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P12495

- GAG_HV1Z2

UniProt

P12495 - GAG_HV1Z2

Protein

Gag polyprotein

Gene

gag

Organism
Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 131 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu.
    Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.
    Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers.
    p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei133 – 1342Cleavage; by viral proteaseBy similarity
    Sitei364 – 3652Cleavage; by viral proteaseBy similarity
    Sitei379 – 3802Cleavage; by viral proteaseBy similarity
    Sitei434 – 4352Cleavage; by viral proteaseBy similarity
    Sitei450 – 4512Cleavage; by viral proteaseBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri392 – 40918CCHC-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri413 – 43018CCHC-type 2PROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. RNA binding Source: UniProtKB-KW
    2. structural molecule activity Source: InterPro
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. viral budding via host ESCRT complex Source: UniProtKB-KW
    2. viral release from host cell Source: UniProtKB-KW

    Keywords - Biological processi

    Host-virus interaction, Viral budding, Viral budding via the host ESCRT complexes, Virus exit from host cell

    Keywords - Ligandi

    Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Gag polyprotein
    Alternative name(s):
    Pr55Gag
    Cleaved into the following 6 chains:
    Gene namesi
    Name:gag
    OrganismiHuman immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
    Taxonomic identifieri11683 [NCBI]
    Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
    Virus hostiHomo sapiens (Human) [TaxID: 9606]

    Subcellular locationi

    Chain Matrix protein p17 : Virion Curated. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane Curated; Lipid-anchor Curated
    Note: Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane By similarity.By similarity

    GO - Cellular componenti

    1. host cell cytoplasm Source: UniProtKB-SubCell
    2. host cell nucleus Source: UniProtKB-SubCell
    3. host cell plasma membrane Source: UniProtKB-SubCell
    4. membrane Source: UniProtKB-KW
    5. viral nucleocapsid Source: UniProtKB-KW

    Keywords - Cellular componenti

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

    Pathology & Biotechi

    Keywords - Diseasei

    AIDS

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed; by hostBy similarity
    Chaini2 – 501500Gag polyproteinPRO_0000261239Add
    BLAST
    Chaini2 – 133132Matrix protein p17By similarityPRO_0000038499Add
    BLAST
    Chaini134 – 364231Capsid protein p24By similarityPRO_0000038500Add
    BLAST
    Peptidei365 – 37915Spacer peptide p2By similarityPRO_0000038501Add
    BLAST
    Chaini380 – 43455Nucleocapsid protein p7By similarityPRO_0000038502Add
    BLAST
    Peptidei435 – 45016Spacer peptide p1By similarityPRO_0000038503Add
    BLAST
    Chaini451 – 50151p6-gagBy similarityPRO_0000038504Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity
    Modified residuei389 – 3891Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6By similarity
    Modified residuei411 – 4111Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6By similarity

    Post-translational modificationi

    Capsid protein p24 is phosphorylated.
    Specific enzymatic cleavages by the viral protease yield mature proteins. The polyprotein is cleaved during and after budding, this process is termed maturation By similarity.By similarity
    Nucleocapsid protein p7 is methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription.By similarity

    Keywords - PTMi

    Lipoprotein, Methylation, Myristate, Phosphoprotein

    Interactioni

    Subunit structurei

    Matrix protein p17, and probably Pr55Gag form hexamer rings of trimers. Oligomerization possibly creates a central hole into which the cytoplasmic tail of the gp41 envelope protein may be inserted. Pr55Gag interacts with host TRIM22; this interaction seems to disrupt proper trafficking of Gag polyprotein and may interfere with budding. p6-gag interacts with Vpr. p6-gag interacts with host TSG101. p6-gag interacts with host PDCD6IP/AIP1 By similarity. Pr55Gag interacts with host PDZD8 By similarity.By similarity

    Structurei

    Secondary structure

    1
    501
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni178 – 1803

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SJEX-ray2.45C167-182[»]
    1SJHX-ray2.25C167-179[»]
    3D3TX-ray2.80P446-455[»]
    ProteinModelPortaliP12495.
    SMRiP12495. Positions 2-434, 451-501.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12495.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi16 – 227Nuclear export signalBy similarity
    Motifi26 – 327Nuclear localization signalBy similarity
    Motifi457 – 4604PTAP/PSAP motif
    Motifi484 – 49310LYPX(n)L motif

    Domaini

    Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. p6-gag contains two L domains: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 and a LYPX(n)L motif which interacts with PDCD6IP/AIP1 By similarity.By similarity

    Sequence similaritiesi

    Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri392 – 40918CCHC-type 1PROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri413 – 43018CCHC-type 2PROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Family and domain databases

