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Protein

Capsid protein

Gene

ORF2

Organism
San Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1)
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 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).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei152 – 1532Cleavage; by 3C-like proteaseBy similarity

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein
Alternative name(s):
Coat protein
Short name:
CP
VP1
Gene namesi
ORF Names:ORF2
OrganismiSan Miguel sea lion virus serotype 1 (SMSV-1) (SMSV serotype 1)
Taxonomic identifieri36406 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostiOtariidae (fur seals & sea lions) [TaxID: 9702]
ProteomesiUP000007224 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
Propeptidei1 – 152152By similarityPRO_0000036882Add
BLAST
Chaini153 – 702550Capsid proteinBy similarityPRO_0000036883Add
BLAST

Post-translational modificationi

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

Interactioni

Subunit structurei

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

Structurei

3D structure databases

ProteinModelPortaliP36284.
SMRiP36284. Positions 163-696.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P36284-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATTHTLLSF DDLEFLLHKK DLTDLYGERC GTLNLVINPY DLFLPDDLDD
60 70 80 90 100
DWCDDPFNCC FSDVYTSIGT EYSYIDPPDL IYEEHCATNG HWPDGTPCEP
110 120 130 140 150
ILPPFVIEGT HHYYATKPGE AVSGILSKLG SAWDPDLQST VDTKPDFVFR
160 170 180 190 200
AESDGPGGAD IVTEEQGTVV QQQPVPAQSA LTTLAAASTG KTVDCEWTTF
210 220 230 240 250
FSYHTAVNWS TTEAQGKILF SRALSPELNP YLRHISSLYS TWSGGIDVRF
260 270 280 290 300
TVSGSGVFGG KLAALIVPPG IEPVESPTML QYPHVLFDAR QTEPVIFTIP
310 320 330 340 350
DIRKTLYHSM DDTDTTRLVI MVYNELINPY EQSEPKSSCS ITVETRPSSD
360 370 380 390 400
FTFSLLKPPG SLLKHGSIPS DLIPRNSRHW MGNRWWSTID GFVVQPRVFQ
410 420 430 440 450
SNRHFDFDST TTGWSTPYYI PIEVTLEKLD RGGQYFKVTD TEKSLVPGLP
460 470 480 490 500
DGWPDTTIPT AMTASNGNYD YTVAEYRITN NGTHFKGFYI MGNLTTKVKG
510 520 530 540 550
SDNLGETQQT SRTLFASVGN YKDQNTINPT HKITSNSLVV YDANNVSAAT
560 570 580 590 600
AKTTTWHSTM SHLGYVLVDE SPVGSDSTKV VRIATLPEAF TNGGNFPVFF
610 620 630 640 650
TNKIQIGHFD RAHTKCFNSQ VLMTSQKLAE NHYTLPPDSL LVYRITDAAS
660 670 680 690 700
SWFDLGINHD GFSYVGISTI PELDFPLTFN LHGVQLAKVK LASKVKTSKT

TI
Length:702
Mass (Da):77,850
Last modified:June 1, 1994 - v1
Checksum:iE6E5A58523DEE3D7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87481 Unassigned DNA. Translation: AAA16217.1.
PIRiA48562.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87481 Unassigned DNA. Translation: AAA16217.1.
PIRiA48562.

3D structure databases

ProteinModelPortaliP36284.
SMRiP36284. Positions 163-696.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  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].

Entry informationi

Entry nameiCAPSD_SMSV1
AccessioniPrimary (citable) accession number: P36284
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: June 24, 2015
This is version 53 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.