. 1 Publication1
Mutagenesisi1159L → I: Loss of cleavage between reverse transcriptase/ribonuclease H and integrase. 1 Publication1

Keywords - Diseasei

AIDS

Chemistry databases

ChEMBLiCHEMBL5823.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostBy similarity
ChainiPRO_00002612612 – 1447Gag-Pol polyproteinAdd BLAST1446
ChainiPRO_00000422852 – 132Matrix protein p17By similarityAdd BLAST131
ChainiPRO_0000042286133 – 363Capsid protein p24By similarityAdd BLAST231
PeptideiPRO_0000042287364 – 377Spacer peptide 1By similarityAdd BLAST14
ChainiPRO_0000042288378 – 432Nucleocapsid protein p7By similarityAdd BLAST55
PeptideiPRO_0000246710433 – 440Transframe peptideSequence analysis8
ChainiPRO_0000042289441 – 500p6-polSequence analysisAdd BLAST60
ChainiPRO_0000038647501 – 599ProteaseBy similarityAdd BLAST99
ChainiPRO_0000042290600 – 1159Reverse transcriptase/ribonuclease HBy similarityAdd BLAST560
ChainiPRO_0000042291600 – 1039p51 RTBy similarityAdd BLAST440
ChainiPRO_00000422921040 – 1159p15Add BLAST120
ChainiPRO_00000422931160 – 1447IntegraseBy similarityAdd BLAST288

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by hostBy similarity1
Modified residuei132Phosphotyrosine; by hostBy similarity1
Modified residuei387Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT61 Publication1
Modified residuei409Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT61 Publication1

Post-translational modificationi

Gag-Pol polyprotein: Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation. Proteolytic cleavage of p66 RT removes the RNase H domain to yield the p51 RT subunit. Nucleocapsid protein p7 might be further cleaved after virus entry.PROSITE-ProRule annotationBy similarity
Matrix protein p17: Tyrosine phosphorylated presumably in the virion by a host kinase. Phosphorylation is apparently not a major regulator of membrane association.By similarity
Capsid protein p24: Phosphorylated possibly by host MAPK1; this phosphorylation is necessary for Pin1-mediated virion uncoating.By similarity
Nucleocapsid protein p7: Methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei132 – 133Cleavage; by viral proteaseBy similarity2
Sitei363 – 364Cleavage; by viral proteaseBy similarity2
Sitei377 – 378Cleavage; by viral proteaseBy similarity2
Sitei432 – 433Cleavage; by viral proteaseSequence analysis2
Sitei440 – 441Cleavage; by viral protease2
Sitei500 – 501Cleavage; by viral protease2
Sitei599 – 600Cleavage; by viral proteaseBy similarity2
Sitei1039 – 1040Cleavage; by viral protease; partial2
Sitei1159 – 1160Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Methylation, Myristate, Phosphoprotein

Interactioni

Subunit structurei

Matrix protein p17: Homotrimer; further assembles as hexamers of trimers (By similarity). Matrix protein p17: Interacts with gp41 (via C-terminus) (By similarity). Matrix protein p17: interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group (By similarity). Matrix protein p17: interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly (By similarity). Matrix protein p17: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase (By similarity). Capsid protein p24: Homodimer; the homodimer further multimerizes as homohexamers or homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA (By similarity); This interaction stabilizes the capsid. Capsid protein p24: Interacts with human NUP153 (By similarity). Capsid protein p24: Interacts with host PDZD8; this interaction stabilizes the capsid (By similarity). Capsid protein p24: Interacts with monkey TRIM5; this interaction destabilizes the capsid (By similarity).Protease: Homodimer, whose active site consists of two apposed aspartic acid residues. Reverse transcriptase/ribonuclease H: Heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase: Homodimer; possibly can form homotetramer. Integrase: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Integrase: Interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1. Integrase: Interacts with human KPNA3; this interaction might play a role in nuclear import of the pre-integration complex (By similarity). Integrase: Interacts with human NUP153; this interaction might play a role in nuclear import of the pre-integration complex (By similarity).By similarity

Protein-protein interaction databases

IntActiP03366. 38 interactors.
MINTiMINT-111903.