    Gene3Di1.10.1200.30. 1 hit.
    1.10.150.90. 1 hit.
    1.10.375.10. 1 hit.
    4.10.60.10. 1 hit.
    InterProiIPR000721. Gag_p24.
    IPR014817. Gag_p6.
    IPR000071. Lentvrl_matrix_N.
    IPR012344. Matrix_N_HIV/RSV.
    IPR008916. Retrov_capsid_C.
    IPR008919. Retrov_capsid_N.
    IPR010999. Retrovr_matrix_N.
    IPR001878. Znf_CCHC.
    [Graphical view]
    PfamiPF00540. Gag_p17. 1 hit.
    PF00607. Gag_p24. 1 hit.
    PF08705. Gag_p6. 1 hit.
    PF00098. zf-CCHC. 2 hits.
    [Graphical view]
    PRINTSiPR00234. HIV1MATRIX.
    SMARTiSM00343. ZnF_C2HC. 2 hits.
    [Graphical view]
    SUPFAMiSSF47353. SSF47353. 1 hit.
    SSF47836. SSF47836. 1 hit.
    SSF47943. SSF47943. 1 hit.
    SSF57756. SSF57756. 1 hit.
    PROSITEiPS50158. ZF_CCHC. 2 hits.
    [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. Align

    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.

    Isoform Gag polyprotein (identifier: P12495-1) [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

    MGARASVLSG GKLDAWEKIR LRPGGKKKYR LKHLVWASRE LERFALNPGL    50
    LETSDGCKQI IGQLQPAIRT GSEELRSLFN TVATLYCVHE RIEVKDTKEA 100
    LEKMEEEQNK SKNKKAQQAA ADAGNNSQVS QNYPIVQNLQ GQMVHQAISP 150
    RTLNAWVKVI EEKAFSPEVI PMFSALSEGA TPQDLNTMLN TVGGHQAAMQ 200
    MLKETINEEA AEWDRLHPVH AGPIAPGQMR EPRGSDIAGT TSTLQEQIAW 250
    MTSNPPIPVG EIYKRWIILG LNKIVRMYSP VSILDIRQGP KEPFRDYVDR 300
    FYKTLRAEQA SQEVKGWMTE TLLVQNANPD CKTILKALGP QATLEEMMTA 350
    CQGVGGPSHK ARVLAEAMSQ ATNSAAAVMM QRGNFKGPRK TIKCFNCGKE 400
    GHIAKNCRAP RRKGCWKCGK EGHQLKDCTE RQANFLGKIW PSHKGRPGNF 450
    LQSRPEPTAP PAESFGFGEE ITPSQKQEQK DKELYPSTAL KSLFGNDPLL 500
    Q 501

    Note: Produced by conventional translation.

    Length:501
    Mass (Da):55,678
    Last modified:January 23, 2007 - v3
    Checksum:i827C2609BC3E5963
    GO
    Isoform Gag-Pol polyprotein (identifier: P12499-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry P12499.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by -1 ribosomal frameshifting.

    Length:1,436
    Mass (Da):161,899
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M22639 Genomic RNA. Translation: AAA45365.1.
    PIRiS54377.

    Keywords - Coding sequence diversityi

    Ribosomal frameshifting

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M22639 Genomic RNA. Translation: AAA45365.1 .
    PIRi S54377.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1SJE X-ray 2.45 C 167-182 [» ]
    1SJH X-ray 2.25 C 167-179 [» ]
    3D3T X-ray 2.80 P 446-455 [» ]
    ProteinModelPortali P12495.
    SMRi P12495. Positions 2-434, 451-501.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P12495.

    Family and domain databases

    Gene3Di 1.10.1200.30. 1 hit.
    1.10.150.90. 1 hit.
    1.10.375.10. 1 hit.
    4.10.60.10. 1 hit.
    InterProi IPR000721. Gag_p24.
    IPR014817. Gag_p6.
    IPR000071. Lentvrl_matrix_N.
    IPR012344. Matrix_N_HIV/RSV.
    IPR008916. Retrov_capsid_C.
    IPR008919. Retrov_capsid_N.
    IPR010999. Retrovr_matrix_N.
    IPR001878. Znf_CCHC.
    [Graphical view ]
    Pfami PF00540. Gag_p17. 1 hit.
    PF00607. Gag_p24. 1 hit.
    PF08705. Gag_p6. 1 hit.
    PF00098. zf-CCHC. 2 hits.
    [Graphical view ]
    PRINTSi PR00234. HIV1MATRIX.
    SMARTi SM00343. ZnF_C2HC. 2 hits.
    [Graphical view ]
    SUPFAMi SSF47353. SSF47353. 1 hit.
    SSF47836. SSF47836. 1 hit.
    SSF47943. SSF47943. 1 hit.
    SSF57756. SSF57756. 1 hit.
    PROSITEi PS50158. ZF_CCHC. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Theodore T., Buckler-White A.J.
      Submitted (JUL-1989) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. "Role of HIV-1 Gag domains in viral assembly."
      Scarlata S., Carter C.
      Biochim. Biophys. Acta 1614:62-72(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.

    Entry informationi

    Entry nameiGAG_HV1Z2
    AccessioniPrimary (citable) accession number: P12495
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 131 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).

    Keywords - Technical termi

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3