Capsid protein VP1 - Norwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US)

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Q83884 (CAPSD_NVN68) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 62. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Capsid protein VP1
Short name=CP

Alternative name(s):
p59

Cleaved into the following chain:

Soluble capsid protein
Alternative name(s):
Protein 30k
Short name=p30

Gene names

ORF Names:

ORF2

Organism

Norwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US) [Reference proteome]

Taxonomic identifier

524364 [NCBI]

Taxonomic lineage

Viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Norovirus ›

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	530 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

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. Ref.8 Soluble capsid protein may play a role in viral immunoevasion. Ref.8
Subunit structure	Homodimerizes, then multimerizes. Binds to histo-blood group antigens at surface of target cells.
Subcellular location	Virion. Host cytoplasm.
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. Ref.2
Sequence similarities	Belongs to the caliciviridae capsid protein family.

Ontologies

Keywords
Cellular component	Host cytoplasm Virion
Molecular function	Capsid protein T=3 icosahedral capsid protein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Cellular_component	T=3 icosahedral viral capsid Inferred from electronic annotation. Source: UniProtKB-KW host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 530

530

Capsid protein VP1

PRO_0000341626

Chain

228 – 530

303

Soluble capsid protein

PRO_0000341627

Regions

Region

1 – 225

225

Shell domain

Region

226 – 530

305

Protruding domain

Region

226 – 278

P1 su-bdomain 1

Region

279 – 405

127

P2 sub-domain

Region

406 – 530

125

P1 sub-domain 2

Sites

Site

227 – 228

Cleavage; by host

Secondary structure

530

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q83884 [UniParc].

Last modified July 11, 2006. Version 2.
Checksum: 7AEF61A8F66D139C
Show »

FASTA

530

56,589

        10         20         30         40         50         60 
MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF 

        70         80         90        100        110        120 
VQAPQGEFTI SPNNTPGDVL FDLSLGPHLN PFLLHLSQMY NGWVGNMRVR IMLAGNAFTA 

       130        140        150        160        170        180 
GKIIVSCIPP GFGSHNLTIA QATLFPHVIA DVRTLDPIEV PLEDVRNVLF HNNDRNQQTM 

       190        200        210        220        230        240 
RLVCMLYTPL RTGGGTGDSF VVAGRVMTCP SPDFNFLFLV PPTVEQKTRP FTLPNLPLSS 

       250        260        270        280        290        300 
LSNSRAPLPI SSMGISPDNV QSVQFQNGRC TLDGRLVGTT PVSLSHVAKI RGTSNGTVIN 

       310        320        330        340        350        360 
LTELDGTPFH PFEGPAPIGF PDLGGCDWHI NMTQFGHSSQ TQYDVDTTPD TFVPHLGSIQ 

       370        380        390        400        410        420 
ANGIGSGNYV GVLSWISPPS HPSGSQVDLW KIPNYGSSIT EATHLAPSVY PPGFGEVLVF 

       430        440        450        460        470        480 
FMSKMPGPGA YNLPCLLPQE YISHLASEQA PTVGEAALLH YVDPDTGRNL GEFKAYPDGF 

       490        500        510        520        530 
LTCVPNGASS GPQQLPINGV FVFVSWVSRF YQLKPVGTAS SARGRLGLRR

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References

[1]	"Sequence and genomic organization of Norwalk virus." Jiang X., Wang M., Wang K., Estes M.K. Virology 195:51-61(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Specific proteolytic cleavage of recombinant Norwalk virus capsid protein." Hardy M.E., White L.J., Ball J.M., Estes M.K. J. Virol. 69:1693-1698(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CLEAVAGE.
[3]	"Attachment and entry of recombinant Norwalk virus capsids to cultured human and animal cell lines." White L.J., Ball J.M., Hardy M.E., Tanaka T.N., Kitamoto N., Estes M.K. J. Virol. 70:6589-6597(1996) [PubMed] [Europe PMC] [Abstract] Cited for: CELL-RECEPTOR BINDING.
[4]	"Biochemical characterization of a smaller form of recombinant Norwalk virus capsids assembled in insect cells." White L.J., Hardy M.E., Estes M.K. J. Virol. 71:8066-8072(1997) [PubMed] [Europe PMC] [Abstract] Cited for: CAPSID ASSEMBLY.
[5]	"Norwalk virus binds to histo-blood group antigens present on gastroduodenal epithelial cells of secretor individuals." Marionneau S., Ruvoen N., Le Moullac-Vaidye B., Clement M., Cailleau-Thomas A., Ruiz-Palacois G., Huang P., Jiang X., Le Pendu J. Gastroenterology 122:1967-1977(2002) [PubMed] [Europe PMC] [Abstract] Cited for: CELL-RECEPTOR BINDING.
[6]	"The 3' end of Norwalk virus mRNA contains determinants that regulate the expression and stability of the viral capsid protein VP1: a novel function for the VP2 protein." Bertolotti-Ciarlet A., Crawford S.E., Hutson A.M., Estes M.K. J. Virol. 77:11603-11615(2003) [PubMed] [Europe PMC] [Abstract] Cited for: STABILIZATION BY VP2.
[7]	"Noroviruses bind to human ABO, Lewis, and secretor histo-blood group antigens: identification of 4 distinct strain-specific patterns." Huang P., Farkas T., Marionneau S., Zhong W., Ruvoen-Clouet N., Morrow A.L., Altaye M., Pickering L.K., Newburg D.S., LePendu J., Jiang X. J. Infect. Dis. 188:19-31(2003) [PubMed] [Europe PMC] [Abstract] Cited for: CELL-RECEPTOR BINDING.
[8]	"C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein." Tan M., Meller J., Jiang X. J. Virol. 80:7322-7331(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Norovirus protein structure and function." Hardy M.E. FEMS Microbiol. Lett. 253:1-8(2005) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[10]	"X-ray crystallographic structure of the Norwalk virus capsid." Prasad B.V.V., Hardy M.E., Dokland T., Bella J., Rossmann M.G., Estes M.K. Science 286:287-290(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M87661 Genomic RNA. Translation: AAB50466.2.

PIR

B37471.

RefSeq

NP_056821.2. NC_001959.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IHM	X-ray	3.40	A/B/C	1-530	[»]
2ZL5	X-ray	1.47	A/B	225-518	[»]
2ZL6	X-ray	1.43	A/B	225-519	[»]
2ZL7	X-ray	1.35	A/B	225-519	[»]
3BY1	X-ray	2.69	A	218-530	[»]
3BY2	X-ray	2.60	A	218-522	[»]
3D26	X-ray	2.30	A/B	230-530	[»]

ProteinModelPortal

Q83884.

SMR

Q83884. Positions 10-520.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1491972.

Family and domain databases

InterPro

IPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
[Graphical view]

Pfam

PF00915. Calici_coat. 1 hit.
PF08435. Calici_coat_C. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q83884.

Entry information

Entry name

CAPSD_NVN68

Accession

Primary (citable) accession number: Q83884

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 2008
Last sequence update:	July 11, 2006
Last modified:	April 3, 2013
This is version 62 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Cleaved into the following chain:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Family and domain databases

Other

Entry information

Relevant documents