Structurei

Secondary structure

11447
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni393 – 395Combined sources3
Beta strandi398 – 400Combined sources3
Turni402 – 404Combined sources3
Beta strandi414 – 416Combined sources3
Beta strandi419 – 421Combined sources3
Turni423 – 425Combined sources3
Beta strandi426 – 429Combined sources4
Beta strandi502 – 504Combined sources3
Beta strandi505 – 507Combined sources3
Beta strandi510 – 515Combined sources6
Beta strandi518 – 524Combined sources7
Beta strandi529 – 533Combined sources5
Beta strandi542 – 549Combined sources8
Beta strandi552 – 566Combined sources15
Beta strandi569 – 578Combined sources10
Beta strandi581 – 585Combined sources5
Helixi587 – 590Combined sources4
Turni591 – 594Combined sources4
Beta strandi596 – 598Combined sources3
Beta strandi602 – 604Combined sources3
Beta strandi611 – 614Combined sources4
Helixi627 – 642Combined sources16
Beta strandi645 – 648Combined sources4
Beta strandi651 – 653Combined sources3
Beta strandi659 – 663Combined sources5
Beta strandi665 – 668Combined sources4
Beta strandi670 – 674Combined sources5
Helixi677 – 682Combined sources6
Helixi684 – 687Combined sources4
Helixi689 – 691Combined sources3
Helixi696 – 698Combined sources3
Helixi699 – 701Combined sources3
Beta strandi703 – 709Combined sources7
Helixi710 – 712Combined sources3
Helixi713 – 716Combined sources4
Helixi721 – 727Combined sources7
Beta strandi729 – 731Combined sources3
Helixi734 – 736Combined sources3
Beta strandi737 – 739Combined sources3
Beta strandi741 – 747Combined sources7
Beta strandi752 – 754Combined sources3
Helixi755 – 773Combined sources19
Beta strandi774 – 776Combined sources3
Beta strandi777 – 782Combined sources6
Beta strandi785 – 790Combined sources6
Helixi794 – 808Combined sources15
Helixi809 – 811Combined sources3
Helixi817 – 819Combined sources3
Beta strandi820 – 822Combined sources3
Beta strandi824 – 828Combined sources5
Beta strandi831 – 833Combined sources3
Helixi835 – 837Combined sources3
Beta strandi838 – 841Combined sources4
Beta strandi849 – 852Combined sources4
Helixi853 – 866Combined sources14
Turni867 – 869Combined sources3
Beta strandi870 – 872Combined sources3
Helixi876 – 879Combined sources4
Helixi880 – 882Combined sources3
Turni883 – 885Combined sources3
Beta strandi886 – 888Combined sources3
Beta strandi890 – 892Combined sources3
Helixi896 – 908Combined sources13
Beta strandi909 – 911Combined sources3
Beta strandi913 – 916Combined sources4
Beta strandi920 – 922Combined sources3
Beta strandi925 – 932Combined sources8
Beta strandi935 – 943Combined sources9
Beta strandi946 – 954Combined sources9
Beta strandi957 – 961Combined sources5
Helixi963 – 982Combined sources20
Beta strandi987 – 992Combined sources6
Helixi994 – 1003Combined sources10
Beta strandi1004 – 1006Combined sources3
Beta strandi1012 – 1015Combined sources4
Beta strandi1017 – 1019Combined sources3
Beta strandi1020 – 1022Combined sources3
Helixi1023 – 1026Combined sources4
Beta strandi1029 – 1031Combined sources3
Beta strandi1036 – 1045Combined sources10
Turni1047 – 1049Combined sources3
Beta strandi1052 – 1058Combined sources7
Beta strandi1059 – 1061Combined sources3
Beta strandi1063 – 1070Combined sources8
Helixi1073 – 1087Combined sources15
Beta strandi1090 – 1096Combined sources7
