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Entry version 117 (18 Sep 2019)
Sequence version 2 (10 Aug 2010)
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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Rous sarcoma virus (strain Schmidt-Ruppin B) (RSV-SRB)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Capsid protein p27: Self-associates to form the irregular polyhedron core composed of hexamers and pentamers, that encapsulates the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro.By similarity
Spacer peptide: Plays a role in the oligomerization of the Gag polyprotein and in the stabilization of the immature particle. Essential layering element during tube assembly.By similarity
Nucleocapsid protein p12: Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs.Curated
Protease p15: 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.PROSITE-ProRule annotation
Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions (PubMed:9218451). This recombination event is an essential step in the viral replication cycle. Has a strong preference for using the 3'-OH at the viral DNA end as a nucleophile.By similarity1 Publication

Miscellaneous

Reverse transcriptase: Error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template switching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs.PROSITE-ProRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei418Involved in capsid protein dimerization upon acidificationBy similarity1
Sitei430Involved in capsid protein dimerization upon acidificationBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei614For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi815Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi890Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi891Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1158Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1192Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1213Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1272Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1344Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1 Publication1
Metal bindingi1401Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1 Publication1
Metal bindingi1437Magnesium; catalytic; for integrase activityBy similarity1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri507 – 524CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri533 – 550CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1280 – 1321Integrase-typePROSITE-ProRule annotationAdd BLAST42
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi1502 – 1550Integrase-typePROSITE-ProRule annotationAdd BLAST49

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, RNA-directed DNA polymerase, Transferase
Biological processDNA integration, DNA recombination, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Gag-Pol polyprotein
Cleaved into the following 13 chains:
Protease p15 (EC:3.4.23.-PROSITE-ProRule annotation)
Reverse transcriptase alpha-subunit (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
RT-alpha
Integrase (EC:2.7.7.-1 Publication, EC:3.1.-.-1 Publication)
Short name:
IN
Alternative name(s):
pp32
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:gag-pol
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRous sarcoma virus (strain Schmidt-Ruppin B) (RSV-SRB)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri269447 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesOrterviralesRetroviridaeOrthoretrovirinaeAlpharetrovirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiGallus gallus (Chicken) [TaxID: 9031]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000159275 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Matrix protein p19 :
Capsid protein p27, alternate cleaved 1 :
Capsid protein p27, alternate cleaved 2 :
Nucleocapsid protein p12 :

GO - Cellular componenti

  • virion Source: UniProtKB-SubCell

Keywords - Cellular componenti

Virion

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi1344D → N: Complete loss of activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004424801 – 1603Gag-Pol polyproteinAdd BLAST1603
ChainiPRO_00003970581 – 155Matrix protein p19Add BLAST155
ChainiPRO_0000397059156 – 166p2AAdd BLAST11
ChainiPRO_0000397060167 – 177p2BAdd BLAST11
ChainiPRO_0000397061178 – 239p10Add BLAST62
ChainiPRO_0000397062240 – 479Capsid protein p27, alternate cleaved 2Add BLAST240
ChainiPRO_0000442481240 – 476Capsid protein p27, alternate cleaved 1Add BLAST237
ChainiPRO_0000397063480 – 488p39
ChainiPRO_0000397064489 – 577Nucleocapsid protein p12Add BLAST89
ChainiPRO_0000397065578 – 708Protease p15Add BLAST131
ChainiPRO_0000397066709 – 1567Reverse transcriptase beta-subunitAdd BLAST859
ChainiPRO_0000040984709 – 1280Reverse transcriptase alpha-subunitAdd BLAST572
ChainiPRO_00000409851281 – 1567IntegraseAdd BLAST287
ChainiPRO_00003970671568 – 1603p4Add BLAST36

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Gag-pol polyprotein: Specific enzymatic cleavages in vivo yield mature proteins.By similarity
Capsid protein p27: The cleavage at the C-terminus is slowly trimmed by the viral protease, sometimes being cut internally thereby generating the short version of the capsid protein and a capsid protein C-terminally extended by 3 amino acids in a ratio of 2:1.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei155 – 156Cleavage; by viral protease p15By similarity2
Sitei166 – 167Cleavage; by viral protease p15By similarity2
Sitei177 – 178Cleavage; by viral protease p15By similarity2
Sitei239 – 240Cleavage; by viral protease p15By similarity2
Sitei476 – 477Cleavage; by viral protease p15By similarity2
Sitei479 – 480Cleavage; by viral protease p15By similarity2
Sitei488 – 489Cleavage; by viral protease p15By similarity2
Sitei577 – 578Cleavage; by viral protease p15By similarity2
Sitei708 – 709Cleavage; by viral protease p15By similarity2
Sitei1280 – 1281Cleavage; by viral protease p15By similarity2
Sitei1567 – 1568Cleavage; by viral protease p15By similarity2

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Protease p15: Active as a homodimer. Integrase: Homodimer; further associates as a homooctamer (PubMed:9218451, PubMed:28458055). Reverse transcriptase: Heterodimer of alpha and beta subunits. Reverse transcriptase: Three forms of RT exist: alpha-alpha (alpha-Pol), beta-beta (beta-Pol), and alpha-beta, with the major form being the heterodimer. Both the polymerase and RNase H active sites are located in the alpha subunit of heterodimeric RT alpha-beta.

