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P06663

- CAPSD_TCV

UniProt

P06663 - CAPSD_TCV

Protein

Capsid protein

Gene

ORF4

Organism
Turnip crinkle virus (TCV)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 75 (01 Oct 2014)
      Sequence version 1 (01 Jan 1988)
      Previous versions | rss
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    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.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

    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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti252 – 2521D → Q in AAA96971. (PubMed:2718381)Curated

    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 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: October 1, 2014
    This is version 75 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