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P54635 (CAPSD_LORDV) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 48. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Capsid protein

Short name=CP
Alternative name(s):
VP1

Cleaved into the following chain:

  1. Soluble capsid protein
Gene names
ORF Names:ORF2
OrganismLordsdale virus (strain GII/Human/United Kingdom/Lordsdale/1993) (Human enteric calicivirus) (Hu/NV/LD/1993/UK) [Complete proteome]
Taxonomic identifier82658 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length539 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

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 histo-blood group antigens present on gastroduodenal epithelial cells By similarity.

Soluble capsid protein may play a role in viral immunoevasion By similarity.

Subunit structure

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

Subcellular location

Virion. Host cytoplasm By similarity.

Domain

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.

Post-translational modification

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

Sequence similarities

Belongs to the caliciviridae capsid protein family.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 539539Capsid protein
PRO_0000100118
Chain223 – 539317Soluble capsid protein
PRO_0000341982

Regions

Region1 – 221221Shell domain By similarity
Region222 – 539318Protruding domain By similarity
Region222 – 27453P1 su-bdomain 1 By similarity
Region275 – 417143P2 sub-domain By similarity
Region418 – 539122P1 sub-domain 2 By similarity

Sites

Site223 – 2242Cleavage; by host By similarity

Sequences

Sequence LengthMass (Da)Tools
P54635 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 5E5C63E7F2C5FD21

FASTA53958,775
        10         20         30         40         50         60 
MKMASNDANP SDGSAANLVP EVNNEVMALE PVVGAAIAAP VAGQQNVIDP WIRNNFVQAP 

        70         80         90        100        110        120 
GGEFTVSPRN APGEILWSAP LGPDLNPYLS HLSRMYNGYA GGFEVQVILA GNAFTAGKVI 

       130        140        150        160        170        180 
FAAVPPNFPT EGLSPSQVTM FPHIIVDVRQ LEPVLIPLPD VRNNFYHYNQ ANDSTLKLIA 

       190        200        210        220        230        240 
MLYTPLRANN AGDDVFTVSC RVLTRPSPDF DFIFLVPPTV ESRTKPFTVP VLTVEEMSNS 

       250        260        270        280        290        300 
RFPIPLEKLY TGPSSAFVVQ PQNGRCTTDG VLLGTTQLSA VNICNFRGDV THIAGSHDYT 

       310        320        330        340        350        360 
MNLASQNWSN YDPTEEIPAP LGTPDFVGKI QGLLTQTTRA DGSTRAHKAT VSTGSVHFTP 

       370        380        390        400        410        420 
KLGSVQFTTD TNNDFQAGQN TKFTPVGVIQ DGDHHQNEPQ QWSLPNYSGR TGHNVHLAPA 

       430        440        450        460        470        480 
VAPTFPGEQL LFFRSTMPGC SGYPNMNLDC LLPQEWVLHF YQEAAPAQSD VALLRFVNPD 

       490        500        510        520        530 
TGRVLFECKL HKSGYITVAH TGPYDLVLPP NGYFRFDSWV NQFYTLAPMG NGTGRRRAL 

« Hide

References

[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].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X86557 Genomic RNA. Translation: CAA60255.1.

3D structure databases

ProteinModelPortalP54635.
SMRP54635. Positions 224-530.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
[Graphical view]
PfamPF00915. Calici_coat. 1 hit.
PF08435. Calici_coat_C. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameCAPSD_LORDV
AccessionPrimary (citable) accession number: P54635
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: April 3, 2013
This is version 48 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families