CAPSD_TCV
ID CAPSD_TCV Reviewed; 351 AA.
AC P06663; Q7TD18;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 11-NOV-2015, sequence version 2.
DT 29-SEP-2021, entry version 98.
DE RecName: Full=Capsid protein;
DE AltName: Full=Coat protein;
DE AltName: Full=p38;
GN ORFNames=ORF4;
OS Turnip crinkle virus (TCV).
OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Tolucaviricetes;
OC Tolivirales; Tombusviridae; Procedovirinae; Betacarmovirus.
OX NCBI_TaxID=11988;
OH NCBI_TaxID=3709; Brassica napus subsp. rapifera.
OH NCBI_TaxID=5130; Hypomyces.
OH NCBI_TaxID=180540; Moricandia arvensis (Purple mistress) (Brassica arvensis).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=3612806; DOI=10.1016/0022-2836(87)90374-3;
RA Stockley P.G., Morris T.J.;
RT "Structure and assembly of turnip crinkle virus. IV. Analysis of the coat
RT protein gene and implications of the subunit primary structure.";
RL J. Mol. Biol. 194:265-276(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=2718381; DOI=10.1016/0042-6822(89)90369-3;
RA Carrington J.C., Heaton L.A., Zuidema D., Hillman B.I., Morris T.J.;
RT "The genome structure of turnip crinkle virus.";
RL Virology 170:219-226(1989).
RN [3]
RP SEQUENCE REVISION.
RA Carrington J.C., Heaton L.A., Zuidema D., Hillman B.I., Morris T.J.;
RL Submitted (MAY-2014) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RC STRAIN=Infectious clone UK;
RA Ryabov E.V.;
RL Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION.
RX PubMed=11041886; DOI=10.2307/3871202;
RA Ren T., Qu F., Morris T.J.;
RT "HRT gene function requires interaction between a NAC protein and viral
RT capsid protein to confer resistance to turnip crinkle virus.";
RL Plant Cell 12:1917-1926(2000).
RN [6]
RP FUNCTION.
RX PubMed=12477856; DOI=10.1128/jvi.77.1.511-522.2003;
RA Qu F., Ren T., Morris T.J.;
RT "The coat protein of turnip crinkle virus suppresses posttranscriptional
RT gene silencing at an early initiation step.";
RL J. Virol. 77:511-522(2003).
RN [7]
RP FUNCTION.
RX PubMed=12620795; DOI=10.1016/s0042-6822(02)00018-1;
RA Thomas C.L., Leh V., Lederer C., Maule A.J.;
RT "Turnip crinkle virus coat protein mediates suppression of RNA silencing in
RT Nicotiana benthamiana.";
RL Virology 306:33-41(2003).
RN [8]
RP INTERACTION WITH HOST TIP.
RX PubMed=15629774; DOI=10.1016/j.virol.2004.10.039;
RA Ren T., Qu F., Morris T.J.;
RT "The nuclear localization of the Arabidopsis transcription factor TIP is
RT blocked by its interaction with the coat protein of Turnip crinkle virus.";
RL Virology 331:316-324(2005).
RN [9]
RP FUNCTION, INTERACTION WITH ARABIDOPSIS THALIANA AGO1 AND AGO4, AND
RP MUTAGENESIS OF TRP-26 AND TRP-274.
RX PubMed=20439431; DOI=10.1101/gad.1908710;
RA Azevedo J., Garcia D., Pontier D., Ohnesorge S., Yu A., Garcia S.,
RA Braun L., Bergdoll M., Hakimi M.A., Lagrange T., Voinnet O.;
RT "Argonaute quenching and global changes in Dicer homeostasis caused by a
RT pathogen-encoded GW repeat protein.";
RL Genes Dev. 24:904-915(2010).
RN [10]
RP FUNCTION.
RX PubMed=24418554; DOI=10.1016/j.virol.2013.11.018;
RA Donze T., Qu F., Twigg P., Morris T.J.;
RT "Turnip crinkle virus coat protein inhibits the basal immune response to
RT virus invasion in Arabidopsis by binding to the NAC transcription factor
RT TIP.";
RL Virology 449:207-214(2014).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).
RX PubMed=3806676; DOI=10.1016/0022-2836(86)90450-x;
RA Hogle J.M., Maeda A., Harrison S.C.;
RT "Structure and assembly of turnip crinkle virus. I. X-ray crystallographic
RT structure analysis at 3.2-A resolution.";
RL J. Mol. Biol. 191:625-638(1986).
CC -!- FUNCTION: Capsid protein self-assembles to form an icosahedral capsid
CC with a T=3 symmetry, about 32-35 nm in diameter, and consisting of 180
CC capsid proteins. Also acts as a suppressor of RNA-mediated gene
CC silencing known as post-transcriptional gene silencing (PTGS), a
CC mechanism of plant viral defense that limits the accumulation of viral
CC RNAs. May suppress other innate immunity by binding to host TIP
CC protein, thereby preventing it to migrate in the nucleus where it could
CC trigger an antiviral response (PubMed:11041886, PubMed:24418554).
