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Protein

Capsid protein

Gene

ORF4

Organism
Turnip crinkle virus (TCV)
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 32-35 nm in diameter, and consisting of 180 capsid proteins. Also acts as a suppressor of RNA-mediated gene silencing known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. May suppress other innate immunity by binding to host TIP protein, thereby preventing it to migrate in the nucleus where it could trigger an antiviral response (PubMed:11041886, PubMed:24418554).5 Publications

Cofactori

Ca2+By similarityNote: Binds Ca2+. Ca2+ probably promotes virus assembly and stabilize the virus particle.By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Suppressor of RNA silencing

Keywords - Biological processi

Host-virus interaction

Keywords - Ligandi

Calcium, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein
Alternative name(s):
Coat protein
p38
Gene namesi
ORF Names:ORF4
OrganismiTurnip crinkle virus (TCV)
Taxonomic identifieri11988 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTombusviridaeCarmovirus
Virus hostiBrassica napus subsp. rapifera [TaxID: 3709]
Hypomyces [TaxID: 5130]
Moricandia arvensis (Purple mistress) (Brassica arvensis) [TaxID: 180540]
Proteomesi
  • UP000007403 Componenti: Genome
  • UP000009133 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, T=3 icosahedral capsid protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi26W → A: Complete loss of interaction with host AGO1 and AGO4. Complete loss of silencing suppression. 1 Publication1
Mutagenesisi274W → A: Complete loss of interaction with host AGO1 and AGO4. Complete loss of silencing suppression. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002228681 – 351Capsid proteinAdd BLAST351

Proteomic databases

PRIDEiP06663.

Interactioni

Subunit structurei

Homodimer. Homomultimer. Interacts (via GW motifs) with Arabidopsis thaliana AGO1 and AGO4; these interactions inhibit RNA silencing ability of host AGOs. Interacts with host TIP (PubMed:15629774).2 Publications

Structurei

Secondary structure

1351
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi98 – 100Combined sources3
Beta strandi109 – 111Combined sources3
Beta strandi117 – 119Combined sources3
Beta strandi122 – 126Combined sources5
Beta strandi144 – 146Combined sources3
Beta strandi164 – 166Combined sources3
Helixi169 – 171Combined sources3
Beta strandi206 – 209Combined sources4
Turni272 – 274Combined sources3
Beta strandi287 – 290Combined sources4
Beta strandi301 – 304Combined sources4
Beta strandi328 – 330Combined sources3
Beta strandi332 – 334Combined sources3
Beta strandi339 – 341Combined sources3
Beta strandi346 – 349Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZX8electron microscopy11.50A/B/C1-351[»]
3ZX9electron microscopy17.00A/B/C1-351[»]
3ZXAX-ray3.20C1-351[»]
ProteinModelPortaliP06663.
SMRiP06663.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 81R domain, disordered, interaction with RNAAdd BLAST81
Regioni82 – 238S domain, virion shellAdd BLAST157
Regioni239 – 351P domain, projectingAdd BLAST113

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi25 – 26GW motif2
Motifi273 – 274GW motif2

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
InterProiIPR000937. Capsid_prot_S-dom_vir.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00729. Viral_coat. 1 hit.
[Graphical view]
PRINTSiPR00233. ICOSAHEDRAL.
PROSITEiPS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P06663-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ
60 70 80 90 100
PVQKVTRLSA PVALAYREVS TQPRVSTARD GITRSGSELI TTLKKNTDTE
110 120 130 140 150
PKYTTAVLNP SEPGTFNQLI KEAAQYEKYR FTSLRFRYSP MSPSTTGGKV
160 170 180 190 200
ALAFDRDAAK PPPNDLASLY NIEGCVSSVP WTGFILTVPT DSTDRFVADG
210 220 230 240 250
ISDPKLVDFG KLIMATYGQG ANDAAQLGEV RVEYTVQLKN RTGSTSDAQI
260 270 280 290 300
GDFAGVKDGP RLVSWSKTKG TAGWEHDCHF LGTGNFSLTL FYEKAPVSGL
310 320 330 340 350
ENADASDFSV LGEAAAGSVQ WAGVKVAERG QGVKMVTTEE QPKGKWQALR

I
Length:351
Mass (Da):38,125
Last modified:November 11, 2015 - v2
Checksum:i027C9C2020F8F1DC
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti252D → Q in AAA96971 (PubMed:2718381).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti13D → E in strain: Infectious clone UK. 1
Natural varianti28T → S in strain: Infectious clone UK. 1
Natural varianti208D → N in strain: Infectious clone UK. 1
Natural varianti332G → S in strain: Infectious clone UK. 1
Natural varianti343K → R in strain: Infectious clone UK. 1
Natural varianti346W → L.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05193 Genomic RNA. Translation: CAA28823.1.
M22445 Genomic RNA. Translation: AAA96971.2.
AY312063 Genomic RNA. Translation: AAP78489.1.
PIRiJA0111. VCVETC.
RefSeqiNP_620723.2. NC_003821.3.

Genome annotation databases

GeneIDi944390.
KEGGivg:944390.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05193 Genomic RNA. Translation: CAA28823.1.
M22445 Genomic RNA. Translation: AAA96971.2.
AY312063 Genomic RNA. Translation: AAP78489.1.
PIRiJA0111. VCVETC.
RefSeqiNP_620723.2. NC_003821.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ZX8electron microscopy11.50A/B/C1-351[»]
3ZX9electron microscopy17.00A/B/C1-351[»]
3ZXAX-ray3.20C1-351[»]
ProteinModelPortaliP06663.
SMRiP06663.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP06663.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi944390.
KEGGivg:944390.

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
InterProiIPR000937. Capsid_prot_S-dom_vir.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF00729. Viral_coat. 1 hit.
[Graphical view]
PRINTSiPR00233. ICOSAHEDRAL.
PROSITEiPS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_TCV
AccessioniPrimary (citable) accession number: P06663
Secondary accession number(s): Q7TD18
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: November 11, 2015
Last modified: November 30, 2016
This is version 83 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.