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Q04542

- CAPSD_SOUV3

UniProt

Q04542 - CAPSD_SOUV3

Protein

Capsid protein VP1

Gene

ORF2

Organism
Southampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 54 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      Previous versions | rss
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    Functioni

    Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells By similarity.By similarity
    Soluble capsid protein may play a role in viral immunoevasion.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei228 – 2292Cleavage; by hostBy similarity

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Capsid protein VP1
    Short name:
    CP
    Cleaved into the following chain:
    Gene namesi
    ORF Names:ORF2
    OrganismiSouthampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK)
    Taxonomic identifieri37129 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
    Virus hostiHomo sapiens (Human) [TaxID: 9606]
    ProteomesiUP000007226: Genome

    Subcellular locationi

    Virion. Host cytoplasm By similarity

    GO - Cellular componenti

    1. host cell cytoplasm Source: UniProtKB-SubCell
    2. T=3 icosahedral viral capsid Source: UniProtKB-KW

    Keywords - Cellular componenti

    Capsid protein, Host cytoplasm, T=3 icosahedral capsid protein, Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 546546Capsid protein VP1PRO_0000100119Add
    BLAST
    Chaini228 – 546319Soluble capsid proteinPRO_0000341983Add
    BLAST

    Post-translational modificationi

    May be cleaved by host protease to generate soluble capsid protein. Assembled capsid cannot be cleaved By similarity.By similarity

    Interactioni

    Subunit structurei

    Homodimerizes, then multimerizes. Binds to histo-blood group antigens at surface of target cells By similarity.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ04542.
    SMRiQ04542. Positions 11-535.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 226226Shell domainBy similarityAdd
    BLAST
    Regioni227 – 545319Protruding domainBy similarityAdd
    BLAST
    Regioni227 – 27953P1 su-bdomain 1By similarityAdd
    BLAST
    Regioni280 – 416137P2 sub-domainBy similarityAdd
    BLAST
    Regioni417 – 546130P1 sub-domain 2By similarityAdd
    BLAST

    Domaini

    The shell domain (S domain) contains elements essential for the formation of the icosahedron. The Protruding domain (P domain) is divided into sub-domains P1 and P2. P domain interacts in dimeric contacts that increase the stability of the capsid and form the protrusions on the virion. An hypervariable region in P2 is thought to play an important role in receptor binding and immune reactivity.

    Sequence similaritiesi

    Family and domain databases

    Gene3Di2.60.120.20. 1 hit.
    InterProiIPR004005. Calicivirus_coat.
    IPR013643. Calicivirus_coat_C.
    IPR029053. Viral_coat.
    [Graphical view]
    PfamiPF00915. Calici_coat. 1 hit.
    PF08435. Calici_coat_C. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q04542-1 [UniParc]FASTAAdd to Basket

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    MMMASKDAPQ SADGASGAGQ LVPEVNTADP LPMEPVAGPT TAVATAGQVN    50
    MIDPWIVNNF VQSPQGEFTI SPNNTPGDIL FDLQLGPHLN PFLSHLSQMY 100
    NGWVGNMRVR ILLAGNAFSA GKIIVCCVPP GFTSSSLTIA QATLFPHVIA 150
    DVRTLEPIEM PLEDVRNVLY HTNDNQPTMR LVCMLYTPLR TGGGSGNSDS 200
    FVVAGRVLTA PSSDFSFLFL VPPTIEQKTR AFTVPNIPLQ TLSNSRFPSL 250
    IQGMILSPDA SQVVQFQNGR CLIDGQLLGT TPATSGQLFR VRGKINQGAR 300
    TLNLTEVDGK PFMAFDSPAP VGFPDFGKCD WHMRISKTPN NTGSGDPMRS 350
    VSVQTNVQGF VPHLGSIQFD EVFNHPTGDY IGTIEWISQP STPPGTDINL 400
    WEIPDYGSSL SQAANLAPPV FPPGFGEALV YFVSAFPGPN NRSAPNDVPC 450
    LLPQEYITHF VSEQAPTMGD AALLHYVDPD TNRNLGEFKL YPGGYLTCVP 500
    NGVGAGPQQL PLNGVFLFVS WVSRFYQLKP VGTASTARGR LGVRRI 546
    Length:546
    Mass (Da):58,774
    Last modified:October 1, 1994 - v1
    Checksum:iC82B2A85AD4B05EA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L07418 Genomic RNA. Translation: AAA92984.1.
    PIRiB37491.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L07418 Genomic RNA. Translation: AAA92984.1 .
    PIRi B37491.

    3D structure databases

    ProteinModelPortali Q04542.
    SMRi Q04542. Positions 11-535.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 2.60.120.20. 1 hit.
    InterProi IPR004005. Calicivirus_coat.
    IPR013643. Calicivirus_coat_C.
    IPR029053. Viral_coat.
    [Graphical view ]
    Pfami PF00915. Calici_coat. 1 hit.
    PF08435. Calici_coat_C. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and genome organization of a human small round-structured (Norwalk-like) virus."
      Lambden P.R., Caul E.O., Ashley C.R., Clarke I.N.
      Science 259:516-519(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

    Entry informationi

    Entry nameiCAPSD_SOUV3
    AccessioniPrimary (citable) accession number: Q04542
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 54 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3