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Database: UniProt
Entry: VIN3_ARATH
LinkDB: VIN3_ARATH
Original site: VIN3_ARATH 
ID   VIN3_ARATH              Reviewed;         620 AA.
AC   Q9FIE3; Q53YX0;
DT   02-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT   12-JUN-2007, sequence version 2.
DT   24-JAN-2024, entry version 161.
DE   RecName: Full=Protein VERNALIZATION INSENSITIVE 3;
GN   Name=VIN3; OrderedLocusNames=At5g57380; ORFNames=MSF19.4;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE
RP   SPECIFICITY, AND INDUCTION.
RC   STRAIN=cv. Columbia;
RX   PubMed=14712276; DOI=10.1038/nature02195;
RA   Sung S., Amasino R.M.;
RT   "Vernalization in Arabidopsis thaliana is mediated by the PHD finger
RT   protein VIN3.";
RL   Nature 427:159-164(2004).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10048488; DOI=10.1093/dnares/5.6.379;
RA   Asamizu E., Sato S., Kaneko T., Nakamura Y., Kotani H., Miyajima N.,
RA   Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence
RT   features of the regions of 1,081,958 bp covered by seventeen physically
RT   assigned P1 and TAC clones.";
RL   DNA Res. 5:379-391(1998).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH VIL1 AND VIL2, AND
RP   INDUCTION BY COLD.
RC   STRAIN=cv. Columbia;
RX   PubMed=17114575; DOI=10.1101/gad.1493306;
RA   Sung S., Schmitz R.J., Amasino R.M.;
RT   "A PHD finger protein involved in both the vernalization and photoperiod
RT   pathways in Arabidopsis.";
RL   Genes Dev. 20:3244-3248(2006).
RN   [5]
RP   FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY COLD, INTERACTION WITH VIL1,
RP   AND SUBCELLULAR LOCATION.
RC   STRAIN=cv. Landsberg erecta;
RX   PubMed=17174094; DOI=10.1016/j.cub.2006.11.052;
RA   Greb T., Mylne J.S., Crevillen P., Geraldo N., An H., Gendall A.R.,
RA   Dean C.;
RT   "The PHD finger protein VRN5 functions in the epigenetic silencing of
RT   Arabidopsis FLC.";
RL   Curr. Biol. 17:73-78(2007).
RN   [6]
RP   SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX   PubMed=18854416; DOI=10.1073/pnas.0808687105;
RA   De Lucia F., Crevillen P., Jones A.M.E., Greb T., Dean C.;
RT   "A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of
RT   FLC during vernalization.";
RL   Proc. Natl. Acad. Sci. U.S.A. 105:16831-16836(2008).
CC   -!- FUNCTION: Plays a central role in vernalization by mediating the
CC       initial transcriptional repression of the homeotic gene FLC, a floral
CC       repressor, after a cold treatment. However, due to its transient
CC       expression, it cannot maintain repression of FLC, which is then
CC       maintained by Polycomb Group complexes containing VRN2 throughout
CC       development. Required to deacetylate histones on the FLC promoter.
CC       Together with VIL1, required during vernalization for the modifications
CC       of FLC and FLM chromatin that are associated with an epigenetically
CC       silenced state (e.g. chromatin modifications, histone deacetylation,
CC       and trimethylated H3 'Lys-4' H3K4me3 and 'Lys-27' H3K27me3) and with
CC       acquisition of competence to flower. {ECO:0000269|PubMed:14712276,
CC       ECO:0000269|PubMed:17114575, ECO:0000269|PubMed:17174094}.
CC   -!- SUBUNIT: Interacts with VIL1 and VIL2. The heterodimer made of VIN3 and
CC       VIL1 is required for establishing the vernalization-induced epigenetic
CC       silencing of FLC. Component of the plant homeodomain / polycomb
CC       repressive complex 2 (PHD-PRC2) large complex during prolonged cold,
CC       composed of core PRC2 components (VRN2, EZA1, FIE and MSI1), and three
CC       related PHD finger proteins (VIL1, VIL2 and VIN3) that mediates histone
CC       H3 trimethylation on 'Lys-27' (H3K27me3). {ECO:0000269|PubMed:17114575,
CC       ECO:0000269|PubMed:17174094, ECO:0000269|PubMed:18854416}.
CC   -!- INTERACTION:
CC       Q9FIE3; Q8W5B1: VRN2; NbExp=2; IntAct=EBI-2358223, EBI-2128880;
CC   -!- SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Note=Probably DNA-
CC       associated; interacts directly with the FLC regulatory regions.
CC   -!- TISSUE SPECIFICITY: Expressed in shoot and root apices. Displays the
CC       same pattern of expression as FLC. {ECO:0000269|PubMed:14712276}.
CC   -!- INDUCTION: By cold. Expressed only after a duration of cold exposure
CC       that is effective for vernalization. Strongly down-regulated after
CC       return to a warm growth temperature. {ECO:0000269|PubMed:14712276,
CC       ECO:0000269|PubMed:17114575, ECO:0000269|PubMed:17174094}.
CC   -!- DISRUPTION PHENOTYPE: Impaired vernalization response with incomplete
CC       repression of FLC during and after cold exposure, due to a reduction in
CC       vernalization-induced histone H3 deacetylation and methylation (e.g.
CC       H3K4me3 and H3K27me3). {ECO:0000269|PubMed:17114575,
CC       ECO:0000269|PubMed:17174094}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB08475.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AY446960; AAR91717.2; -; mRNA.
DR   EMBL; AB016891; BAB08475.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED96894.1; -; Genomic_DNA.
DR   RefSeq; NP_001332646.1; NM_001345260.1.
DR   RefSeq; NP_200548.2; NM_125121.3.
