Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Capsid protein

Gene

ORF2

Organism
San Miguel sea lion virus serotype 4 (SMSV-4) (SMSV serotype 4)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

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

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 4 (SMSV-4) (SMSV serotype 4)
Taxonomic identifieri36407 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostiOtariidae (fur seals & sea lions) [TaxID: 9702]

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)DescriptionActionsGraphical viewLength
PropeptideiPRO_00000368841 – 152By similarityAdd BLAST152
ChainiPRO_0000036885153 – 702Capsid proteinBy similarityAdd BLAST550

Post-translational modificationi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei152 – 153Cleavage; by calicivirinBy similarity2

Interactioni

Subunit structurei

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

Protein-protein interaction databases

DIPiDIP-61173N.

Structurei

Secondary structure

1703
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi178 – 189Combined sources12
Helixi196 – 198Combined sources3
Beta strandi202 – 213Combined sources12
Beta strandi218 – 223Combined sources6
Helixi226 – 228Combined sources3
Helixi230 – 235Combined sources6
Helixi236 – 238Combined sources3
Beta strandi239 – 243Combined sources5
Beta strandi246 – 253Combined sources8
Beta strandi261 – 267Combined sources7
Helixi277 – 280Combined sources4
Beta strandi285 – 288Combined sources4
Beta strandi295 – 299Combined sources5
Beta strandi304 – 309Combined sources6
Beta strandi317 – 320Combined sources4
Beta strandi332 – 341Combined sources10
Beta strandi365 – 367Combined sources3
Helixi371 – 373Combined sources3
Beta strandi375 – 382Combined sources8
Beta strandi385 – 388Combined sources4
Beta strandi390 – 393Combined sources4
Beta strandi405 – 409Combined sources5
Beta strandi416 – 422Combined sources7
Beta strandi429 – 438Combined sources10
Turni468 – 470Combined sources3
Beta strandi471 – 473Combined sources3
Helixi479 – 481Combined sources3
Turni485 – 488Combined sources4
Beta strandi490 – 498Combined sources9
Helixi508 – 512Combined sources5
Beta strandi519 – 526Combined sources8
Beta strandi528 – 533Combined sources6
Beta strandi542 – 547Combined sources6
Beta strandi550 – 564Combined sources15
Beta strandi568 – 570Combined sources3
Helixi576 – 578Combined sources3
Beta strandi587 – 589Combined sources3
Beta strandi594 – 600Combined sources7
Beta strandi603 – 610Combined sources8
Beta strandi615 – 620Combined sources6
Helixi621 – 629Combined sources9
Beta strandi638 – 645Combined sources8
Beta strandi647 – 649Combined sources3
Beta strandi651 – 656Combined sources6
Beta strandi662 – 665Combined sources4
Beta strandi678 – 686Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2GH8X-ray3.20A/B/C153-703[»]
ProteinModelPortaliP36285.
SMRiP36285.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36285.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR033703. Rhv-like.
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.

P36285-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATTHTLLSF DDLEFLLHRK DLTDLYGERC GTLNLVINPY ELFLPDELDD
60 70 80 90 100
DCCDDPFNCC FPDVYASIGT EYSYIDPPEL IHEEHCATNG TWPNGDPCEP
110 120 130 140 150
ILPPFTITGT HHYYATKPGE VVSGILSKLG SSWDPSLRST ADVSNSFTFR
160 170 180 190 200
AESDGPGSAE IVTEEQGTVV QQQPAPAPTA LATLATASTG KSVEQEWMTF
210 220 230 240 250
FSYHTSINWS TVESQGKILY SQALNPSINP YLDHIAKLYS TWSGGIDVRF
260 270 280 290 300
TVSGSGVFGG KLAALLVPPG VEPIESVSML QYPHVLFDAR QTEPVIFTIP
310 320 330 340 350
DIRKTLFHSM DETDTTKLVI NPYENGVENK TTCSITVETR PSADFTFALL
360 370 380 390 400
KPPGSLIKHG SIPSDLIPRN SAHWMGNRWW STISGFSVQP RVFQSNRHFD
410 420 430 440 450
FDSTTTGWST PYYVPIEIKI QGKVGSNNKW FHVIDTDKAL VPGIPDGWPD
460 470 480 490 500
TTIPDETKAT NGNFSYGESY RAGSTTIKPN ENSTHFKGTY ICGTLSTVEI
510 520 530 540 550
PENDEQQIKT EAEKKSQTMY VVTADFKDTI VKPQHKISPQ KLVVYFDGPE
560 570 580 590 600
KDLTMSATLS PLGYTLVDEQ PVGSVSSRVV RIATLPEAFT QGGNYPIFYV
610 620 630 640 650
NKIKVGYFDR ATTNCYNSQI LMTSQRLAEG NYNLPPDSLA VYRITDSSSQ
660 670 680 690 700
WFDIGINHDG FSYVGLSDLP NDLSFPLTST FMGVQLARVK LASKVKAHTI

TAK
Length:703
Mass (Da):77,721
Last modified:June 1, 1994 - v1
Checksum:iC5DAD8223B261073
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87482 Unassigned RNA. Translation: AAA16220.1.
PIRiC48562.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87482 Unassigned RNA. Translation: AAA16220.1.
PIRiC48562.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2GH8X-ray3.20A/B/C153-703[»]
ProteinModelPortaliP36285.
SMRiP36285.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-61173N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP36285.

Family and domain databases

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR033703. Rhv-like.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_SMSV4
AccessioniPrimary (citable) accession number: P36285
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: November 30, 2016
This is version 65 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

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.