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P36285 (CAPSD_SMSV4) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 52. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Capsid protein
Alternative name(s):
Coat protein
Short name=CP
VP1
Gene names
ORF Names:ORF2
OrganismSan Miguel sea lion virus serotype 4 (SMSV-4) (SMSV serotype 4)
Taxonomic identifier36407 [NCBI]
Taxonomic lineageViruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Vesivirus ›
Virus hostOtariidae (fur seals & sea lions) [TaxID: 9702]

Protein attributes

Sequence length703 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 to feline junctional adhesion molecule A (F11R) and/or to alpha-2,6-linked sialic acid. Once attached, the virion is endocytosed. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm By similarity.

Subunit structure

Homodimerizes, then multimerizes. May bind to VP3 and Vpg proteins By similarity.

Subcellular location

Virion. Host cytoplasm By similarity.

Post-translational modification

Cleaved by virus calcivirin to produce mature capsid protein By similarity.

Sequence similarities

Belongs to the caliciviridae capsid protein family.

Ontologies

Keywords
   Cellular componentHost cytoplasm
Virion
   Molecular functionCapsid protein
T=3 icosahedral capsid protein
   Technical term3D-structure
Gene Ontology (GO)
   Cellular_componentT=3 icosahedral viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

host cell cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Propeptide1 – 152152 By similarity
PRO_0000036884
Chain153 – 702550Capsid protein By similarity
PRO_0000036885

Sites

Site152 – 1532Cleavage; by calicivirin By similarity

Secondary structure

1 ......................................................................................... 703
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P36285 [UniParc].

Last modified June 1, 1994. Version 1.
Checksum: C5DAD8223B261073

FASTA70377,721
        10         20         30         40         50         60 
MATTHTLLSF DDLEFLLHRK DLTDLYGERC GTLNLVINPY ELFLPDELDD DCCDDPFNCC 

        70         80         90        100        110        120 
FPDVYASIGT EYSYIDPPEL IHEEHCATNG TWPNGDPCEP ILPPFTITGT HHYYATKPGE 

       130        140        150        160        170        180 
VVSGILSKLG SSWDPSLRST ADVSNSFTFR AESDGPGSAE IVTEEQGTVV QQQPAPAPTA 

       190        200        210        220        230        240 
LATLATASTG KSVEQEWMTF FSYHTSINWS TVESQGKILY SQALNPSINP YLDHIAKLYS 

       250        260        270        280        290        300 
TWSGGIDVRF TVSGSGVFGG KLAALLVPPG VEPIESVSML QYPHVLFDAR QTEPVIFTIP 

       310        320        330        340        350        360 
DIRKTLFHSM DETDTTKLVI NPYENGVENK TTCSITVETR PSADFTFALL KPPGSLIKHG 

       370        380        390        400        410        420 
SIPSDLIPRN SAHWMGNRWW STISGFSVQP RVFQSNRHFD FDSTTTGWST PYYVPIEIKI 

       430        440        450        460        470        480 
QGKVGSNNKW FHVIDTDKAL VPGIPDGWPD TTIPDETKAT NGNFSYGESY RAGSTTIKPN 

       490        500        510        520        530        540 
ENSTHFKGTY ICGTLSTVEI PENDEQQIKT EAEKKSQTMY VVTADFKDTI VKPQHKISPQ 

       550        560        570        580        590        600 
KLVVYFDGPE KDLTMSATLS PLGYTLVDEQ PVGSVSSRVV RIATLPEAFT QGGNYPIFYV 

       610        620        630        640        650        660 
NKIKVGYFDR ATTNCYNSQI LMTSQRLAEG NYNLPPDSLA VYRITDSSSQ WFDIGINHDG 

       670        680        690        700 
FSYVGLSDLP NDLSFPLTST FMGVQLARVK LASKVKAHTI TAK

« Hide

References

[1]"Nucleotide sequence of the capsid protein gene of two serotypes of San Miguel sea lion virus: identification of conserved and non-conserved amino acid sequences among calicivirus capsid proteins."
Neill J.D.
Virus Res. 24:211-222(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"X-ray structure of a native calicivirus: structural insights into antigenic diversity and host specificity."
Chen R., Neill J.D., Estes M.K., Prasad B.V.V.
Proc. Natl. Acad. Sci. U.S.A. 103:8048-8053(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 153-703.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M87482 Unassigned RNA. Translation: AAA16220.1.
PIRC48562.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2GH8X-ray3.20A/B/C153-703[»]
ProteinModelPortalP36285.
SMRP36285. Positions 160-696.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR004005. Calicivirus_coat.
[Graphical view]
PfamPF00915. Calici_coat. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP36285.

Entry information

Entry nameCAPSD_SMSV4
AccessionPrimary (citable) accession number: P36285
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: April 3, 2013
This is version 52 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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