Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q83884 (CAPSD_NVN68) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 65. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Capsid protein VP1

Short name=CP
Alternative name(s):
p59

Cleaved into the following chain:

  1. Soluble capsid protein
    Alternative name(s):
    Protein 30k
    Short name=p30
Gene names
ORF Names:ORF2
OrganismNorwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US) [Reference proteome]
Taxonomic identifier524364 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length530 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.8

Soluble capsid protein may play a role in viral immunoevasion. Ref.8

Subunit structure

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

Subcellular location

Virion. Host cytoplasm.

Domain

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.

Post-translational modification

May be cleaved by host protease to generate soluble capsid protein. Assembled capsid cannot be cleaved. Ref.2

Sequence similarities

Belongs to the caliciviridae capsid protein family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 530530Capsid protein VP1
PRO_0000341626
Chain228 – 530303Soluble capsid protein
PRO_0000341627

Regions

Region1 – 225225Shell domain
Region226 – 530305Protruding domain
Region226 – 27853P1 su-bdomain 1
Region279 – 405127P2 sub-domain
Region406 – 530125P1 sub-domain 2

Sites

Site227 – 2282Cleavage; by host

Secondary structure

........................................................................................... 530
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q83884 [UniParc].

Last modified July 11, 2006. Version 2.
Checksum: 7AEF61A8F66D139C

FASTA53056,589
        10         20         30         40         50         60 
MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF 

        70         80         90        100        110        120 
VQAPQGEFTI SPNNTPGDVL FDLSLGPHLN PFLLHLSQMY NGWVGNMRVR IMLAGNAFTA 

       130        140        150        160        170        180 
GKIIVSCIPP GFGSHNLTIA QATLFPHVIA DVRTLDPIEV PLEDVRNVLF HNNDRNQQTM 

       190        200        210        220        230        240 
RLVCMLYTPL RTGGGTGDSF VVAGRVMTCP SPDFNFLFLV PPTVEQKTRP FTLPNLPLSS 

       250        260        270        280        290        300 
LSNSRAPLPI SSMGISPDNV QSVQFQNGRC TLDGRLVGTT PVSLSHVAKI RGTSNGTVIN 

       310        320        330        340        350        360 
LTELDGTPFH PFEGPAPIGF PDLGGCDWHI NMTQFGHSSQ TQYDVDTTPD TFVPHLGSIQ 

       370        380        390        400        410        420 
ANGIGSGNYV GVLSWISPPS HPSGSQVDLW KIPNYGSSIT EATHLAPSVY PPGFGEVLVF 

       430        440        450        460        470        480 
FMSKMPGPGA YNLPCLLPQE YISHLASEQA PTVGEAALLH YVDPDTGRNL GEFKAYPDGF 

       490        500        510        520        530 
LTCVPNGASS GPQQLPINGV FVFVSWVSRF YQLKPVGTAS SARGRLGLRR 

« Hide

References

[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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M87661 Genomic RNA. Translation: AAB50466.2.
PIRB37471.
RefSeqNP_056821.2. NC_001959.2.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalQ83884.
SMRQ83884. Positions 10-520.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1491972.

Family and domain databases

Gene3D2.60.120.20. 1 hit.
InterProIPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
IPR029053. Viral_coat.
[Graphical view]
PfamPF00915. Calici_coat. 1 hit.
PF08435. Calici_coat_C. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ83884.

Entry information

Entry nameCAPSD_NVN68
AccessionPrimary (citable) accession number: Q83884
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: July 11, 2006
Last modified: July 9, 2014
This is version 65 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references