2 PublicationsBy similarity

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

11603
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
O92956

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
O92956

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini609 – 690Peptidase A2PROSITE-ProRule annotationAdd BLAST82
Domaini750 – 938Reverse transcriptasePROSITE-ProRule annotationAdd BLAST189
Domaini1163 – 1280RNase HPROSITE-ProRule annotationAdd BLAST118
Domaini1333 – 1496Integrase catalyticPROSITE-ProRule annotationAdd BLAST164

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1548 – 1567Involved in homooctamerizationBy similarityAdd BLAST20

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi172 – 175PPXY motifBy similarity4
Motifi180 – 184LYPX(n)L motifBy similarity5
Motifi219 – 229Nuclear export signalBy similarityAdd BLAST11

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi171 – 174Poly-Pro4

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Gag-Pol polyprotein: Late-budding domains (L domains) are short sequence motifs essential for viral particle release. They can occur individually or in close proximity within structural proteins. They interacts with sorting cellular proteins of the multivesicular body (MVB) pathway. Most of these proteins are class E vacuolar protein sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes. P2B contains two L domain: a PPXY motif which probably binds to the WW domains of HECT (homologous to E6-AP C-terminus) E3 ubiquitin ligases and a LYPX(n)L domain which is known to bind the Alix adaptator protein.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).By similarity
Gag-Pol polyprotein: contains a nuclear export signal in p10 and a nucleolar localization signal in nucleocapsid protein p12.By similarity
Capsid protein p27: Proton-driven dimerization of the C-terminus facilitates capsid assembly.By similarity

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri507 – 524CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri533 – 550CCHC-typePROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1280 – 1321Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05482 HIV_retropepsin_like, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.10.200, 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

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR004028 Gag_M
IPR000721 Gag_p24
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR012344 Matrix_HIV/RSV_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010661 RVT_thumb
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF02813 Retro_M, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF06817 RVT_thumb, 1 hit
PF00098 zf-CCHC, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00343 ZnF_C2HC, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF46919 SSF46919, 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

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50175 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, 1 hit
PS50876 ZF_INTEGRASE, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (2)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by ribosomal frameshifting. AlignAdd to basket
Note: Translation results in the formation of the Gag polyprotein. Ribosomal frameshifting at the gag/pol genes boundary produces the Gag-Pol polyprotein.
Isoform Gag-Pol polyprotein (identifier: O92956-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali 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
MEAVIKVISS ACKTYCGKTS PSKKEIGAML SLLQKEGLLM SPSDLYSPGS
60 70 80 90 100
WDPITAALSQ RAMVLGKSGE LKTWGLVLGA LKAAREEQVT SEQAKFWLGL
110 120 130 140 150
GGGRVSPPGP ECIEKPATER RIDKGEEVGE TTVQRDAKMA PEETATPKTV
160 170 180 190 200
GTSCYHCGTA IGCNCATASA PPPPYVGSGL YPSLAGVGEQ QGQGGDTPRG
210 220 230 240 250
AEQPRAEPGH AGLAPGPALT DWARIREELA STGPPVVAMP VVIKTEGPAW
260 270 280 290 300
TPLEPKLITR LADTVRTKGL RSPITMAEVE ALMSSPLLPH DVTNLMRVIL
310 320 330 340 350
GPAPYALWMD AWGVQLQTVI AAATRDPRHP ANGQGRGERT NLDRLKGLAD
360 370 380 390 400
GMVGNPQGQA ALLRPGELVA ITASALQAFR EVARLAEPAG PWADITQGPS
410 420 430 440 450
ESFVDFANRL IKAVEGSDLP PSARAPVIID CFRQKSQPDI QQLIRAAPST
460 470 480 490 500
LTTPGEIIKY VLDRQKIAPL TDQGIAAAMS SAIQPLVMAV VNRERDGQTG
510 520 530 540 550
SGGRARRLCY TCGSPGHYQA QCPKKRKSGN SRERCQLCDG MGHNAKQCRR
560 570 580 590 600
RDSNQGQRPG RGLSSGPWPV SEQPAVSLAM TMEHKDRPLV RVILTNTGSH
610 620 630 640 650
PVKQRSVYIT ALLDSGADIT IISEEDWPTD WPVVDTANPQ IHGIGGGIPM
660 670 680 690 700
RKSRDMIELG VINRDGSLER PLLLFPAVAM VRGSILGRDC LQGLGLRLTN
710 720 730 740 750
LVGRATVLTV ALHLAIPLKW KPDHTPVWID QWPLPEGKLV ALTQLVEKEL
760 770 780 790 800
QLGHIEPSLS CWNTPVFVIR KASGSYRLLH DLRAVNAKLV PFGAVQQGAP
810 820 830 840 850
VLSALPRGWP LMVLDLKDCF FSIPLAEQDR EAFAFTLPSV NNQAPARRFQ
860 870 880 890 900
WKVLPQGMTC SPTICQLVVG QVLEPLRLKH PSLRMLHYMD DLLLAASSHD
910 920 930 940 950
GLEAAGEEVI NTLERAGFTI SPDKIQREPG VQYLGYKLGS TYVAPVGLVA
960 970 980 990 1000
EPRIATLWDV QKLVGSLQWL RPALGIPPRL MGPFYEQLRG SDPNEAREWN
1010 1020 1030 1040 1050
LDMKMAWREI VQLSTTAALE RWDPALPLEG AVVRCEQGAI GVLGQGLSTH
1060 1070 1080 1090 1100
PRPCLWLFST QPTKAFTAWL EVLTLLITKL RASAVRTFGK EVDILLLPAC
1110 1120 1130 1140 1150
FREDLPLPEG ILLALRGFAG KIRSSDTPSI FDIARPLHVS LKVRVTDHPV
1160 1170 1180 1190 1200
PGPTVFTDAS SSTHKGVVVW REGPRWEIKE IADLGASVQQ LEARAVAMAL
1210 1220 1230 1240 1250
LLWPTTPTNV VTDSAFVAKM LLKMGQEGVP STAAAFILED ALSQRSAMAA
1260 1270 1280 1290 1300
VLHVRSHSEV PGFFTEGNDV ADSQATFQAY PLREAKDLHT TLHIGPRALS
1310 1320 1330 1340 1350
KACNISMQQA REVVQTCPHC NSAPALEAGV NPRGLGPLQI WQTDFTLEPR
1360 1370 1380 1390 1400
MAPRSWLAVT VDTASSAIVV TQHGRVTSVA AQHHWATAIA VLGRPKAIKT
1410 1420 1430 1440 1450
DNGSCFTSKS TREWLARWGI AHTTGIPGNS QGQAMVERAN RLLKDKIRVL
1460 1470 1480 1490 1500
AEGDGFMKRI PASKQGELLA KAMYALNHFE RGENTKTPVQ KHWRPTVLTE
1510 1520 1530 1540 1550
GPPVKIRIET GEWEKGWNVL VWGRGYAAVK NRDTDKVIWV PSRKVKPDIT
1560 1570 1580 1590 1600
QKDEVTKKDE ASPLFAGSSD WIPWGDEQEG LQEEAASNKQ EGPGEDTLAA

