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P36285

- CAPSD_SMSV4

UniProt

P36285 - CAPSD_SMSV4

Protein

Capsid protein

Gene

ORF2

Organism
San Miguel sea lion virus serotype 4 (SMSV-4) (SMSV serotype 4)
Status
Reviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 55 (01 Oct 2014)
      Sequence version 1 (01 Jun 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 to feline junctional adhesion molecule A (F11R) and/or to alpha-2,6-linked sialic acid. Once attached, the virion is endocytosed. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei152 – 1532Cleavage; by calicivirinBy similarity

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Capsid protein
    Alternative name(s):
    Coat protein
    Short name:
    CP
    VP1
    Gene namesi
    ORF Names:ORF2
    OrganismiSan Miguel sea lion virus serotype 4 (SMSV-4) (SMSV serotype 4)
    Taxonomic identifieri36407 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
    Virus hostiOtariidae (fur seals & sea lions) [TaxID: 9702]

    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
    Propeptidei1 – 152152By similarityPRO_0000036884Add
    BLAST
    Chaini153 – 702550Capsid proteinBy similarityPRO_0000036885Add
    BLAST

    Post-translational modificationi

    Cleaved by virus calcivirin to produce mature capsid protein.By similarity

    Interactioni

    Subunit structurei

    Homodimerizes, then multimerizes. May bind to VP3 and Vpg proteins By similarity.By similarity

    Structurei

    Secondary structure

    1
    703
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi178 – 18912
    Helixi196 – 1983
    Beta strandi202 – 21312
    Beta strandi218 – 2236
    Helixi226 – 2283
    Helixi230 – 2356
    Helixi236 – 2383
    Beta strandi239 – 2435
    Beta strandi246 – 2538
    Beta strandi261 – 2677
    Helixi277 – 2804
    Beta strandi285 – 2884
    Beta strandi295 – 2995
    Beta strandi304 – 3096
    Beta strandi317 – 3204
    Beta strandi332 – 34110
    Beta strandi365 – 3673
    Helixi371 – 3733
    Beta strandi375 – 3828
    Beta strandi385 – 3884
    Beta strandi390 – 3934
    Beta strandi405 – 4095
    Beta strandi416 – 4227
    Beta strandi429 – 43810
    Turni468 – 4703
    Beta strandi471 – 4733
    Helixi479 – 4813
    Turni485 – 4884
    Beta strandi490 – 4989
    Helixi508 – 5125
    Beta strandi519 – 5268
    Beta strandi528 – 5336
    Beta strandi542 – 5476
    Beta strandi550 – 56415
    Beta strandi568 – 5703
    Helixi576 – 5783
    Beta strandi587 – 5893
    Beta strandi594 – 6007
    Beta strandi603 – 6108
    Beta strandi615 – 6206
    Helixi621 – 6299
    Beta strandi638 – 6458
    Beta strandi647 – 6493
    Beta strandi651 – 6566
    Beta strandi662 – 6654
    Beta strandi678 – 6869

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GH8X-ray3.20A/B/C153-703[»]
    ProteinModelPortaliP36285.
    SMRiP36285. Positions 160-696.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP36285.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di2.60.120.20. 1 hit.
    InterProiIPR004005. Calicivirus_coat.
    IPR029053. Viral_coat.
    [Graphical view]
    PfamiPF00915. Calici_coat. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P36285-1 [UniParc]FASTAAdd to Basket

    « Hide

    MATTHTLLSF DDLEFLLHRK DLTDLYGERC GTLNLVINPY ELFLPDELDD    50
    DCCDDPFNCC FPDVYASIGT EYSYIDPPEL IHEEHCATNG TWPNGDPCEP 100
    ILPPFTITGT HHYYATKPGE VVSGILSKLG SSWDPSLRST ADVSNSFTFR 150
    AESDGPGSAE IVTEEQGTVV QQQPAPAPTA LATLATASTG KSVEQEWMTF 200
    FSYHTSINWS TVESQGKILY SQALNPSINP YLDHIAKLYS TWSGGIDVRF 250
    TVSGSGVFGG KLAALLVPPG VEPIESVSML QYPHVLFDAR QTEPVIFTIP 300
    DIRKTLFHSM DETDTTKLVI NPYENGVENK TTCSITVETR PSADFTFALL 350
    KPPGSLIKHG SIPSDLIPRN SAHWMGNRWW STISGFSVQP RVFQSNRHFD 400
    FDSTTTGWST PYYVPIEIKI QGKVGSNNKW FHVIDTDKAL VPGIPDGWPD 450
    TTIPDETKAT NGNFSYGESY RAGSTTIKPN ENSTHFKGTY ICGTLSTVEI 500
    PENDEQQIKT EAEKKSQTMY VVTADFKDTI VKPQHKISPQ KLVVYFDGPE 550
    KDLTMSATLS PLGYTLVDEQ PVGSVSSRVV RIATLPEAFT QGGNYPIFYV 600
    NKIKVGYFDR ATTNCYNSQI LMTSQRLAEG NYNLPPDSLA VYRITDSSSQ 650
    WFDIGINHDG FSYVGLSDLP NDLSFPLTST FMGVQLARVK LASKVKAHTI 700
    TAK 703
    Length:703
    Mass (Da):77,721
    Last modified:June 1, 1994 - v1
    Checksum:iC5DAD8223B261073
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M87482 Unassigned RNA. Translation: AAA16220.1.
    PIRiC48562.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M87482 Unassigned RNA. Translation: AAA16220.1 .
    PIRi C48562.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2GH8 X-ray 3.20 A/B/C 153-703 [» ]
    ProteinModelPortali P36285.
    SMRi P36285. Positions 160-696.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P36285.

    Family and domain databases

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

    Publicationsi

    1. "Nucleotide sequence of the capsid protein gene of two serotypes of San Miguel sea lion virus: identification of conserved and non-conserved amino acid sequences among calicivirus capsid proteins."
      Neill J.D.
      Virus Res. 24:211-222(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. "X-ray structure of a native calicivirus: structural insights into antigenic diversity and host specificity."
      Chen R., Neill J.D., Estes M.K., Prasad B.V.V.
      Proc. Natl. Acad. Sci. U.S.A. 103:8048-8053(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 153-703.

    Entry informationi

    Entry nameiCAPSD_SMSV4
    AccessioniPrimary (citable) accession number: P36285
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: June 1, 1994
    Last modified: October 1, 2014
    This is version 55 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

    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