Helixi1099 – 1105Combined sources7
Beta strandi1110 – 1114Combined sources5
Helixi1115 – 1126Combined sources12
Beta strandi1128 – 1134Combined sources7
Beta strandi1137 – 1139Combined sources3
Beta strandi1140 – 1142Combined sources3
Helixi1144 – 1152Combined sources9
Turni1153 – 1155Combined sources3
Beta strandi1219 – 1227Combined sources9
Beta strandi1230 – 1237Combined sources8
Turni1238 – 1240Combined sources3
Beta strandi1243 – 1250Combined sources8
Helixi1253 – 1266Combined sources14
Beta strandi1271 – 1273Combined sources3
Helixi1277 – 1281Combined sources5
Helixi1283 – 1292Combined sources10
Beta strandi1295 – 1297Combined sources3
Helixi1305 – 1324Combined sources20
Helixi1325 – 1327Combined sources3
Helixi1331 – 1344Combined sources14
Helixi1355 – 1367Combined sources13
Beta strandi1380 – 1386Combined sources7
Beta strandi1395 – 1403Combined sources9
Beta strandi1405 – 1420Combined sources16
Helixi1421 – 1423Combined sources3
Beta strandi1424 – 1428Combined sources5
Helixi1436 – 1439Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A9MX-ray2.30A/B501-599[»]
1AJVX-ray2.00A/B501-599[»]
1AJXX-ray2.00A/B501-599[»]
1AXAX-ray2.00A/B501-599[»]
1BQMX-ray3.10A600-1155[»]
B600-1029[»]
1BQNX-ray3.30A600-1440[»]
B600-1029[»]
1D4HX-ray1.81A/B501-599[»]
1D4IX-ray1.81A/B501-599[»]
1D4JX-ray1.81A/B501-599[»]
1DLOX-ray2.70A600-1155[»]
B600-1026[»]
1DW6X-ray1.88C/D501-599[»]
1EBKX-ray2.06C/D/E/F501-599[»]
1EBWX-ray1.81A/B501-599[»]
1EBYX-ray2.29A/B501-599[»]
1EBZX-ray2.01A/B501-599[»]
1EC0X-ray1.79A/B501-599[»]
1EC1X-ray2.10A/B501-599[»]
1EC2X-ray2.00A/B501-599[»]
1EC3X-ray1.80A/B501-599[»]
1EETX-ray2.73A600-1156[»]
B600-1026[»]
1G35X-ray1.80A/B501-599[»]
1GNMX-ray2.30A/B501-599[»]
1GNNX-ray2.30A/B501-599[»]
1GNOX-ray2.30A/B501-599[»]
1HARX-ray2.20A600-815[»]
1HBVX-ray2.30A/B501-599[»]
1HEFX-ray2.20E501-599[»]
1HEGX-ray2.20E501-599[»]
1HIHX-ray2.20A/B501-599[»]
1HMVX-ray3.20A/C/E/G600-1159[»]
B/D/F/H600-1039[»]
1HNIX-ray2.80A600-1157[»]
1HNVX-ray3.00A600-1157[»]
B600-1026[»]
1HOSX-ray2.30A/B501-599[»]
1HPSX-ray2.30A/B501-599[»]
1HPZX-ray3.00A600-1159[»]
B600-1029[»]
1HQEX-ray2.70A600-1159[»]
B600-1029[»]
1HQUX-ray2.70A600-1159[»]
B600-1029[»]
1HRHX-ray2.40A/B1026-1161[»]
1HTEX-ray2.80A/B501-599[»]
1HTFX-ray2.20A/B501-599[»]
1HTGX-ray2.00A/B501-599[»]
1HVIX-ray1.80A/B501-599[»]
1HVKX-ray1.80A/B501-599[»]
1HVPmodel-A/B501-599[»]
1HVUX-ray4.75A/D/G/J600-1153[»]
B/E/H/K604-1026[»]
1HYSX-ray3.00A600-1152[»]
B600-1024[»]
1IKVX-ray3.00A600-1159[»]
B600-1026[»]
1IKWX-ray3.00A600-1159[»]
B600-1026[»]
1IKXX-ray2.80A600-1159[»]
B600-1026[»]
1IKYX-ray3.00A600-1159[»]
B600-1026[»]
1J5OX-ray3.50A600-1157[»]
B600-1029[»]
1KJHX-ray2.00P1155-1164[»]
1MERX-ray1.90A/B501-599[»]
1MESX-ray1.90A/B501-599[»]
1METX-ray1.90A/B501-599[»]
1MEUX-ray1.90A/B501-599[»]
1N5YX-ray3.10A600-1157[»]
B600-1029[»]
1N6QX-ray3.00A600-1157[»]
B600-1029[»]
1NPAX-ray2.00A/B501-599[»]
1NPVX-ray2.00A/B501-599[»]
1NPWX-ray2.00A/B501-599[»]
1QE1X-ray2.85A600-1157[»]
B600-1026[»]
1QMCNMR-A/B1379-1429[»]
1R0AX-ray2.80A600-1157[»]
B600-1028[»]
1RDHX-ray2.80A/B1026-1159[»]
1RTDX-ray3.20A/C600-1153[»]
1RVLmodel-A600-1155[»]
B600-1027[»]
1RVMmodel-A600-1155[»]
B600-1027[»]
1RVNmodel-A600-1155[»]
B600-1027[»]
1RVOmodel-A600-1155[»]
B600-1027[»]
1RVPmodel-A600-1155[»]
B600-1027[»]
1RVQmodel-A600-1155[»]
