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P06663 (CAPSD_TCV) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 74. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Capsid protein
Alternative name(s):
Coat protein
p38
Gene names
ORF Names:ORF4
OrganismTurnip crinkle virus (TCV) [Complete proteome]
Taxonomic identifier11988 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageTombusviridaeCarmovirus
Virus hostBrassica napus subsp. rapifera [TaxID: 3709]
Hypomyces [TaxID: 5130]
Moricandia arvensis (Purple mistress) (Brassica arvensis) [TaxID: 180540]

Protein attributes

Sequence length351 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.5 Ref.6

Cofactor

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

Subunit structure

Homodimer. Homomultimer. Interacts (via GW motifs) with Arabidopsis thaliana AGO1 and AGO4; these interactions inhibit RNA silencing ability of host AGOs. Ref.6

Subcellular location

Virion.

Sequence similarities

Belongs to the icosahedral plant coat protein family.

Ontologies

Keywords
   Biological processHost-virus interaction
   Cellular componentCapsid protein
T=3 icosahedral capsid protein
Virion
   LigandCalcium
RNA-binding
   Molecular functionSuppressor of RNA silencing
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processviral process

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentT=3 icosahedral viral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

structural molecule activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 351351Capsid protein
PRO_0000222868

Regions

Region1 – 8181R domain, disordered, interaction with RNA
Region82 – 238157S domain, virion shell
Region239 – 351113P domain, projecting
Motif25 – 262GW motif
Motif273 – 2742GW motif

Natural variations

Natural variant131D → E in strain: Infectious clone UK.
Natural variant281T → S in strain: Infectious clone UK.
Natural variant2081D → N in strain: Infectious clone UK.
Natural variant3321G → S in strain: Infectious clone UK.
Natural variant3431K → R in strain: Infectious clone UK.
Natural variant3461L → W in strain: Infectious clone UK.

Experimental info

Mutagenesis261W → A: Complete loss of interaction with host AGO1 and AGO4. Complete loss of silencing suppression. Ref.6
Mutagenesis2741W → A: Complete loss of interaction with host AGO1 and AGO4. Complete loss of silencing suppression. Ref.6
Sequence conflict2521D → Q in AAA96971. Ref.2

Secondary structure

............................... 351
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06663 [UniParc].

Last modified January 1, 1988. Version 1.
Checksum: 027C9C2020ECA1DC

FASTA35138,052
        10         20         30         40         50         60 
MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ PVQKVTRLSA 

        70         80         90        100        110        120 
PVALAYREVS TQPRVSTARD GITRSGSELI TTLKKNTDTE PKYTTAVLNP SEPGTFNQLI 

       130        140        150        160        170        180 
KEAAQYEKYR FTSLRFRYSP MSPSTTGGKV ALAFDRDAAK PPPNDLASLY NIEGCVSSVP 

       190        200        210        220        230        240 
WTGFILTVPT DSTDRFVADG ISDPKLVDFG KLIMATYGQG ANDAAQLGEV RVEYTVQLKN 

       250        260        270        280        290        300 
RTGSTSDAQI GDFAGVKDGP RLVSWSKTKG TAGWEHDCHF LGTGNFSLTL FYEKAPVSGL 

       310        320        330        340        350 
ENADASDFSV LGEAAAGSVQ WAGVKVAERG QGVKMVTTEE QPKGKLQALR I 

« Hide

References

[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]"The genome structure of turnip crinkle virus."
Carrington J.C., Heaton L.A., Zuidema D., Hillman B.I., Morris T.J.
Virology 170:219-226(1989) [PubMed] [Europe PMC] [Abstract]
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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X05193 Genomic RNA. Translation: CAA28823.1.
M22445 Genomic RNA. Translation: AAA96971.1.
AY312063 Genomic RNA. Translation: AAP78489.1.
PIRVCVETC. JA0111.
RefSeqNP_620723.2. NC_003821.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZX8electron microscopy11.50A/B/C1-351[»]
3ZX9electron microscopy17.00A/B/C1-351[»]
3ZXAX-ray3.20C1-351[»]
ProteinModelPortalP06663.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID944390.

Family and domain databases

Gene3D2.60.120.20. 1 hit.
InterProIPR000937. Capsid_prot_S-dom_vir.
IPR029053. Viral_coat.
[Graphical view]
PfamPF00729. Viral_coat. 1 hit.
[Graphical view]
PRINTSPR00233. ICOSAHEDRAL.
PROSITEPS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameCAPSD_TCV
AccessionPrimary (citable) accession number: P06663
Secondary accession number(s): Q7TD18
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references