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Q04542 (CAPSD_SOUV3) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 53. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | 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

Cleaved into the following chain:

  1. Soluble capsid protein
Gene names
ORF Names:ORF2
OrganismSouthampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK) [Complete proteome]
Taxonomic identifier37129 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length546 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

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 By similarity.

Soluble capsid protein may play a role in viral immunoevasion By similarity.

Subunit structure

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

Subcellular location

Virion. Host cytoplasm By similarity.

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 By similarity.

Sequence similarities

Belongs to the caliciviridae capsid protein family.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 546546Capsid protein VP1
PRO_0000100119
Chain228 – 546319Soluble capsid protein
PRO_0000341983

Regions

Region1 – 226226Shell domain By similarity
Region227 – 545319Protruding domain By similarity
Region227 – 27953P1 su-bdomain 1 By similarity
Region280 – 416137P2 sub-domain By similarity
Region417 – 546130P1 sub-domain 2 By similarity

Sites

Site228 – 2292Cleavage; by host By similarity

Sequences

Sequence LengthMass (Da)Tools
Q04542 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: C82B2A85AD4B05EA

FASTA54658,774
        10         20         30         40         50         60 
MMMASKDAPQ SADGASGAGQ LVPEVNTADP LPMEPVAGPT TAVATAGQVN MIDPWIVNNF 

        70         80         90        100        110        120 
VQSPQGEFTI SPNNTPGDIL FDLQLGPHLN PFLSHLSQMY NGWVGNMRVR ILLAGNAFSA 

       130        140        150        160        170        180 
GKIIVCCVPP GFTSSSLTIA QATLFPHVIA DVRTLEPIEM PLEDVRNVLY HTNDNQPTMR 

       190        200        210        220        230        240 
LVCMLYTPLR TGGGSGNSDS FVVAGRVLTA PSSDFSFLFL VPPTIEQKTR AFTVPNIPLQ 

       250        260        270        280        290        300 
TLSNSRFPSL IQGMILSPDA SQVVQFQNGR CLIDGQLLGT TPATSGQLFR VRGKINQGAR 

       310        320        330        340        350        360 
TLNLTEVDGK PFMAFDSPAP VGFPDFGKCD WHMRISKTPN NTGSGDPMRS VSVQTNVQGF 

       370        380        390        400        410        420 
VPHLGSIQFD EVFNHPTGDY IGTIEWISQP STPPGTDINL WEIPDYGSSL SQAANLAPPV 

       430        440        450        460        470        480 
FPPGFGEALV YFVSAFPGPN NRSAPNDVPC LLPQEYITHF VSEQAPTMGD AALLHYVDPD 

       490        500        510        520        530        540 
TNRNLGEFKL YPGGYLTCVP NGVGAGPQQL PLNGVFLFVS WVSRFYQLKP VGTASTARGR 


LGVRRI 

« Hide

References

[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].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L07418 Genomic RNA. Translation: AAA92984.1.
PIRB37491.

3D structure databases

ProteinModelPortalQ04542.
SMRQ04542. Positions 11-535.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

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...

Entry information

Entry nameCAPSD_SOUV3
AccessionPrimary (citable) accession number: Q04542
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: July 9, 2014
This is version 53 of the entry and version 1 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