B600-1027[»]
1RVRmodel-A600-1155[»]
B600-1027[»]
1S6PX-ray2.90A600-1159[»]
B600-1029[»]
1S6QX-ray3.00A600-1159[»]
B600-1029[»]
1S9EX-ray2.60A600-1159[»]
B600-1029[»]
1S9GX-ray2.80A600-1159[»]
B600-1029[»]
1SBGX-ray2.30A/B501-599[»]
1SUQX-ray3.00A600-1159[»]
B600-1029[»]
1SV5X-ray2.90A600-1159[»]
B600-1029[»]
1T03X-ray3.10A600-1157[»]
B600-1028[»]
1T05X-ray3.00A600-1157[»]
1T7KX-ray2.10A/B501-599[»]
1TV6X-ray2.80A600-1159[»]
B600-1039[»]
1TVRX-ray3.00A600-1157[»]
B600-1026[»]
1UWBX-ray3.20A600-1157[»]
B600-1026[»]
1W5VX-ray1.80A/B490-599[»]
1W5WX-ray1.80A/B490-599[»]
1W5XX-ray1.90A/B490-599[»]
1W5YX-ray1.90A/B490-599[»]
1YT9X-ray3.00A/B501-599[»]
1ZP8X-ray2.02A501-599[»]
1ZPAX-ray2.02A501-599[»]
1ZSFX-ray1.98A/B501-599[»]
1ZSRX-ray2.06A/B501-599[»]
2AQUX-ray2.00A/B501-599[»]
2B5JX-ray2.90A600-1159[»]
B600-1029[»]
2B6AX-ray2.65A600-1159[»]
B600-1029[»]
2BANX-ray2.95A600-1159[»]
B600-1029[»]
2BBBX-ray1.70A/B501-599[»]
2BE2X-ray2.43A600-1159[»]
B600-1029[»]
2EXFNMR-A390-432[»]
2G69X-ray1.35A501-599[»]
2HB3X-ray1.35A/B501-598[»]
2HMIX-ray2.80A600-1157[»]
B600-1029[»]
2HNZX-ray3.00B606-1027[»]
2HS1X-ray0.84A/B501-599[»]
2HS2X-ray1.22A/B501-599[»]
2I4DX-ray1.50A/B501-599[»]
2I4UX-ray1.50A/B501-599[»]
2I4VX-ray1.50A/B501-599[»]
2I4WX-ray1.55A/B501-599[»]
2I4XX-ray1.55A/B501-599[»]
2I5JX-ray3.15A600-1150[»]
B600-1027[»]
2IAJX-ray2.50A600-1158[»]
B600-1045[»]
2IC3X-ray3.00A600-1158[»]
B600-1045[»]
2IDWX-ray1.10A/B501-599[»]
2IEOX-ray1.53A/B501-599[»]
2JZWNMR-A390-432[»]
2L45NMR-A411-429[»]
2L46NMR-A411-429[»]
2L4LNMR-A388-432[»]
2UXZX-ray1.75A/B501-599[»]
2UY0X-ray1.76A/B501-599[»]
2VG5X-ray2.80A600-1156[»]
B600-1027[»]
2VG6X-ray3.01A600-1156[»]
B600-1027[»]
2VG7X-ray2.82A600-1156[»]
B600-1027[»]
2X4UX-ray2.10C/F908-916[»]
2YKMX-ray2.90A600-1156[»]
B600-1027[»]
2YKNX-ray2.12A600-1156[»]
B600-1027[»]
2ZD1X-ray1.80A600-1154[»]
B600-1027[»]
2ZE2X-ray2.90A600-1154[»]
B600-1027[»]
3AVIX-ray1.70A/B1209-1371[»]
3BGRX-ray2.10A600-1154[»]
B600-1027[»]
3DLKX-ray1.85A600-1154[»]
B605-1027[»]
3GGAX-ray2.50A/B/C/D/G/H501-599[»]
3GGVX-ray3.09A/B/C/D/E/F/G/H/I501-599[»]
3GGXX-ray2.70A/B/C/D/E/F/G/H501-599[»]
3HVTX-ray2.90A600-1155[»]
B600-1027[»]
3IG1X-ray2.80A600-1154[»]
B600-1027[»]
3IRXX-ray2.80A600-1154[»]
B600-1027[»]
3IS9X-ray2.55A600-1154[»]
B600-1027[»]
3ISNX-ray2.50C600-1159[»]
D600-1026[»]
3ITHX-ray2.80A/C600-1159[»]
B/D600-1026[»]
3JSMX-ray3.00A600-1157[»]
B600-1028[»]
3JYTX-ray3.30A600-1157[»]
B600-1028[»]
3K2PX-ray2.04A/B1026-1159[»]
3K4VX-ray1.39A/B/C/D501-599[»]
3KLEX-ray3.20A/E/I/M600-1157[»]
B/F/J/N600-1027[»]
3KLFX-ray3.15A/E/I/M600-1154[»]
B/F/J/N600-1027[»]
3KLGX-ray3.65A/E600-1157[»]
B/F600-1027[»]
3KLHX-ray2.90A600-1159[»]
B600-1027[»]
3KLIX-ray2.65A600-1157[»]
B600-1027[»]
3NDTX-ray1.72A/B/C/D501-599[»]
3NU3X-ray1.02A/B501-599[»]
3NU4X-ray1.20A/B501-599[»]
3NU5X-ray1.29A/B501-599[»]
3NU6X-ray1.16A/B501-599[»]
3NU9X-ray1.85A/B501-599[»]
3NUJX-ray1.50A/B501-599[»]
3NUOX-ray1.35A/B501-599[»]
3OK9X-ray1.27A/B501-599[»]
3PSUX-ray2.07A501-599[»]
3QAAX-ray1.40A/B501-599[»]
3QLHX-ray2.70A600-1153[»]
B605-1027[»]
3QO9X-ray2.60A600-1154[»]
B600-1027[»]
3TKGX-ray1.36A/B/C/D497-599[»]
3TKWX-ray1.55A/B497-599[»]
3TL9X-ray1.32A/B497-599[»]
3TLHX-ray2.00A501-599[»]
3V4IX-ray2.80A/C600-1153[»]
B/D600-1027[»]
3V6DX-ray2.70A/C600-1153[»]
