SWI3D_ARATH
ID SWI3D_ARATH Reviewed; 985 AA.
AC Q8VY05; O65671; Q3E9R6; Q8GZ04; Q9SZ08;
DT 04-JAN-2005, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2008, sequence version 3.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=SWI/SNF complex subunit SWI3D;
DE Short=AtSWI3D;
DE AltName: Full=Transcription regulatory protein SWI3D;
GN Name=SWI3D; Synonyms=CHB3; OrderedLocusNames=At4g34430;
GN ORFNames=F10M10.200, T4L20.10;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP TISSUE SPECIFICITY.
RX PubMed=14682613; DOI=10.1023/b:plan.0000004305.60407.8b;
RA Zhou C., Miki B., Wu K.;
RT "CHB2, a member of the SWI3 gene family, is a global regulator in
RT Arabidopsis.";
RL Plant Mol. Biol. 52:1125-1134(2003).
RN [6]
RP DISRUPTION PHENOTYPE, AND INTERACTION WITH SWI3B AND BSH.
RX PubMed=16055636; DOI=10.1105/tpc.105.031203;
RA Sarnowski T.J., Rios G., Jasik J., Swiezewski S., Kaczanowski S., Li Y.,
RA Kwiatkowska A., Pawlikowska K., Kozbial M., Kozbial P., Koncz C.,
RA Jerzmanowski A.;
RT "SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play
RT distinct roles during Arabidopsis development.";
RL Plant Cell 17:2454-2472(2005).
RN [7]
RP SUBUNIT.
RX PubMed=24465213; DOI=10.1371/journal.pgen.1003948;
RA Liu Z.-W., Shao C.-R., Zhang C.-J., Zhou J.-X., Zhang S.-W., Li L.,
RA Chen S., Huang H.-W., Cai T., He X.-J.;
RT "The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy
RT at RNA-directed DNA methylation loci.";
RL PLoS Genet. 10:E1003948-E1003948(2014).
RN [8]
RP INTERACTION WITH MORC6 AND SUVH9.
RX PubMed=27171427; DOI=10.1371/journal.pgen.1006026;
RA Liu Z.-W., Zhou J.-X., Huang H.-W., Li Y.-Q., Shao C.-R., Li L., Cai T.,
RA Chen S., He X.-J.;
RT "Two components of the RNA-Directed DNA methylation pathway associate with
RT MORC6 and silence loci targeted by MORC6 in Arabidopsis.";
RL PLoS Genet. 12:E1006026-E1006026(2016).
CC -!- FUNCTION: Component of a multiprotein complex equivalent of the SWI/SNF
CC complex, an ATP-dependent chromatin-remodeling complex, which is
CC required for the positive and negative regulation of gene expression of
CC a large number of genes. It changes chromatin structure by altering
CC DNA-histone contacts within a nucleosome, leading eventually to a
CC change in nucleosome position, thus facilitating or repressing binding
CC of gene-specific transcription factors.
CC -!- SUBUNIT: Interacts with SWI3B, but not with BSH. Component of a RNA-
CC directed DNA methylation (RdDM) complex that contains at least MORC6,
CC MORC1/CRT1, MORC2, SWI3D and SUVH9 (PubMed:24465213). Interacts with
CC MORC6 and SUVH9 (PubMed:27171427). {ECO:0000269|PubMed:16055636,
CC ECO:0000269|PubMed:24465213, ECO:0000269|PubMed:27171427}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00624}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q8VY05-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8VY05-2; Sequence=VSP_012493;
CC Name=3;
CC IsoId=Q8VY05-3; Sequence=VSP_034846;
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed.
CC {ECO:0000269|PubMed:14682613}.
CC -!- DISRUPTION PHENOTYPE: Plants are viable but have alterations in leaf,
CC root and flower development, and are early flowering.
CC {ECO:0000269|PubMed:16055636}.
CC -!- CAUTION: Was originally incorrectly assigned as CHB4. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA18822.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB36720.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80160.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL023094; CAA18822.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL035521; CAB36720.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161585; CAB80160.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86373.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86374.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86375.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86376.1; -; Genomic_DNA.
DR EMBL; AK117284; BAC41956.1; -; mRNA.
DR EMBL; AY074306; AAL67003.1; -; mRNA.
DR EMBL; AY096454; AAM20094.1; -; mRNA.
DR PIR; T04789; T04789.
DR PIR; T05263; T05263.
DR RefSeq; NP_195169.3; NM_119608.3. [Q8VY05-2]
DR RefSeq; NP_849563.1; NM_179232.1. [Q8VY05-1]
DR RefSeq; NP_849564.1; NM_179233.2. [Q8VY05-1]
DR RefSeq; NP_974682.1; NM_202953.1. [Q8VY05-3]
DR AlphaFoldDB; Q8VY05; -.
DR SMR; Q8VY05; -.
DR BioGRID; 14876; 29.
DR IntAct; Q8VY05; 5.
DR STRING; 3702.AT4G34430.4; -.
DR iPTMnet; Q8VY05; -.
DR PaxDb; Q8VY05; -.
DR PRIDE; Q8VY05; -.
DR ProteomicsDB; 226538; -. [Q8VY05-1]
DR EnsemblPlants; AT4G34430.1; AT4G34430.1; AT4G34430. [Q8VY05-1]
DR EnsemblPlants; AT4G34430.2; AT4G34430.2; AT4G34430. [Q8VY05-1]
DR EnsemblPlants; AT4G34430.3; AT4G34430.3; AT4G34430. [Q8VY05-2]
DR EnsemblPlants; AT4G34430.4; AT4G34430.4; AT4G34430. [Q8VY05-3]
DR GeneID; 829594; -.
