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   27-MAR-2024, entry version 103.
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;
OC   Betacarmovirus brassicae.
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=10.1105/tpc.12.10.1917;
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   GeneID; 944390; -.
DR   KEGG; vg:944390; -.
DR   OrthoDB; 17533at10239; -.
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   Gene3D; 2.60.40.3420; -; 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   SUPFAM; SSF88633; Positive stranded ssRNA viruses; 1.
DR   PROSITE; PS00555; ICOSAH_VIR_COAT_S; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Calcium; Capsid protein; Host-virus interaction;
KW   Inhibition of host innate immune response by virus; Reference proteome;
KW   RNA-binding; Suppressor of RNA silencing; T=3 icosahedral capsid protein;
KW   Viral immunoevasion; 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
//