ID COE3_HUMAN Reviewed; 596 AA.
AC Q9H4W6; A0AUY1; Q5T6H9; Q9H4W5;
DT 04-MAY-2001, integrated into UniProtKB/Swiss-Prot.
DT 04-MAY-2001, sequence version 2.
DT 27-MAR-2024, entry version 182.
DE RecName: Full=Transcription factor COE3;
DE AltName: Full=Early B-cell factor 3;
DE Short=EBF-3;
DE AltName: Full=Olf-1/EBF-like 2;
DE Short=O/E-2;
DE Short=OE-2;
GN Name=EBF3; Synonyms=COE3;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (ISOFORMS LONG AND SHORT).
RX PubMed=15164054; DOI=10.1038/nature02462;
RA Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L.,
RA Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K.,
RA Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L.,
RA Taylor A., Battles J., Bird C.P., Ainscough R., Almeida J.P.,
RA Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J.,
RA Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N.,
RA Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A.,
RA Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C.,
RA Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D.,
RA Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C.,
RA Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K.,
RA Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A.,
RA Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S.,
RA McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S.,
RA Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V.,
RA Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A.,
RA Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M.,
RA Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A.,
RA Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P.,
RA Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y.,
RA Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D.,
RA Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.;
RT "The DNA sequence and comparative analysis of human chromosome 10.";
RL Nature 429:375-381(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM SHORT).
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP TISSUE SPECIFICITY.
RX PubMed=12355068; DOI=10.1038/ng1007;
RA Zardo G., Tiirikainen M.I., Hong C., Misra A., Feuerstein B.G., Volik S.,
RA Collins C.C., Lamborn K.R., Bollen A., Pinkel D., Albertson D.G.,
RA Costello J.F.;
RT "Integrated genomic and epigenomic analyses pinpoint biallelic gene
RT inactivation in tumors.";
RL Nat. Genet. 32:453-458(2002).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 261-415.
RX PubMed=20592035; DOI=10.1074/jbc.c110.150482;
RA Siponen M.I., Wisniewska M., Lehtio L., Johansson I., Svensson L.,
RA Raszewski G., Nilsson L., Sigvardsson M., Berglund H.;
RT "Structural determination of functional domains in early B-cell factor
RT (EBF) family of transcription factors reveals similarities to Rel DNA-
RT binding proteins and a novel dimerization motif.";
RL J. Biol. Chem. 285:25875-25879(2010).
RN [6]
RP VARIANTS HADDS ASP-66; CYS-141; HIS-GLU-ILE-159 INS; ASP-171; LEU-177 AND
RP TRP-209, CHARACTERIZATION OF VARIANTS HADDS ASP-66; CYS-141;
RP HIS-GLU-ILE-159 INS; ASP-171; LEU-177 AND TRP-209, INVOLVEMENT IN HADDS,
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=28017373; DOI=10.1016/j.ajhg.2016.11.012;
RA Harms F.L., Girisha K.M., Hardigan A.A., Kortuem F., Shukla A., Alawi M.,
RA Dalal A., Brady L., Tarnopolsky M., Bird L.M., Ceulemans S., Bebin M.,
RA Bowling K.M., Hiatt S.M., Lose E.J., Primiano M., Chung W.K., Juusola J.,
RA Akdemir Z.C., Bainbridge M., Charng W.L., Drummond-Borg M., Eldomery M.K.,
RA El-Hattab A.W., Saleh M.A., Bezieau S., Cogne B., Isidor B., Kuery S.,
RA Lupski J.R., Myers R.M., Cooper G.M., Kutsche K.;
RT "Mutations in EBF3 disturb transcriptional profiles and cause intellectual
RT disability, ataxia, and facial dysmorphism.";
RL Am. J. Hum. Genet. 100:117-127(2017).
RN [7]
RP VARIANTS HADDS GLN-163 AND LEU-163, CHARACTERIZATION OF VARIANTS HADDS
RP GLN-163 AND LEU-163, AND FUNCTION.
RX PubMed=28017372; DOI=10.1016/j.ajhg.2016.11.018;
RA Chao H.T., Davids M., Burke E., Pappas J.G., Rosenfeld J.A., McCarty A.J.,
RA Davis T., Wolfe L., Toro C., Tifft C., Xia F., Stong N., Johnson T.K.,
RA Warr C.G., Yamamoto S., Adams D.R., Markello T.C., Gahl W.A., Bellen H.J.,
RA Wangler M.F., Malicdan M.C.;
RT "A syndromic neurodevelopmental disorder caused by de novo variants in
RT EBF3.";
RL Am. J. Hum. Genet. 100:128-137(2017).