B/D600-1027[»]
3V81X-ray2.85A/C600-1153[»]
B/D600-1027[»]
3ZPSX-ray1.55A/B501-599[»]
3ZPTX-ray1.54A/B501-599[»]
3ZPUX-ray1.80A/B501-599[»]
4COEX-ray2.45A/B501-599[»]
4CP7X-ray1.80A/B501-599[»]
4CPQX-ray2.35A/B501-599[»]
4CPRX-ray1.80A/B501-599[»]
4CPSX-ray1.55A/B501-599[»]
4CPTX-ray1.70A/B501-599[»]
4CPUX-ray1.82A/B501-599[»]
4CPWX-ray1.70A/B501-599[»]
4CPXX-ray1.85A/B501-599[»]
4DG1X-ray2.15A600-1148[»]
B600-1026[»]
4G1QX-ray1.51A600-1154[»]
B600-1027[»]
4G8GX-ray2.40C263-272[»]
4G8IX-ray1.60C263-272[»]
4G9DX-ray1.60C263-272[»]
4G9FX-ray1.90C263-272[»]
4H4MX-ray2.85A600-1154[»]
B600-1027[»]
4H4OX-ray2.90A600-1154[»]
B600-1027[»]
4I2PX-ray2.30A600-1154[»]
B600-1027[»]
4I2QX-ray2.70A600-1154[»]
B600-1027[»]
4ICLX-ray1.80A600-1154[»]
B600-1027[»]
4ID5X-ray1.95A600-1154[»]
B600-1027[»]
4IDKX-ray2.10A600-1154[»]
B600-1027[»]
4IFVX-ray2.05A600-1154[»]
B600-1027[»]
4IFYX-ray2.10A600-1154[»]
B600-1027[»]
4IG0X-ray2.50A600-1154[»]
B600-1027[»]
4IG3X-ray1.95A600-1154[»]
B600-1027[»]
4KFBX-ray1.85A600-1154[»]
B604-1027[»]
4KKOX-ray2.89A600-1154[»]
B600-1027[»]
4KO0X-ray1.95A600-1154[»]
B600-1027[»]
4LSLX-ray2.69A600-1154[»]
B600-1027[»]
4LSNX-ray3.10A600-1154[»]
B600-1027[»]
4MFBX-ray2.88A600-1154[»]
B600-1027[»]
4O44X-ray2.89A600-1154[»]
B600-1027[»]
4O4GX-ray2.71A600-1154[»]
B600-1027[»]
4OJRX-ray1.82A1209-1371[»]
4PQUX-ray2.51A/C600-1153[»]
B/D600-1027[»]
4PUOX-ray2.90A/C600-1153[»]
B/D600-1027[»]
4PWDX-ray3.00A/C600-1153[»]
B/D600-1027[»]
4Q0BX-ray3.30A/C600-1153[»]
B/D600-1027[»]
4QAGX-ray1.71A/B1024-1156[»]
4R5PX-ray2.89A/C600-1153[»]
B/D600-1027[»]
4RW4X-ray2.67A600-1154[»]
B600-1027[»]
4RW6X-ray2.63A600-1154[»]
B600-1027[»]
4RW7X-ray3.01A600-1154[»]
B600-1027[»]
4RW8X-ray2.88A600-1154[»]
B600-1027[»]
4RW9X-ray2.99A600-1154[»]
B600-1027[»]
4U8WX-ray1.30A/B501-599[»]
4WE1X-ray2.49A600-1154[»]
B600-1027[»]
4YE3X-ray1.35A/B501-599[»]
4YHQX-ray1.30A/B501-599[»]
4ZIPX-ray1.11A/B501-599[»]
4ZLSX-ray1.53A/B501-599[»]
5AGZX-ray1.20A/B501-599[»]
5AH6X-ray1.50A/B501-599[»]
5AH7X-ray1.55A/B501-599[»]
5AH8X-ray1.26A/B501-599[»]
5AH9X-ray1.44A/B501-599[»]
5AHAX-ray1.35A/B501-599[»]
5AHBX-ray1.50A/B501-599[»]
5AHCX-ray1.50A/B501-599[»]
5BRYX-ray1.34A/B501-599[»]
5BS4X-ray1.29A/B501-599[»]
5C24X-ray2.60A600-1144[»]
B604-1027[»]
5C25X-ray2.84A600-1154[»]
B600-1027[»]
5C42X-ray3.50A600-1154[»]
B600-1027[»]
5CYMX-ray2.10A600-1154[»]
B600-1027[»]
5CYQX-ray2.15A600-1154[»]
B600-1027[»]
5D3GX-ray2.30A/C600-1154[»]
B/D600-1027[»]
5FDLX-ray3.10A600-1156[»]
B600-1039[»]
5HBMX-ray3.04A600-1154[»]
B600-1027[»]
5HLFX-ray2.95A/C600-1154[»]
B/D600-1027[»]
5HP1X-ray2.90A/C600-1154[»]
B/D600-1027[»]
5HROX-ray2.75A/C600-1154[»]
B/D600-1027[»]
5I3UX-ray3.00A/C600-1154[»]
B/D600-1027[»]
5I42X-ray3.30A/C600-1154[»]
B/D600-1027[»]
5J1EX-ray2.90A/C600-1154[»]
B/D600-1027[»]
5JFPX-ray1.49A/B501-599[»]
5JFUX-ray1.70A/B501-599[»]
5JG1X-ray1.16A/B501-599[»]
ProteinModelPortaliP03366.
SMRiP03366.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03366.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini520 – 589Peptidase A2PROSITE-ProRule annotationAdd BLAST70
Domaini643 – 833Reverse transcriptasePROSITE-ProRule annotationAdd BLAST191
Domaini1033 – 1156RNase HPROSITE-ProRule annotationAdd BLAST124
Domaini1213 – 1363Integrase catalyticPROSITE-ProRule annotationAdd BLAST151

