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P36285

- CAPSD_SMSV4

UniProt

P36285 - CAPSD_SMSV4

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Protein

Capsid protein

Gene

ORF2

Organism
San Miguel sea lion virus serotype 4 (SMSV-4) (SMSV serotype 4)
Status
Reviewed - 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei152 – 1532Cleavage; by calicivirinBy 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 positive-strand viruses, no DNA stageCaliciviridaeVesivirus
Virus hostiOtariidae (fur seals & sea lions) [TaxID: 9702]

Subcellular locationi

Virion. Host cytoplasm By similarity

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-KW
  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
Propeptidei1 – 152152By similarityPRO_0000036884Add
BLAST
Chaini153 – 702550Capsid proteinBy similarityPRO_0000036885Add
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

Secondary structure

1
703
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi178 – 18912
Helixi196 – 1983
Beta strandi202 – 21312
Beta strandi218 – 2236
Helixi226 – 2283
Helixi230 – 2356
Helixi236 – 2383
Beta strandi239 – 2435
Beta strandi246 – 2538
Beta strandi261 – 2677
Helixi277 – 2804
Beta strandi285 – 2884
Beta strandi295 – 2995
Beta strandi304 – 3096
Beta strandi317 – 3204
Beta strandi332 – 34110
Beta strandi365 – 3673
Helixi371 – 3733
Beta strandi375 – 3828
Beta strandi385 – 3884
Beta strandi390 – 3934
Beta strandi405 – 4095
Beta strandi416 – 4227
Beta strandi429 – 43810
Turni468 – 4703
Beta strandi471 – 4733
Helixi479 – 4813
Turni485 – 4884
Beta strandi490 – 4989
Helixi508 – 5125
Beta strandi519 – 5268
Beta strandi528 – 5336
Beta strandi542 – 5476
Beta strandi550 – 56415
Beta strandi568 – 5703
Helixi576 – 5783
Beta strandi587 – 5893
Beta strandi594 – 6007
Beta strandi603 – 6108
Beta strandi615 – 6206
Helixi621 – 6299
Beta strandi638 – 6458
Beta strandi647 – 6493
Beta strandi651 – 6566
Beta strandi662 – 6654
Beta strandi678 – 6869

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GH8X-ray3.20A/B/C153-703[»]
ProteinModelPortaliP36285.
SMRiP36285. Positions 160-696.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36285.

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.

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:
EMBL
GenBank
DDBJ
Links Updated
M87482 Unassigned RNA. Translation: AAA16220.1.
PIRiC48562.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M87482 Unassigned RNA. Translation: AAA16220.1 .
PIRi C48562.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2GH8 X-ray 3.20 A/B/C 153-703 [» ]
ProteinModelPortali P36285.
SMRi P36285. Positions 160-696.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P36285.

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
InterProi IPR004005. Calicivirus_coat.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF00915. Calici_coat. 1 hit.
[Graphical view ]
ProtoNeti Search...

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].
  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.

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: October 29, 2014
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

3D-structure

Documents

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

External Data

Dasty 3