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Protein

Capsid protein VP1

Gene

ORF2

Organism
Southampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei228 – 2292Cleavage; by hostBy similarity

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein VP1
Short name:
CP
Cleaved into the following chain:
Gene namesi
ORF Names:ORF2
OrganismiSouthampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK)
Taxonomic identifieri37129 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000007226 Componenti: Genome

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
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 – 546546Capsid protein VP1PRO_0000100119Add
BLAST
Chaini228 – 546319Soluble capsid proteinPRO_0000341983Add
BLAST

Post-translational modificationi

May be cleaved by host protease to generate soluble capsid protein. Assembled capsid cannot be cleaved (By similarity).By similarity

Interactioni

Subunit structurei

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

Structurei

3D structure databases

ProteinModelPortaliQ04542.
SMRiQ04542. Positions 11-535.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 226226Shell domainBy similarityAdd
BLAST
Regioni227 – 545319Protruding domainBy similarityAdd
BLAST
Regioni227 – 27953P1 su-bdomain 1By similarityAdd
BLAST
Regioni280 – 416137P2 sub-domainBy similarityAdd
BLAST
Regioni417 – 546130P1 sub-domain 2By similarityAdd
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.

Q04542-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMMASKDAPQ SADGASGAGQ LVPEVNTADP LPMEPVAGPT TAVATAGQVN
60 70 80 90 100
MIDPWIVNNF VQSPQGEFTI SPNNTPGDIL FDLQLGPHLN PFLSHLSQMY
110 120 130 140 150
NGWVGNMRVR ILLAGNAFSA GKIIVCCVPP GFTSSSLTIA QATLFPHVIA
160 170 180 190 200
DVRTLEPIEM PLEDVRNVLY HTNDNQPTMR LVCMLYTPLR TGGGSGNSDS
210 220 230 240 250
FVVAGRVLTA PSSDFSFLFL VPPTIEQKTR AFTVPNIPLQ TLSNSRFPSL
260 270 280 290 300
IQGMILSPDA SQVVQFQNGR CLIDGQLLGT TPATSGQLFR VRGKINQGAR
310 320 330 340 350
TLNLTEVDGK PFMAFDSPAP VGFPDFGKCD WHMRISKTPN NTGSGDPMRS
360 370 380 390 400
VSVQTNVQGF VPHLGSIQFD EVFNHPTGDY IGTIEWISQP STPPGTDINL
410 420 430 440 450
WEIPDYGSSL SQAANLAPPV FPPGFGEALV YFVSAFPGPN NRSAPNDVPC
460 470 480 490 500
LLPQEYITHF VSEQAPTMGD AALLHYVDPD TNRNLGEFKL YPGGYLTCVP
510 520 530 540
NGVGAGPQQL PLNGVFLFVS WVSRFYQLKP VGTASTARGR LGVRRI
Length:546
Mass (Da):58,774
Last modified:September 30, 1994 - v1
Checksum:iC82B2A85AD4B05EA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07418 Genomic RNA. Translation: AAA92984.1.
PIRiB37491.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07418 Genomic RNA. Translation: AAA92984.1.
PIRiB37491.

3D structure databases

ProteinModelPortaliQ04542.
SMRiQ04542. Positions 11-535.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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 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(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiCAPSD_SOUV3
AccessioniPrimary (citable) accession number: Q04542
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 30, 1994
Last sequence update: September 30, 1994
Last modified: January 6, 2015
This is version 56 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

Complete proteome

Documents

  1. 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.