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni7 – 31Interaction with Gp41By similarityAdd BLAST25
Regioni8 – 43Interaction with host CALM1By similarityAdd BLAST36
Regioni12 – 19Interaction with host AP3D1By similarity8
Regioni14 – 33Interaction with membrane phosphatidylinositol 4,5-bisphosphate and RNABy similarityAdd BLAST20
Regioni73 – 77Interaction with membrane phosphatidylinositol 4,5-bisphosphateBy similarity5
Regioni189 – 227Interaction with human PPIA/CYPA and NUP153By similarityAdd BLAST39
Regioni277 – 363Dimerization/Multimerization of capsid protein p24By similarityAdd BLAST87
Regioni501 – 505Dimerization of proteaseBy similarity5
Regioni549 – 555Dimerization of proteaseBy similarity7
Regioni588 – 600Dimerization of proteaseBy similarityAdd BLAST13
Regioni826 – 834RT 'primer grip'9

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi16 – 22Nuclear export signalBy similarity7
Motifi26 – 32Nuclear localization signalBy similarity7
Motifi997 – 1013Tryptophan repeat motifAdd BLAST17

Domaini

Reverse transcriptase/ribonuclease H: RT is structured in five subdomains: finger, palm, thumb, connection and RNase H. Within the palm subdomain, the 'primer grip' region is thought to be involved in the positioning of the primer terminus for accommodating the incoming nucleotide. The RNase H domain stabilizes the association of RT with primer-template.By similarity
Reverse transcriptase/ribonuclease H: The tryptophan repeat motif is involved in RT p66/p51 dimerization (By similarity).By similarity
Integrase: The core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein.By similarity

Sequence similaritiesi

Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 integrase-type DNA-binding domain.PROSITE-ProRule annotation
Contains 1 integrase-type zinc finger.PROSITE-ProRule annotation
Contains 1 peptidase A2 domain.PROSITE-ProRule annotation
Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
Contains 1 RNase H domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri390 – 407CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri411 – 428CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1162 – 1203Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Repeat, Zinc-finger

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
1.10.1200.30. 1 hit.
1.10.150.90. 1 hit.
1.10.375.10. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
3.30.420.10. 2 hits.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_HIV/RSV.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06815. RVT_connect. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00234. HIV1MATRIX.
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF53098. SSF53098. 2 hits.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 2 hits.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Note: Translation results in the formation of the Gag polyprotein most of the time. Ribosomal frameshifting at the gag-pol genes boundary occurs at low frequency and produces the Gag-Pol polyprotein. This strategy of translation probably allows the virus to modulate the quantity of each viral protein. Maintenance of a correct Gag to Gag-Pol ratio is essential for RNA dimerization and viral infectivity.1 Publication
Isoform Gag-Pol polyprotein (identifier: P03366-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL
60 70 80 90 100
LETSEGCRQI LGQLQPSLQT GSEELRSLYN TVATLYCVHQ RIEIKDTKEA
110 120 130 140 150
LDKIEEEQNK SKKKAQQAAA DTGHSSQVSQ NYPIVQNIQG QMVHQAISPR
160 170 180 190 200
TLNAWVKVVE EKAFSPEVIP MFSALSEGAT PQDLNTMLNT VGGHQAAMQM
210 220 230 240 250
LKETINEEAA EWDRVHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM
260 270 280 290 300
TNNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK EPFRDYVDRF
310 320 330 340 350
YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC
360 370 380 390 400
QGVGGPGHKA RVLAEAMSQV TNTATIMMQR GNFRNQRKMV KCFNCGKEGH
410 420 430 440 450
TARNCRAPRK KGCWKCGKEG HQMKDCTERQ ANFLREDLAF LQGKAREFSS
460 470 480 490 500
EQTRANSPTI SSEQTRANSP TRRELQVWGR DNNSPSEAGA DRQGTVSFNF
510 520 530 540 550
PQITLWQRPL VTIKIGGQLK EALLDTGADD TVLEEMSLPG RWKPKMIGGI
560 570 580 590 600
GGFIKVRQYD QILIEICGHK AIGTVLVGPT PVNIIGRNLL TQIGCTLNFP
610 620 630 640 650
ISPIETVPVK LKPGMDGPKV KQWPLTEEKI KALVEICTEM EKEGKISKIG
660 670 680 690 700
PENPYNTPVF AIKKKDSTKW RKLVDFRELN KRTQDFWEVQ LGIPHPAGLK
710 720 730 740 750
KKKSVTVLDV GDAYFSVPLD EDFRKYTAFT IPSINNETPG IRYQYNVLPQ
760 770 780 790 800
GWKGSPAIFQ SSMTKILEPF KKQNPDIVIY QYMDDLYVGS DLEIGQHRTK
810 820 830 840 850
IEELRQHLLR WGLTTPDKKH QKEPPFLWMG YELHPDKWTV QPIVLPEKDS
860 870 880 890 900
WTVNDIQKLV GKLNWASQIY PGIKVRQLCK LLRGTKALTE VIPLTEEAEL
910 920 930 940 950
ELAENREILK EPVHGVYYDP SKDLIAEIQK QGQGQWTYQI YQEPFKNLKT
960 970 980 990 1000
GKYARMRGAH TNDVKQLTEA VQKITTESIV IWGKTPKFKL PIQKETWETW
1010 1020 1030 1040 1050
WTEYWQATWI PEWEFVNTPP LVKLWYQLEK EPIVGAETFY VDGAANRETK
1060 1070 1080 1090 1100
LGKAGYVTNK GRQKVVPLTN TTNQKTELQA IYLALQDSGL EVNIVTDSQY
1110 1120 1130 1140 1150
ALGIIQAQPD KSESELVNQI IEQLIKKEKV YLAWVPAHKG IGGNEQVDKL
1160 1170 1180 1190 1200
VSAGIRKILF LDGIDKAQDE HEKYHSNWRA MASDFNLPPV VAKEIVASCD
1210 1220 1230 1240 1250
KCQLKGEAMH GQVDCSPGIW QLDCTHLEGK VILVAVHVAS GYIEAEVIPA
1260 1270 1280 1290 1300
ETGQETAYFL LKLAGRWPVK TIHTDNGSNF TSATVKAACW WAGIKQEFGI
1310 1320 1330 1340 1350
PYNPQSQGVV ESMNKELKKI IGQVRDQAEH LKTAVQMAVF IHNFKRKGGI
1360 1370 1380 1390 1400
GGYSAGERIV DIIATDIQTK ELQKQITKIQ NFRVYYRDSR NPLWKGPAKL
1410 1420 1430 1440
LWKGEGAVVI QDNSDIKVVP RRKAKIIRDY GKQMAGDDCV ASRQDED
Note: Produced by -1 ribosomal frameshifting.
Length:1,447
Mass (Da):163,288
Last modified:January 23, 2007 - v3
Checksum:iAC3EE1439592E0AD
GO
Isoform Gag polyprotein (identifier: P03347-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P03347.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:512
Mass (Da):57,256
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti297V → L in strain: Isolate PV22. 1
Natural varianti434L → F.1
Natural varianti771K → R in strain: Isolate PV22. 1
Natural varianti1050K → R in strain: Isolate PV22. 1
Natural varianti1057V → L in strain: Isolate PV22. 1
Natural varianti1111K → Q in strain: Isolate PV22. 1
Natural varianti1128E → Q in strain: Isolate PV22. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15654 Genomic RNA. Translation: AAA44198.1. Sequence problems.
K02083 Genomic DNA. Translation: AAB59867.1. Sequence problems.
X01762 Genomic RNA. No translation available.
PIRiA03965. GNVWH3.
A03967. GNVWVL.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Web resourcesi

