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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: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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 virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000000826 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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
Helixi14 – 163Combined sources
Helixi42 – 443Combined sources
Turni54 – 585Combined sources
Beta strandi61 – 7010Combined sources
Beta strandi79 – 846Combined sources
Helixi87 – 893Combined sources
Helixi91 – 977Combined sources
Beta strandi100 – 1045Combined sources
Beta strandi107 – 1148Combined sources
Beta strandi117 – 1204Combined sources
Beta strandi122 – 1287Combined sources
Helixi139 – 1424Combined sources
Beta strandi145 – 1517Combined sources
Beta strandi158 – 1625Combined sources
Beta strandi167 – 1693Combined sources
Beta strandi171 – 1733Combined sources
Beta strandi181 – 1866Combined sources
Beta strandi202 – 2109Combined sources
Helixi238 – 2403Combined sources
Beta strandi244 – 2474Combined sources
Beta strandi252 – 2543Combined sources
Beta strandi266 – 2683Combined sources
Helixi284 – 2863Combined sources
Beta strandi289 – 2946Combined sources
Beta strandi296 – 3027Combined sources
Beta strandi306 – 3083Combined sources
Helixi311 – 3133Combined sources
Beta strandi315 – 3173Combined sources
Beta strandi325 – 3339Combined sources
Beta strandi341 – 3455Combined sources
Helixi354 – 3563Combined sources
Beta strandi358 – 3603Combined sources
Beta strandi366 – 37712Combined sources
Beta strandi380 – 3823Combined sources
Beta strandi396 – 3983Combined sources
Beta strandi416 – 42510Combined sources
Beta strandi427 – 4293Combined sources
Beta strandi431 – 4377Combined sources
Helixi439 – 44810Combined sources
Beta strandi455 – 4628Combined sources
Turni464 – 4663Combined sources
Beta strandi469 – 4768Combined sources
Turni477 – 4793Combined sources
Beta strandi480 – 4834Combined sources
Turni487 – 4893Combined sources
Helixi492 – 4943Combined sources
Beta strandi500 – 5078Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN
60 70 80 90 100
PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHLN PFLLHLSQMY
110 120 130 140 150
NGWVGNMRVR IMLAGNAFTA GKIIVSCIPP GFGSHNLTIA QATLFPHVIA
160 170 180 190 200
DVRTLDPIEV PLEDVRNVLF HNNDRNQQTM RLVCMLYTPL RTGGGTGDSF
210 220 230 240 250
VVAGRVMTCP SPDFNFLFLV PPTVEQKTRP FTLPNLPLSS LSNSRAPLPI
260 270 280 290 300
SSMGISPDNV QSVQFQNGRC TLDGRLVGTT PVSLSHVAKI RGTSNGTVIN
310 320 330 340 350
LTELDGTPFH PFEGPAPIGF PDLGGCDWHI NMTQFGHSSQ TQYDVDTTPD
360 370 380 390 400
TFVPHLGSIQ ANGIGSGNYV GVLSWISPPS HPSGSQVDLW KIPNYGSSIT
410 420 430 440 450
EATHLAPSVY PPGFGEVLVF FMSKMPGPGA YNLPCLLPQE YISHLASEQA
460 470 480 490 500
PTVGEAALLH YVDPDTGRNL GEFKAYPDGF LTCVPNGASS GPQQLPINGV
510 520 530
FVFVSWVSRF YQLKPVGTAS SARGRLGLRR
Length:530
Mass (Da):56,589
Last modified:July 11, 2006 - v2
Checksum:i7AEF61A8F66D139C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87661 Genomic RNA. Translation: AAB50466.2.
PIRiB37471.
RefSeqiNP_056821.2. NC_001959.2.

Genome annotation databases

GeneIDi1491972.
KEGGivg:1491972.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87661 Genomic RNA. Translation: AAB50466.2.
PIRiB37471.
RefSeqiNP_056821.2. NC_001959.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1491972.
KEGGivg:1491972.

Miscellaneous databases

EvolutionaryTraceiQ83884.

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]
ProtoNetiSearch...

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: June 24, 2015
This is version 72 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.