Q04542 (CAPSD_SOUV3) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Capsid protein VP1
Short name=CP

Cleaved into the following chain:

1. Soluble capsid protein

Gene names

ORF Names:

ORF2

Organism

Southampton virus (strain GI/Human/United Kingdom/Southampton/1991) (SHV) (Hu/NV/SHV/1991/UK) [Complete proteome]

Taxonomic identifier

37129 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Norovirus › Norwalk virus › Norovirus genogroup I › Southampton virus

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	546 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred 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

Keywords
Cellular component	Host cytoplasm Virion
Molecular function	Capsid protein T=3 icosahedral capsid protein
Technical term	Complete 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 – 546	546	Capsid protein VP1		PRO_0000100119
	Chain	228 – 546	319	Soluble capsid protein		PRO_0000341983
Regions
	Region	1 – 226	226	Shell domain By similarity
	Region	227 – 545	319	Protruding domain By similarity
	Region	227 – 279	53	P1 su-bdomain 1 By similarity
	Region	280 – 416	137	P2 sub-domain By similarity
	Region	417 – 546	130	P1 sub-domain 2 By similarity
Sites
	Site	228 – 229	2	Cleavage; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q04542 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: C82B2A85AD4B05EA	FASTA	546	58,774
	10 20 30 40 50 60 MMMASKDAPQ SADGASGAGQ LVPEVNTADP LPMEPVAGPT TAVATAGQVN MIDPWIVNNF 70 80 90 100 110 120 VQSPQGEFTI SPNNTPGDIL FDLQLGPHLN PFLSHLSQMY NGWVGNMRVR ILLAGNAFSA 130 140 150 160 170 180 GKIIVCCVPP GFTSSSLTIA QATLFPHVIA DVRTLEPIEM PLEDVRNVLY HTNDNQPTMR 190 200 210 220 230 240 LVCMLYTPLR TGGGSGNSDS FVVAGRVLTA PSSDFSFLFL VPPTIEQKTR AFTVPNIPLQ 250 260 270 280 290 300 TLSNSRFPSL IQGMILSPDA SQVVQFQNGR CLIDGQLLGT TPATSGQLFR VRGKINQGAR 310 320 330 340 350 360 TLNLTEVDGK PFMAFDSPAP VGFPDFGKCD WHMRISKTPN NTGSGDPMRS VSVQTNVQGF 370 380 390 400 410 420 VPHLGSIQFD EVFNHPTGDY IGTIEWISQP STPPGTDINL WEIPDYGSSL SQAANLAPPV 430 440 450 460 470 480 FPPGFGEALV YFVSAFPGPN NRSAPNDVPC LLPQEYITHF VSEQAPTMGD AALLHYVDPD 490 500 510 520 530 540 TNRNLGEFKL YPGGYLTCVP NGVGAGPQQL PLNGVFLFVS WVSRFYQLKP VGTASTARGR LGVRRI

References

[1]	"Sequence and genome organization of a human small round-structured (Norwalk-like) virus." Lambden P.R., Caul E.O., Ashley C.R., Clarke I.N. Science 259:516-519(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	L07418 Genomic RNA. Translation: AAA92984.1.
PIR	B37491.
3D structure databases
ProteinModelPortal	Q04542.
SMR	Q04542. Positions 11-535.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
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...

Entry information

Entry name

CAPSD_SOUV3

Accession

Primary (citable) accession number: Q04542

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	April 3, 2013
This is version 51 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program