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Q83884

- CAPSD_NVN68

UniProt

Q83884 - CAPSD_NVN68

Protein

Capsid protein VP1

Gene

ORF2

Organism
Norwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 66 (01 Oct 2014)
      Sequence version 2 (11 Jul 2006)
      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.1 Publication
    Soluble capsid protein may play a role in viral immunoevasion.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei227 – 2282Cleavage; by host

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Capsid protein VP1
    Short name:
    CP
    Alternative name(s):
    p59
    Cleaved into the following chain:
    Alternative name(s):
    Protein 30k
    Short name:
    p30
    Gene namesi
    ORF Names:ORF2
    OrganismiNorwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US)
    Taxonomic identifieri524364 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
    Virus hostiHomo sapiens (Human) [TaxID: 9606]
    ProteomesiUP000000826: Genome

    Subcellular locationi

    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 – 530530Capsid protein VP1PRO_0000341626Add
    BLAST
    Chaini228 – 530303Soluble capsid proteinPRO_0000341627Add
    BLAST

    Post-translational modificationi

    May be cleaved by host protease to generate soluble capsid protein. Assembled capsid cannot be cleaved.1 Publication

    Interactioni

    Subunit structurei

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

    Structurei

    Secondary structure

    1
    530
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi42 – 443
    Turni54 – 585
    Beta strandi61 – 7010
    Beta strandi79 – 846
    Helixi87 – 893
    Helixi91 – 977
    Beta strandi100 – 1045
    Beta strandi107 – 1148
    Beta strandi117 – 1204
    Beta strandi122 – 1287
    Helixi139 – 1424
    Beta strandi145 – 1517
    Beta strandi158 – 1625
    Beta strandi167 – 1693
    Beta strandi171 – 1733
    Beta strandi181 – 1866
    Beta strandi202 – 2109
    Helixi238 – 2403
    Beta strandi244 – 2474
    Beta strandi252 – 2543
    Beta strandi266 – 2683
    Helixi284 – 2863
    Beta strandi289 – 2946
    Beta strandi296 – 3027
    Beta strandi306 – 3083
    Helixi311 – 3133
    Beta strandi315 – 3173
    Beta strandi325 – 3339
    Beta strandi341 – 3455
    Helixi354 – 3563
    Beta strandi358 – 3603
    Beta strandi366 – 37712
    Beta strandi380 – 3823
    Beta strandi396 – 3983
    Beta strandi416 – 42510
    Beta strandi427 – 4293
    Beta strandi431 – 4377
    Helixi439 – 44810
    Beta strandi455 – 4628
    Turni464 – 4663
    Beta strandi469 – 4768
    Turni477 – 4793
    Beta strandi480 – 4834
    Turni487 – 4893
    Helixi492 – 4943
    Beta strandi500 – 5078

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1IHMX-ray3.40A/B/C1-530[»]
    2ZL5X-ray1.47A/B225-518[»]
    2ZL6X-ray1.43A/B225-519[»]
    2ZL7X-ray1.35A/B225-519[»]
    3BY1X-ray2.69A218-530[»]
    3BY2X-ray2.60A218-522[»]
    3D26X-ray2.30A/B230-530[»]
    ProteinModelPortaliQ83884.
    SMRiQ83884. Positions 10-520.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ83884.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 225225Shell domainAdd
    BLAST
    Regioni226 – 530305Protruding domainAdd
    BLAST
    Regioni226 – 27853P1 su-bdomain 1Add
    BLAST
    Regioni279 – 405127P2 sub-domainAdd
    BLAST
    Regioni406 – 530125P1 sub-domain 2Add
    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.