HIV drug resistance mutations
hivdb

HIV drug resistance database

BioAfrica: HIV bioinformatics in Africa

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15654 Genomic RNA. Translation: AAA44198.1. Sequence problems.
K02083 Genomic DNA. Translation: AAB59867.1. Sequence problems.
X01762 Genomic RNA. No translation available.
PIRiA03965. GNVWH3.
A03967. GNVWVL.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A9MX-ray2.30A/B501-599[»]
1AJVX-ray2.00A/B501-599[»]
1AJXX-ray2.00A/B501-599[»]
1AXAX-ray2.00A/B501-599[»]
1BQMX-ray3.10A600-1155[»]
B600-1029[»]
1BQNX-ray3.30A600-1440[»]
B600-1029[»]
1D4HX-ray1.81A/B501-599[»]
1D4IX-ray1.81A/B501-599[»]
1D4JX-ray1.81A/B501-599[»]
1DLOX-ray2.70A600-1155[»]
B600-1026[»]
1DW6X-ray1.88C/D501-599[»]
1EBKX-ray2.06C/D/E/F501-599[»]
1EBWX-ray1.81A/B501-599[»]
1EBYX-ray2.29A/B501-599[»]
1EBZX-ray2.01A/B501-599[»]
1EC0X-ray1.79A/B501-599[»]
1EC1X-ray2.10A/B501-599[»]
1EC2X-ray2.00A/B501-599[»]
1EC3X-ray1.80A/B501-599[»]
1EETX-ray2.73A600-1156[»]
B600-1026[»]
1G35X-ray1.80A/B501-599[»]
1GNMX-ray2.30A/B501-599[»]
1GNNX-ray2.30A/B501-599[»]
1GNOX-ray2.30A/B501-599[»]
1HARX-ray2.20A600-815[»]
1HBVX-ray2.30A/B501-599[»]
1HEFX-ray2.20E501-599[»]
1HEGX-ray2.20E501-599[»]
1HIHX-ray2.20A/B501-599[»]
1HMVX-ray3.20A/C/E/G600-1159[»]
B/D/F/H600-1039[»]
1HNIX-ray2.80A600-1157[»]
1HNVX-ray3.00A600-1157[»]
B600-1026[»]
1HOSX-ray2.30A/B501-599[»]
1HPSX-ray2.30A/B501-599[»]
1HPZX-ray3.00A600-1159[»]
B600-1029[»]
1HQEX-ray2.70A600-1159[»]
B600-1029[»]
1HQUX-ray2.70A600-1159[»]
B600-1029[»]
1HRHX-ray2.40A/B1026-1161[»]
1HTEX-ray2.80A/B501-599[»]
1HTFX-ray2.20A/B501-599[»]
1HTGX-ray2.00A/B501-599[»]
1HVIX-ray1.80A/B501-599[»]
1HVKX-ray1.80A/B501-599[»]
1HVPmodel-A/B501-599[»]
1HVUX-ray4.75A/D/G/J600-1153[»]
B/E/H/K604-1026[»]
1HYSX-ray3.00A600-1152[»]
B600-1024[»]
1IKVX-ray3.00A600-1159[»]
B600-1026[»]
1IKWX-ray3.00A600-1159[»]
B600-1026[»]
1IKXX-ray2.80A600-1159[»]
B600-1026[»]
1IKYX-ray3.00A600-1159[»]
B600-1026[»]
1J5OX-ray3.50A600-1157[»]
B600-1029[»]
1KJHX-ray2.00P1155-1164[»]
1MERX-ray1.90A/B501-599[»]
1MESX-ray1.90A/B501-599[»]
1METX-ray1.90A/B501-599[»]
1MEUX-ray1.90A/B501-599[»]
1N5YX-ray3.10A600-1157[»]
B600-1029[»]
1N6QX-ray3.00A600-1157[»]
B600-1029[»]
1NPAX-ray2.00A/B501-599[»]
1NPVX-ray2.00A/B501-599[»]
1NPWX-ray2.00A/B501-599[»]
1QE1X-ray2.85A600-1157[»]
B600-1026[»]
1QMCNMR-A/B1379-1429[»]
1R0AX-ray2.80A600-1157[»]
B600-1028[»]
1RDHX-ray2.80A/B1026-1159[»]
