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P06663

- CAPSD_TCV

UniProt

P06663 - CAPSD_TCV

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Protein

Capsid protein

Gene
ORF4
Organism
Turnip crinkle virus (TCV)
Status
Reviewed - 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, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs.3 Publications

Cofactori

Binds calcium ions. Calcium ions probably promote virus assembly and stabilize the virus particle By similarity.

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW
  2. structural molecule activity Source: InterPro

GO - Biological processi

  1. viral process Source: UniProtKB-KW
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 positive-strand viruses, no DNA stageTombusviridaeCarmovirus
Virus hostiBrassica napus subsp. rapifera [TaxID: 3709]
Hypomyces [TaxID: 5130]
Moricandia arvensis (Purple mistress) (Brassica arvensis) [TaxID: 180540]
ProteomesiUP000007403: Genome, UP000009133: Genome

Subcellular locationi

GO - Cellular componenti

  1. T=3 icosahedral viral capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, T=3 icosahedral capsid protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi26 – 261W → A: Complete loss of interaction with host AGO1 and AGO4. Complete loss of silencing suppression. 1 Publication
Mutagenesisi274 – 2741W → A: Complete loss of interaction with host AGO1 and AGO4. Complete loss of silencing suppression. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 351351Capsid proteinPRO_0000222868Add
BLAST

Interactioni

Subunit structurei

Homodimer. Homomultimer. Interacts (via GW motifs) with Arabidopsis thaliana AGO1 and AGO4; these interactions inhibit RNA silencing ability of host AGOs.1 Publication

Structurei

Secondary structure

1
351
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi98 – 1003
Beta strandi109 – 1113
Beta strandi117 – 1193
Beta strandi122 – 1265
Beta strandi144 – 1463
Beta strandi164 – 1663
Helixi169 – 1713
Beta strandi206 – 2094
Turni272 – 2743
Beta strandi287 – 2904
Beta strandi301 – 3044
Beta strandi328 – 3303
Beta strandi332 – 3343
Beta strandi339 – 3413
Beta strandi346 – 3494

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZX8electron microscopy11.50A/B/C1-351[»]
3ZX9electron microscopy17.00A/B/C1-351[»]
3ZXAX-ray3.20C1-351[»]
ProteinModelPortaliP06663.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8181R domain, disordered, interaction with RNAAdd
BLAST
Regioni82 – 238157S domain, virion shellAdd
BLAST
Regioni239 – 351113P domain, projectingAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi25 – 262GW motif
Motifi273 – 2742GW motif

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

MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ    50
PVQKVTRLSA PVALAYREVS TQPRVSTARD GITRSGSELI TTLKKNTDTE 100
PKYTTAVLNP SEPGTFNQLI KEAAQYEKYR FTSLRFRYSP MSPSTTGGKV 150
ALAFDRDAAK PPPNDLASLY NIEGCVSSVP WTGFILTVPT DSTDRFVADG 200
ISDPKLVDFG KLIMATYGQG ANDAAQLGEV RVEYTVQLKN RTGSTSDAQI 250
GDFAGVKDGP RLVSWSKTKG TAGWEHDCHF LGTGNFSLTL FYEKAPVSGL 300
ENADASDFSV LGEAAAGSVQ WAGVKVAERG QGVKMVTTEE QPKGKLQALR 350
I 351
Length:351
Mass (Da):38,052
Last modified:January 1, 1988 - v1
Checksum:i027C9C2020ECA1DC
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti13 – 131D → E in strain: Infectious clone UK.
Natural varianti28 – 281T → S in strain: Infectious clone UK.
Natural varianti208 – 2081D → N in strain: Infectious clone UK.
Natural varianti332 – 3321G → S in strain: Infectious clone UK.
Natural varianti343 – 3431K → R in strain: Infectious clone UK.
Natural varianti346 – 3461L → W in strain: Infectious clone UK.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti252 – 2521D → Q in AAA96971. 1 Publication

Sequence databases

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

Genome annotation databases

GeneIDi944390.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X05193 Genomic RNA. Translation: CAA28823.1 .
M22445 Genomic RNA. Translation: AAA96971.1 .
AY312063 Genomic RNA. Translation: AAP78489.1 .
PIRi JA0111. VCVETC.
RefSeqi NP_620723.2. NC_003821.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3ZX8 electron microscopy 11.50 A/B/C 1-351 [» ]
3ZX9 electron microscopy 17.00 A/B/C 1-351 [» ]
3ZXA X-ray 3.20 C 1-351 [» ]
ProteinModelPortali P06663.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 944390.

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
InterProi IPR000937. Capsid_prot_S-dom_vir.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF00729. Viral_coat. 1 hit.
[Graphical view ]
PRINTSi PR00233. ICOSAHEDRAL.
PROSITEi PS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Structure and assembly of turnip crinkle virus. IV. Analysis of the coat protein gene and implications of the subunit primary structure."
    Stockley P.G., Morris T.J.
    J. Mol. Biol. 194:265-276(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  3. Ryabov E.V.
    Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Infectious clone UK.
  4. "The coat protein of turnip crinkle virus suppresses posttranscriptional gene silencing at an early initiation step."
    Qu F., Ren T., Morris T.J.
    J. Virol. 77:511-522(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Turnip crinkle virus coat protein mediates suppression of RNA silencing in Nicotiana benthamiana."
    Thomas C.L., Leh V., Lederer C., Maule A.J.
    Virology 306:33-41(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein."
    Azevedo J., Garcia D., Pontier D., Ohnesorge S., Yu A., Garcia S., Braun L., Bergdoll M., Hakimi M.A., Lagrange T., Voinnet O.
    Genes Dev. 24:904-915(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH ARABIDOPSIS THALIANA AGO1 AND AGO4, MUTAGENESIS OF TRP-26 AND TRP-274.
  7. "Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2-A resolution."
    Hogle J.M., Maeda A., Harrison S.C.
    J. Mol. Biol. 191:625-638(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).

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: January 1, 1988
Last modified: July 9, 2014
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

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

External Data

Dasty 3

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