DR   PDB; 7O6T; X-ray; 2.02 A; A/B=531-603.
DR   PDB; 7O6U; X-ray; 1.84 A; A=532-601.
DR   PDB; 7OQV; X-ray; 2.40 A; AAA/BBB/CCC/DDD=529-603.
DR   PDBsum; 7O6T; -.
DR   PDBsum; 7O6U; -.
DR   PDBsum; 7OQV; -.
DR   AlphaFoldDB; Q9FIE3; -.
DR   SMR; Q9FIE3; -.
DR   BioGRID; 21088; 3.
DR   DIP; DIP-48611N; -.
DR   IntAct; Q9FIE3; 3.
DR   STRING; 3702.Q9FIE3; -.
DR   PaxDb; 3702-AT5G57380-1; -.
DR   EnsemblPlants; AT5G57380.1; AT5G57380.1; AT5G57380.
DR   GeneID; 835844; -.
DR   Gramene; AT5G57380.1; AT5G57380.1; AT5G57380.
DR   KEGG; ath:AT5G57380; -.
DR   Araport; AT5G57380; -.
DR   TAIR; AT5G57380; VIN3.
DR   eggNOG; ENOG502QR8D; Eukaryota.
DR   HOGENOM; CLU_016873_0_0_1; -.
DR   InParanoid; Q9FIE3; -.
DR   OMA; NALIRCC; -.
DR   OrthoDB; 664204at2759; -.
DR   PhylomeDB; Q9FIE3; -.
DR   PRO; PR:Q9FIE3; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9FIE3; baseline and differential.
DR   GO; GO:0005677; C:chromatin silencing complex; IDA:UniProtKB.
DR   GO; GO:0016607; C:nuclear speck; IDA:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0070417; P:cellular response to cold; IEP:UniProtKB.
DR   GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IMP:UniProtKB.
DR   GO; GO:0009409; P:response to cold; IEP:UniProtKB.
DR   GO; GO:0001666; P:response to hypoxia; IMP:TAIR.
DR   GO; GO:0010048; P:vernalization response; IMP:UniProtKB.
DR   CDD; cd00063; FN3; 1.
DR   CDD; cd15521; PHD_VIN3_plant; 1.
DR   Gene3D; 2.60.40.10; Immunoglobulins; 1.
DR   InterPro; IPR003961; FN3_dom.
DR   InterPro; IPR036116; FN3_sf.
DR   InterPro; IPR013783; Ig-like_fold.
DR   InterPro; IPR032881; Oberon-like_PHD.
DR   InterPro; IPR044514; VIN3-like.
DR   PANTHER; PTHR46286:SF7; PROTEIN VERNALIZATION INSENSITIVE 3; 1.
DR   PANTHER; PTHR46286; VIN3-LIKE PROTEIN 2-RELATED; 1.
DR   Pfam; PF07227; PHD_Oberon; 1.
DR   SUPFAM; SSF49265; Fibronectin type III; 1.
DR   PROSITE; PS50853; FN3; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA-binding; Metal-binding; Nucleus; Reference proteome;
KW   Repressor; Stress response; Transcription; Transcription regulation; Zinc;
KW   Zinc-finger.
FT   CHAIN           1..620
FT                   /note="Protein VERNALIZATION INSENSITIVE 3"
FT                   /id="PRO_0000059334"
FT   DOMAIN          314..412
FT                   /note="Fibronectin type-III"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00316"
FT   ZN_FING         148..206
FT                   /note="PHD-type"
FT   REGION          411..466
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          512..620
FT                   /note="VIN3-Interacting Domain (VID)"
FT                   /evidence="ECO:0000250"
FT   MOTIF           213..220
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   MOTIF           493..500
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   COMPBIAS        418..451
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        452..466
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   HELIX           533..545
FT                   /evidence="ECO:0007829|PDB:7O6U"
FT   HELIX           551..563
FT                   /evidence="ECO:0007829|PDB:7O6U"
FT   HELIX           567..599
FT                   /evidence="ECO:0007829|PDB:7O6U"
SQ   SEQUENCE   620 AA;  69347 MW;  C145D4E88D3BD588 CRC64;
     MQAASLSKIW RFDGNVGPEN MDSSSFEDNE CIETCKPNVL NVSERRELIH ALSNQPEEAS
     ELLNSWSRNE IMKIICAEMG KERKYTGLNK PKLIENLLNL VSRPLGETSC SDRRNSRKKE
     KKMIGYIICC ENLACRAALG CDDTFCRRCS CCICQKFDDN KDPSLWLTCD ACGSSCHLEC
     GLKQDRYGIG SDDLDGRFYC AYCGKDNDLL GCWRKQVKVA KETRRVDVLC YRLSLGQKLL
     RGTTKYRNLL ELMDEAVKKL EGDVGPLSGW AMKMARGIVN RLSSGVHVQK LCSQAMEALD
     KVVSPSESVS GQGDKMTVRV EEIQARSVTV RVDSEEPSSS TQNKITGFRL FCRKSKDEEC
     SSQGNCVVYL PETTSAIQGL EPDTEFCLRV VSFNEEGDLD ESELRFTTLK DDGDEAGDQQ
     SPLTNSSSGL CSNPSLPEDE SNNVNKSCSK GNGDKDNTEH CSAGEVESEL EEERLVKRKA
     NKIDGRDLLV TPCKRDIYKG KQGGNKRFKS RTVSLNEKPE INNAANGVGD KDLGHIVKTI
     RCLEEEGHID KSFRERFLTW YSLRATHREV RVVKIFVETF MEDLSSLGQQ LVDTFSESIL
     SKRSSTNGVV PAGICLKLWH
//
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