DR Gramene; AT4G34430.1; AT4G34430.1; AT4G34430. [Q8VY05-1]
DR Gramene; AT4G34430.2; AT4G34430.2; AT4G34430. [Q8VY05-1]
DR Gramene; AT4G34430.3; AT4G34430.3; AT4G34430. [Q8VY05-2]
DR Gramene; AT4G34430.4; AT4G34430.4; AT4G34430. [Q8VY05-3]
DR KEGG; ath:AT4G34430; -.
DR Araport; AT4G34430; -.
DR TAIR; locus:2116159; AT4G34430.
DR eggNOG; KOG1279; Eukaryota.
DR InParanoid; Q8VY05; -.
DR OMA; KGNTMET; -.
DR OrthoDB; 683891at2759; -.
DR PhylomeDB; Q8VY05; -.
DR PRO; PR:Q8VY05; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8VY05; baseline and differential.
DR Genevisible; Q8VY05; AT.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0060255; P:regulation of macromolecule metabolic process; IEA:UniProt.
DR GO; GO:0051171; P:regulation of nitrogen compound metabolic process; IEA:UniProt.
DR GO; GO:0080090; P:regulation of primary metabolic process; IEA:UniProt.
DR CDD; cd00167; SANT; 1.
DR CDD; cd02336; ZZ_RSC8; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.30.60.90; -; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017930; Myb_dom.
DR InterPro; IPR041984; Rsc8/Ssr1/Ssr2_ZZ.
DR InterPro; IPR001005; SANT/Myb.
DR InterPro; IPR017884; SANT_dom.
DR InterPro; IPR032451; SMARCC_C.
DR InterPro; IPR007526; SWIRM.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR000433; Znf_ZZ.
DR InterPro; IPR043145; Znf_ZZ_sf.
DR Pfam; PF00249; Myb_DNA-binding; 1.
DR Pfam; PF04433; SWIRM; 1.
DR Pfam; PF16495; SWIRM-assoc_1; 1.
DR Pfam; PF00569; ZZ; 1.
DR SMART; SM00717; SANT; 1.
DR SMART; SM00291; ZnF_ZZ; 1.
DR SUPFAM; SSF46689; SSF46689; 2.
DR PROSITE; PS51293; SANT; 1.
DR PROSITE; PS50934; SWIRM; 1.
DR PROSITE; PS01357; ZF_ZZ_1; 1.
DR PROSITE; PS50135; ZF_ZZ_2; 1.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Chromatin regulator; Coiled coil;
KW Developmental protein; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..985
FT /note="SWI/SNF complex subunit SWI3D"
FT /id="PRO_0000197119"
FT DOMAIN 145..242
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT DOMAIN 362..413
FT /note="SANT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00624"
FT ZN_FING 305..359
FT /note="ZZ-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT REGION 1..55
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 428..502
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 591..814
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 944..985
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 108..133
FT /evidence="ECO:0000255"
FT COILED 839..900
FT /evidence="ECO:0000255"
FT COMPBIAS 591..660
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 671..685
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 706..720
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 721..739
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 742..774
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 782..804
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 944..959
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 965..985
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 310
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 313
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 333
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 336
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT VAR_SEQ 605..606
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11910074"
FT /id="VSP_012493"
FT VAR_SEQ 867
FT /note="K -> KQ (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_034846"
FT CONFLICT 591
FT /note="E -> G (in Ref. 3; BAC41956)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 985 AA; 107797 MW; FDF941F23E23337A CRC64;
MEEKRRDSAG TLAFAGSSGD SPASEPMPAP RRRGGGLKRK ANALGGSNFF SSAPSKRMLT
REKAMLASFS PVHNGPLTRA RQAPSIMPSA ADGVKSEVLN VAVGADGEKP KEEEERNKAI
REWEALEAKI EADFEAIRSR DSNVHVVPNH CGWFSWEKIH PLEERSLPSF FNGKLEGRTS
EVYREIRNWI MGKFHSNPNI QIELKDLTEL EVGDSEAKQE VMEFLDYWGL INFHPFPPTD
TGSTASDHDD LGDKESLLNS LYRFQVDEAC PPLVHKPRFT AQATPSGLFP DPMAADELLK
QEGPAVEYHC NSCSADCSRK RYHCPKQADF DLCTECFNSG KFSSDMSSSD FILMEPAEAP
GVGSGKWTDQ ETLLLLEALE IFKENWNEIA EHVATKTKAQ CMLHFLQMPI EDAFLDQIDY
KDPISKDTTD LAVSKDDNSV LKDAPEEAEN KKRVDEDETM KEVPEPEDGN EEKVSQESSK
PGDASEETNE MEAEQKTPKL ETAIEERCKD EADENIALKA LTEAFEDVGH SSTPEASFSF
ADLGNPVMGL AAFLVRLAGS DVATASARAS IKSLHSNSGM LLATRHCYIL EDPPDNKKDP
TKSKSCSADA EGNDDNSHKD DQPEEKSKKA EEVSLNSDDR EMPDTDTGKE TQDSVSEEKQ
PGSRTENSTT KLDAVQEKRS SKPVTTDNSE KPVDIICPSQ DKCSGKELQE PLKDGNKLSS
ENKDASQSTV SQSAADASQP EASRDVEMKD TLQSEKDPED VVKTVGEKVQ LAKEEGANDV
LSTPDKSVSQ QPIGSASAPE NGTAGGNPNI EGKKEKDICE GTKDKYNIEK LKRAAISAIS
AAAVKAKNLA KQEEDQIRQL SGSLIEKQLH KLEAKLSIFN EAESLTMRVR EQLERSRQRL
YHERAQIIAA RLGVPPSMSS KASLPTNRIA ANFANVAQRP PMGMAFPRPP MPRPPGFPVP
GSFVAATTMT GSSDPSPGSD NVSSV
