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Protein

Capsid protein VP1

Gene

ORF2

Organism
Norwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US)
Status
Reviewed-Annotation score: Annotation score: 4 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 histo-blood group antigens present on gastroduodenal epithelial cells.1 Publication
Soluble capsid protein may play a role in viral immunoevasion.1 Publication

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein VP1
Short name:
CP
Alternative name(s):
p59
Cleaved into the following chain:
Alternative name(s):
Protein 30k
Short name:
p30
Gene namesi
ORF Names:ORF2
OrganismiNorwalk virus (strain GI/Human/United States/Norwalk/1968) (Hu/NV/NV/1968/US)
Taxonomic identifieri524364 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageCaliciviridaeNorovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000000826 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cytoplasm, T=3 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003416261 – 530Capsid protein VP1Add BLAST530
ChainiPRO_0000341627228 – 530Soluble capsid proteinAdd BLAST303

Post-translational modificationi

May be cleaved by host protease to generate soluble capsid protein. Assembled capsid cannot be cleaved.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei227 – 228Cleavage; by host2

Interactioni

Subunit structurei

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

Structurei

Secondary structure

1530
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 16Combined sources3
Helixi42 – 44Combined sources3
Turni54 – 58Combined sources5
Beta strandi61 – 70Combined sources10
Beta strandi79 – 84Combined sources6
Helixi87 – 89Combined sources3
Helixi91 – 97Combined sources7
Beta strandi100 – 104Combined sources5
Beta strandi107 – 114Combined sources8
Beta strandi117 – 120Combined sources4
Beta strandi122 – 128Combined sources7
Helixi139 – 142Combined sources4
Beta strandi145 – 151Combined sources7
Beta strandi158 – 162Combined sources5
Beta strandi167 – 169Combined sources3
Beta strandi171 – 173Combined sources3
Beta strandi181 – 186Combined sources6
Beta strandi202 – 210Combined sources9
Helixi238 – 240Combined sources3
Beta strandi244 – 247Combined sources4
Beta strandi252 – 254Combined sources3
Beta strandi266 – 268Combined sources3
Helixi284 – 286Combined sources3
Beta strandi289 – 294Combined sources6
Beta strandi296 – 302Combined sources7
Beta strandi306 – 308Combined sources3
Helixi311 – 313Combined sources3
Beta strandi315 – 317Combined sources3
Beta strandi325 – 333Combined sources9
Beta strandi341 – 345Combined sources5
Helixi354 – 356Combined sources3
Beta strandi358 – 360Combined sources3
Beta strandi366 – 377Combined sources12
Beta strandi380 – 382Combined sources3
Beta strandi396 – 398Combined sources3
Beta strandi416 – 425Combined sources10
Beta strandi427 – 429Combined sources3
Beta strandi431 – 437Combined sources7
Helixi439 – 448Combined sources10
Beta strandi455 – 462Combined sources8
Turni464 – 466Combined sources3
Beta strandi469 – 476Combined sources8
Turni477 – 479Combined sources3
Beta strandi480 – 483Combined sources4
Turni487 – 489Combined sources3
Helixi492 – 494Combined sources3
Beta strandi500 – 507Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IHMX-ray3.40A/B/C1-530[»]
2ZL5X-ray1.47A/B225-518[»]
2ZL6X-ray1.43A/B225-519[»]
2ZL7X-ray1.35A/B225-519[»]
3BY1X-ray2.69A218-530[»]
3BY2X-ray2.60A218-522[»]
3D26X-ray2.30A/B230-530[»]
5KW9X-ray2.30A225-518[»]
ProteinModelPortaliQ83884.
SMRiQ83884.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ83884.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 225Shell domainAdd BLAST225
Regioni226 – 530Protruding domainAdd BLAST305
Regioni226 – 278P1 su-bdomain 1Add BLAST53
Regioni279 – 405P2 sub-domainAdd BLAST127
Regioni406 – 530P1 sub-domain 2Add BLAST125

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

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
IPR033703. Rhv-like.
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.

Q83884-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN
60 70 80 90 100
PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHLN PFLLHLSQMY
110 120 130 140 150
NGWVGNMRVR IMLAGNAFTA GKIIVSCIPP GFGSHNLTIA QATLFPHVIA
160 170 180 190 200
DVRTLDPIEV PLEDVRNVLF HNNDRNQQTM RLVCMLYTPL RTGGGTGDSF
210 220 230 240 250
VVAGRVMTCP SPDFNFLFLV PPTVEQKTRP FTLPNLPLSS LSNSRAPLPI
260 270 280 290 300
SSMGISPDNV QSVQFQNGRC TLDGRLVGTT PVSLSHVAKI RGTSNGTVIN
310 320 330 340 350
LTELDGTPFH PFEGPAPIGF PDLGGCDWHI NMTQFGHSSQ TQYDVDTTPD
360 370 380 390 400
TFVPHLGSIQ ANGIGSGNYV GVLSWISPPS HPSGSQVDLW KIPNYGSSIT
410 420 430 440 450
EATHLAPSVY PPGFGEVLVF FMSKMPGPGA YNLPCLLPQE YISHLASEQA
460 470 480 490 500
PTVGEAALLH YVDPDTGRNL GEFKAYPDGF LTCVPNGASS GPQQLPINGV
510 520 530
FVFVSWVSRF YQLKPVGTAS SARGRLGLRR
Length:530
Mass (Da):56,589
Last modified:July 11, 2006 - v2
Checksum:i7AEF61A8F66D139C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87661 Genomic RNA. Translation: AAB50466.2.
PIRiB37471.
RefSeqiNP_056821.2. NC_001959.2.

Genome annotation databases

GeneIDi1491972.
KEGGivg:1491972.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M87661 Genomic RNA. Translation: AAB50466.2.
PIRiB37471.
RefSeqiNP_056821.2. NC_001959.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IHMX-ray3.40A/B/C1-530[»]
2ZL5X-ray1.47A/B225-518[»]
2ZL6X-ray1.43A/B225-519[»]
2ZL7X-ray1.35A/B225-519[»]
3BY1X-ray2.69A218-530[»]
3BY2X-ray2.60A218-522[»]
3D26X-ray2.30A/B230-530[»]
5KW9X-ray2.30A225-518[»]
ProteinModelPortaliQ83884.
SMRiQ83884.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1491972.
KEGGivg:1491972.

Miscellaneous databases

EvolutionaryTraceiQ83884.

Family and domain databases

CDDicd00205. rhv_like. 1 hit.
Gene3Di2.60.120.20. 1 hit.
InterProiIPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
IPR033703. Rhv-like.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00915. Calici_coat. 1 hit.
PF08435. Calici_coat_C. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_NVN68
AccessioniPrimary (citable) accession number: Q83884
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: July 11, 2006
Last modified: November 30, 2016
This is version 78 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.