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P54635

- CAPSD_LORDV

UniProt

P54635 - CAPSD_LORDV

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Protein
Capsid protein
Gene
ORF2
Organism
Lordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK)
Status
Reviewed - Annotation score: 3 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.
Soluble capsid protein may play a role in viral immunoevasion By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei223 – 2242Cleavage; by host By similarity

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein
Short name:
CP
Alternative name(s):
VP1
Cleaved into the following chain:
Gene namesi
ORF Names:ORF2
OrganismiLordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK)
Taxonomic identifieri82658 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000007767: Genome

Subcellular locationi

Virion. Host cytoplasm By similarity

GO - Cellular componenti

  1. T=3 icosahedral viral capsid Source: UniProtKB-KW
  2. host cell cytoplasm Source: UniProtKB-SubCell
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 – 539539Capsid protein
PRO_0000100118Add
BLAST
Chaini223 – 539317Soluble capsid protein
PRO_0000341982Add
BLAST

Post-translational modificationi

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

Interactioni

Subunit structurei

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

Structurei

3D structure databases

ProteinModelPortaliP54635.
SMRiP54635. Positions 224-530.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 221221Shell domain By similarity
Add
BLAST
Regioni222 – 539318Protruding domain By similarity
Add
BLAST
Regioni222 – 27453P1 su-bdomain 1 By similarity
Add
BLAST
Regioni275 – 417143P2 sub-domain By similarity
Add
BLAST
Regioni418 – 539122P1 sub-domain 2 By similarity
Add
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.

P54635-1 [UniParc]FASTAAdd to Basket

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MKMASNDANP SDGSAANLVP EVNNEVMALE PVVGAAIAAP VAGQQNVIDP    50
WIRNNFVQAP GGEFTVSPRN APGEILWSAP LGPDLNPYLS HLSRMYNGYA 100
GGFEVQVILA GNAFTAGKVI FAAVPPNFPT EGLSPSQVTM FPHIIVDVRQ 150
LEPVLIPLPD VRNNFYHYNQ ANDSTLKLIA MLYTPLRANN AGDDVFTVSC 200
RVLTRPSPDF DFIFLVPPTV ESRTKPFTVP VLTVEEMSNS RFPIPLEKLY 250
TGPSSAFVVQ PQNGRCTTDG VLLGTTQLSA VNICNFRGDV THIAGSHDYT 300
MNLASQNWSN YDPTEEIPAP LGTPDFVGKI QGLLTQTTRA DGSTRAHKAT 350
VSTGSVHFTP KLGSVQFTTD TNNDFQAGQN TKFTPVGVIQ DGDHHQNEPQ 400
QWSLPNYSGR TGHNVHLAPA VAPTFPGEQL LFFRSTMPGC SGYPNMNLDC 450
LLPQEWVLHF YQEAAPAQSD VALLRFVNPD TGRVLFECKL HKSGYITVAH 500
TGPYDLVLPP NGYFRFDSWV NQFYTLAPMG NGTGRRRAL 539
Length:539
Mass (Da):58,775
Last modified:October 1, 1996 - v1
Checksum:i5E5C63E7F2C5FD21
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X86557 Genomic RNA. Translation: CAA60255.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X86557 Genomic RNA. Translation: CAA60255.1 .

3D structure databases

ProteinModelPortali P54635.
SMRi P54635. Positions 224-530.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
InterProi IPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF00915. Calici_coat. 1 hit.
PF08435. Calici_coat_C. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Human enteric Caliciviridae: the complete genome sequence and expression of virus-like particles from a genetic group II small round structured virus."
    Dingle K.E., Lambden P.R., Caul E.O., Clarke I.N.
    J. Gen. Virol. 76:2349-2355(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiCAPSD_LORDV
AccessioniPrimary (citable) accession number: P54635
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 9, 2014
This is version 50 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

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