NES
Note: Produced by -1 ribosomal frameshifting.
Length:1,603
Mass (Da):173,990
Last modified:August 10, 2010 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i3BEFAA397C54CDE7
GO
Isoform Gag polyprotein (identifier: O92954-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry O92954.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:701
Mass (Da):74,753
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAC08988 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti1376V → A (PubMed:8805516).Curated1
Sequence conflicti1441R → K (PubMed:8805516).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AF052428 Genomic DNA Translation: AAC08988.1 Different initiation.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF052428 Genomic DNA Translation: AAC08988.1 Different initiation.

3D structure databases

Select the link destinations:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1A5VX-ray1.90A1332-1487[»]
1A5WX-ray2.00A1332-1487[»]
1A5XX-ray1.90A1332-1487[»]
1ASUX-ray1.70A1332-1487[»]
1ASVX-ray2.20A1332-1487[»]
1ASWX-ray1.80A1332-1487[»]
1CXQX-ray1.02A1333-1487[»]
1CXUX-ray1.42A1333-1487[»]
1CZ9X-ray1.20A1333-1487[»]
1CZBX-ray1.06A1333-1487[»]
1VSDX-ray1.70A1335-1479[»]
1VSEX-ray2.20A1335-1479[»]
1VSFX-ray2.05A1335-1479[»]
1VSHX-ray1.95A1335-1479[»]
1VSIX-ray2.20A1335-1479[»]
1VSJX-ray2.10A1335-1479[»]
1VSKX-ray2.20A1334-1479[»]
1VSLX-ray2.20A1334-1479[»]
1VSMX-ray2.15A1334-1479[»]
3O4NX-ray1.80A/B1333-1479[»]
3O4QX-ray1.55A1333-1479[»]
SMRiO92956
ModBaseiSearch...
PDBe-KBiSearch...

Miscellaneous databases

EvolutionaryTraceiO92956

Family and domain databases

CDDicd05482 HIV_retropepsin_like, 1 hit
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
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR004028 Gag_M
IPR000721 Gag_p24
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR012344 Matrix_HIV/RSV_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010661 RVT_thumb
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF02813 Retro_M, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF06817 RVT_thumb, 1 hit
PF00098 zf-CCHC, 1 hit
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF46919 SSF46919, 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
PROSITEiView protein in PROSITE
PS50175 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, 1 hit
PS50876 ZF_INTEGRASE, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

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ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPOL_RSVSB
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O92956
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 27, 2004
Last sequence update: August 10, 2010
Last modified: September 18, 2019
This is version 117 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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