    Q83884-1 [UniParc]FASTAAdd to Basket

    « Hide

    MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN    50
    PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHLN PFLLHLSQMY 100
    NGWVGNMRVR IMLAGNAFTA GKIIVSCIPP GFGSHNLTIA QATLFPHVIA 150
    DVRTLDPIEV PLEDVRNVLF HNNDRNQQTM RLVCMLYTPL RTGGGTGDSF 200
    VVAGRVMTCP SPDFNFLFLV PPTVEQKTRP FTLPNLPLSS LSNSRAPLPI 250
    SSMGISPDNV QSVQFQNGRC TLDGRLVGTT PVSLSHVAKI RGTSNGTVIN 300
    LTELDGTPFH PFEGPAPIGF PDLGGCDWHI NMTQFGHSSQ TQYDVDTTPD 350
    TFVPHLGSIQ ANGIGSGNYV GVLSWISPPS HPSGSQVDLW KIPNYGSSIT 400
    EATHLAPSVY PPGFGEVLVF FMSKMPGPGA YNLPCLLPQE YISHLASEQA 450
    PTVGEAALLH YVDPDTGRNL GEFKAYPDGF LTCVPNGASS GPQQLPINGV 500
    FVFVSWVSRF YQLKPVGTAS SARGRLGLRR 530
    Length:530
    Mass (Da):56,589
    Last modified:July 11, 2006 - v2
    Checksum:i7AEF61A8F66D139C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M87661 Genomic RNA. Translation: AAB50466.2.
    PIRiB37471.
    RefSeqiNP_056821.2. NC_001959.2.

    Genome annotation databases

    GeneIDi1491972.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M87661 Genomic RNA. Translation: AAB50466.2 .
    PIRi B37471.
    RefSeqi NP_056821.2. NC_001959.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1IHM X-ray 3.40 A/B/C 1-530 [» ]
    2ZL5 X-ray 1.47 A/B 225-518 [» ]
    2ZL6 X-ray 1.43 A/B 225-519 [» ]
    2ZL7 X-ray 1.35 A/B 225-519 [» ]
    3BY1 X-ray 2.69 A 218-530 [» ]
    3BY2 X-ray 2.60 A 218-522 [» ]
    3D26 X-ray 2.30 A/B 230-530 [» ]
    ProteinModelPortali Q83884.
    SMRi Q83884. Positions 10-520.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1491972.

    Miscellaneous databases

    EvolutionaryTracei Q83884.

    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 genomic organization of Norwalk virus."
      Jiang X., Wang M., Wang K., Estes M.K.
      Virology 195:51-61(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. "Specific proteolytic cleavage of recombinant Norwalk virus capsid protein."
      Hardy M.E., White L.J., Ball J.M., Estes M.K.
      J. Virol. 69:1693-1698(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: CLEAVAGE.
    3. "Attachment and entry of recombinant Norwalk virus capsids to cultured human and animal cell lines."
      White L.J., Ball J.M., Hardy M.E., Tanaka T.N., Kitamoto N., Estes M.K.
      J. Virol. 70:6589-6597(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CELL-RECEPTOR BINDING.
    4. "Biochemical characterization of a smaller form of recombinant Norwalk virus capsids assembled in insect cells."
      White L.J., Hardy M.E., Estes M.K.
      J. Virol. 71:8066-8072(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: CAPSID ASSEMBLY.
    5. "Norwalk virus binds to histo-blood group antigens present on gastroduodenal epithelial cells of secretor individuals."
      Marionneau S., Ruvoen N., Le Moullac-Vaidye B., Clement M., Cailleau-Thomas A., Ruiz-Palacois G., Huang P., Jiang X., Le Pendu J.
      Gastroenterology 122:1967-1977(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CELL-RECEPTOR BINDING.
    6. "The 3' end of Norwalk virus mRNA contains determinants that regulate the expression and stability of the viral capsid protein VP1: a novel function for the VP2 protein."
      Bertolotti-Ciarlet A., Crawford S.E., Hutson A.M., Estes M.K.
      J. Virol. 77:11603-11615(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: STABILIZATION BY VP2.
    7. "Noroviruses bind to human ABO, Lewis, and secretor histo-blood group antigens: identification of 4 distinct strain-specific patterns."
      Huang P., Farkas T., Marionneau S., Zhong W., Ruvoen-Clouet N., Morrow A.L., Altaye M., Pickering L.K., Newburg D.S., LePendu J., Jiang X.
      J. Infect. Dis. 188:19-31(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: CELL-RECEPTOR BINDING.
    8. "C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein."
      Tan M., Meller J., Jiang X.
      J. Virol. 80:7322-7331(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Norovirus protein structure and function."
      Hardy M.E.
      FEMS Microbiol. Lett. 253:1-8(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    10. "X-ray crystallographic structure of the Norwalk virus capsid."
      Prasad B.V.V., Hardy M.E., Dokland T., Bella J., Rossmann M.G., Estes M.K.
      Science 286:287-290(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS).

    Entry informationi

    Entry nameiCAPSD_NVN68
    AccessioniPrimary (citable) accession number: Q83884
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 2008
    Last sequence update: July 11, 2006
    Last modified: October 1, 2014
    This is version 66 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    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