1RTDX-ray3.20A/C600-1153[»]
1RVLmodel-A600-1155[»]
B600-1027[»]
1RVMmodel-A600-1155[»]
B600-1027[»]
1RVNmodel-A600-1155[»]
B600-1027[»]
1RVOmodel-A600-1155[»]
B600-1027[»]
1RVPmodel-A600-1155[»]
B600-1027[»]
1RVQmodel-A600-1155[»]
B600-1027[»]
1RVRmodel-A600-1155[»]
B600-1027[»]
1S6PX-ray2.90A600-1159[»]
B600-1029[»]
1S6QX-ray3.00A600-1159[»]
B600-1029[»]
1S9EX-ray2.60A600-1159[»]
B600-1029[»]
1S9GX-ray2.80A600-1159[»]
B600-1029[»]
1SBGX-ray2.30A/B501-599[»]
1SUQX-ray3.00A600-1159[»]
B600-1029[»]
1SV5X-ray2.90A600-1159[»]
B600-1029[»]
1T03X-ray3.10A600-1157[»]
B600-1028[»]
1T05X-ray3.00A600-1157[»]
1T7KX-ray2.10A/B501-599[»]
1TV6X-ray2.80A600-1159[»]
B600-1039[»]
1TVRX-ray3.00A600-1157[»]
B600-1026[»]
1UWBX-ray3.20A600-1157[»]
B600-1026[»]
1W5VX-ray1.80A/B490-599[»]
1W5WX-ray1.80A/B490-599[»]
1W5XX-ray1.90A/B490-599[»]
1W5YX-ray1.90A/B490-599[»]
1YT9X-ray3.00A/B501-599[»]
1ZP8X-ray2.02A501-599[»]
1ZPAX-ray2.02A501-599[»]
1ZSFX-ray1.98A/B501-599[»]
1ZSRX-ray2.06A/B501-599[»]
2AQUX-ray2.00A/B501-599[»]
2B5JX-ray2.90A600-1159[»]
B600-1029[»]
2B6AX-ray2.65A600-1159[»]
B600-1029[»]
2BANX-ray2.95A600-1159[»]
B600-1029[»]
2BBBX-ray1.70A/B501-599[»]
2BE2X-ray2.43A600-1159[»]
B600-1029[»]
2EXFNMR-A390-432[»]
2G69X-ray1.35A501-599[»]
2HB3X-ray1.35A/B501-598[»]
2HMIX-ray2.80A600-1157[»]
B600-1029[»]
2HNZX-ray3.00B606-1027[»]
2HS1X-ray0.84A/B501-599[»]
2HS2X-ray1.22A/B501-599[»]
2I4DX-ray1.50A/B501-599[»]
2I4UX-ray1.50A/B501-599[»]
2I4VX-ray1.50A/B501-599[»]
2I4WX-ray1.55A/B501-599[»]
2I4XX-ray1.55A/B501-599[»]
2I5JX-ray3.15A600-1150[»]
B600-1027[»]
2IAJX-ray2.50A600-1158[»]
B600-1045[»]
2IC3X-ray3.00A600-1158[»]
B600-1045[»]
2IDWX-ray1.10A/B501-599[»]
2IEOX-ray1.53A/B501-599[»]
2JZWNMR-A390-432[»]
2L45NMR-A411-429[»]
2L46NMR-A411-429[»]
2L4LNMR-A388-432[»]
2UXZX-ray1.75A/B501-599[»]
2UY0X-ray1.76A/B501-599[»]
2VG5X-ray2.80A600-1156[»]
B600-1027[»]
2VG6X-ray3.01A600-1156[»]
B600-1027[»]
2VG7X-ray2.82A600-1156[»]
B600-1027[»]
2X4UX-ray2.10C/F908-916[»]
2YKMX-ray2.90A600-1156[»]
B600-1027[»]
2YKNX-ray2.12A600-1156[»]
B600-1027[»]
2ZD1X-ray1.80A600-1154[»]
B600-1027[»]
2ZE2X-ray2.90A600-1154[»]
B600-1027[»]
3AVIX-ray1.70A/B1209-1371[»]
3BGRX-ray2.10A600-1154[»]
B600-1027[»]
3DLKX-ray1.85A600-1154[»]
B605-1027[»]
3GGAX-ray2.50A/B/C/D/G/H501-599[»]
3GGVX-ray3.09A/B/C/D/E/F/G/H/I501-599[»]
3GGXX-ray2.70A/B/C/D/E/F/G/H501-599[»]
3HVTX-ray2.90A600-1155[»]
B600-1027[»]
3IG1X-ray2.80A600-1154[»]
B600-1027[»]
3IRXX-ray2.80A600-1154[»]