CC {ECO:0000269|PubMed:11041886, ECO:0000269|PubMed:12477856,
CC ECO:0000269|PubMed:12620795, ECO:0000269|PubMed:20439431,
CC ECO:0000269|PubMed:24418554}.
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000250};
CC Note=Binds Ca(2+). Ca(2+) probably promotes virus assembly and
CC stabilize the virus particle. {ECO:0000250};
CC -!- SUBUNIT: Homodimer. Homomultimer. Interacts (via GW motifs) with
CC Arabidopsis thaliana AGO1 and AGO4; these interactions inhibit RNA
CC silencing ability of host AGOs. Interacts with host TIP
CC (PubMed:15629774). {ECO:0000269|PubMed:15629774,
CC ECO:0000269|PubMed:20439431}.
CC -!- SUBCELLULAR LOCATION: Virion.
CC -!- SIMILARITY: Belongs to the icosahedral plant coat protein family.
CC {ECO:0000305}.
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DR EMBL; X05193; CAA28823.1; -; Genomic_RNA.
DR EMBL; M22445; AAA96971.2; -; Genomic_RNA.
DR EMBL; AY312063; AAP78489.1; -; Genomic_RNA.
DR PIR; JA0111; VCVETC.
DR RefSeq; NP_620723.2; NC_003821.3.
DR PDB; 3ZX8; EM; 11.50 A; A/B/C=1-351.
DR PDB; 3ZX9; EM; 17.00 A; A/B/C=1-351.
DR PDB; 3ZXA; X-ray; 3.20 A; C=1-351.
DR PDBsum; 3ZX8; -.
DR PDBsum; 3ZX9; -.
DR PDBsum; 3ZXA; -.
DR SMR; P06663; -.
DR PRIDE; P06663; -.
DR GeneID; 944390; -.
DR KEGG; vg:944390; -.
DR Proteomes; UP000007403; Genome.
DR Proteomes; UP000009133; Genome.
DR GO; GO:0039617; C:T=3 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR Gene3D; 2.60.120.20; -; 1.
DR InterPro; IPR000937; Capsid_prot_S-dom_vir.
DR InterPro; IPR029053; Viral_coat.
DR Pfam; PF00729; Viral_coat; 1.
DR PRINTS; PR00233; ICOSAHEDRAL.
DR PROSITE; PS00555; ICOSAH_VIR_COAT_S; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Capsid protein; Host-virus interaction;
KW Reference proteome; RNA-binding; Suppressor of RNA silencing;
KW T=3 icosahedral capsid protein; Virion.
FT CHAIN 1..351
FT /note="Capsid protein"
FT /id="PRO_0000222868"
FT REGION 82..238
FT /note="S domain, virion shell"
FT REGION 239..351
FT /note="P domain, projecting"
FT MOTIF 25..26
FT /note="GW motif"
FT MOTIF 273..274
FT /note="GW motif"
FT VARIANT 13
FT /note="D -> E (in strain: Infectious clone UK)"
FT VARIANT 28
FT /note="T -> S (in strain: Infectious clone UK)"
FT VARIANT 208
FT /note="D -> N (in strain: Infectious clone UK)"
FT VARIANT 332
FT /note="G -> S (in strain: Infectious clone UK)"
FT VARIANT 343
FT /note="K -> R (in strain: Infectious clone UK)"
FT VARIANT 346
FT /note="W -> L"
FT MUTAGEN 26
FT /note="W->A: Complete loss of interaction with host AGO1
FT and AGO4. Complete loss of silencing suppression."
FT /evidence="ECO:0000269|PubMed:20439431"
FT MUTAGEN 274
FT /note="W->A: Complete loss of interaction with host AGO1
FT and AGO4. Complete loss of silencing suppression."
FT /evidence="ECO:0000269|PubMed:20439431"
FT CONFLICT 252
FT /note="D -> Q (in Ref. 2; AAA96971)"
FT /evidence="ECO:0000305"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:3ZXA"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:3ZXA"
FT TURN 272..274
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 301..304
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 328..330
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:3ZXA"
FT STRAND 346..349
FT /evidence="ECO:0007829|PDB:3ZXA"
SQ SEQUENCE 351 AA; 38125 MW; 027C9C2020F8F1DC CRC64;
MENDPRVRKF ASDGAQWAIK WQKKGWSTLT SRQKQTARAA MGIKLSPVAQ PVQKVTRLSA
PVALAYREVS TQPRVSTARD GITRSGSELI TTLKKNTDTE PKYTTAVLNP SEPGTFNQLI
KEAAQYEKYR FTSLRFRYSP MSPSTTGGKV ALAFDRDAAK PPPNDLASLY NIEGCVSSVP
WTGFILTVPT DSTDRFVADG ISDPKLVDFG KLIMATYGQG ANDAAQLGEV RVEYTVQLKN
RTGSTSDAQI GDFAGVKDGP RLVSWSKTKG TAGWEHDCHF LGTGNFSLTL FYEKAPVSGL
ENADASDFSV LGEAAAGSVQ WAGVKVAERG QGVKMVTTEE QPKGKWQALR I