RN [8]
RP VARIANTS HADDS PRO-163; LEU-177 AND ASN-193, CHARACTERIZATION OF VARIANTS
RP HADDS PRO-163; LEU-177 AND ASN-193, AND FUNCTION.
RX PubMed=28017370; DOI=10.1016/j.ajhg.2016.11.020;
RA Sleven H., Welsh S.J., Yu J., Churchill M.E., Wright C.F., Henderson A.,
RA Horvath R., Rankin J., Vogt J., Magee A., McConnell V., Green A.,
RA King M.D., Cox H., Armstrong L., Lehman A., Nelson T.N., Williams J.,
RA Clouston P., Hagman J., Nemeth A.H.;
RT "De novo mutations in EBF3 cause a neurodevelopmental syndrome.";
RL Am. J. Hum. Genet. 100:138-150(2017).
CC -!- FUNCTION: Transcriptional activator (PubMed:28017373, PubMed:28017372,
CC PubMed:28017370). Recognizes variations of the palindromic sequence 5'-
CC ATTCCCNNGGGAATT-3' (By similarity). {ECO:0000250|UniProtKB:Q07802,
CC ECO:0000269|PubMed:28017370, ECO:0000269|PubMed:28017372,
CC ECO:0000269|PubMed:28017373}.
CC -!- SUBUNIT: Forms either a homodimer or a heterodimer with a related
CC family member. {ECO:0000250|UniProtKB:O08791}.
CC -!- INTERACTION:
CC Q9H4W6-2; Q8N5M1: ATPAF2; NbExp=3; IntAct=EBI-17233744, EBI-1166928;
CC Q9H4W6-2; Q9HAK2: EBF2; NbExp=3; IntAct=EBI-17233744, EBI-12267154;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:28017373}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=Long;
CC IsoId=Q9H4W6-1; Sequence=Displayed;
CC Name=Short;
CC IsoId=Q9H4W6-2; Sequence=VSP_001113, VSP_001114;
CC -!- TISSUE SPECIFICITY: Expressed in brain. {ECO:0000269|PubMed:12355068}.
CC -!- DISEASE: Hypotonia, ataxia, and delayed development syndrome (HADDS)
CC [MIM:617330]: An autosomal dominant neurodevelopmental syndrome
CC characterized by global developmental delay, moderate to severe
CC intellectual disability, cerebellar ataxia, hypotonia, speech delay,
CC variable dysmorphic features, and genitourinary abnormalities including
CC vesicoureteric reflux. {ECO:0000269|PubMed:28017370,
CC ECO:0000269|PubMed:28017372, ECO:0000269|PubMed:28017373}. Note=The
CC disease is caused by variants affecting the gene represented in this
CC entry.
CC -!- SIMILARITY: Belongs to the COE family. {ECO:0000305}.
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DR EMBL; AL354950; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471066; EAW49160.1; -; Genomic_DNA.
DR EMBL; BC126130; AAI26131.1; -; mRNA.
DR EMBL; BC130479; AAI30480.1; -; mRNA.
DR CCDS; CCDS31314.1; -. [Q9H4W6-2]
DR CCDS; CCDS91376.1; -. [Q9H4W6-1]
DR RefSeq; NP_001005463.1; NM_001005463.2. [Q9H4W6-2]
DR RefSeq; XP_005252725.1; XM_005252668.3.
DR PDB; 3MUJ; X-ray; 1.92 A; A/B=261-395.
DR PDB; 3N50; X-ray; 3.10 A; A/B/C/D/E/F=261-415.
DR PDBsum; 3MUJ; -.
DR PDBsum; 3N50; -.
DR AlphaFoldDB; Q9H4W6; -.
DR SMR; Q9H4W6; -.
DR BioGRID; 128985; 18.
DR IntAct; Q9H4W6; 8.
DR MINT; Q9H4W6; -.
DR STRING; 9606.ENSP00000357637; -.
DR iPTMnet; Q9H4W6; -.
DR PhosphoSitePlus; Q9H4W6; -.
DR BioMuta; EBF3; -.
DR DMDM; 13959320; -.
DR EPD; Q9H4W6; -.
DR MassIVE; Q9H4W6; -.
DR MaxQB; Q9H4W6; -.
DR PaxDb; 9606-ENSP00000357637; -.
DR PeptideAtlas; Q9H4W6; -.
DR ProteomicsDB; 80876; -. [Q9H4W6-1]
DR ProteomicsDB; 80877; -. [Q9H4W6-2]
DR Pumba; Q9H4W6; -.
DR Antibodypedia; 32510; 214 antibodies from 30 providers.
DR DNASU; 253738; -.
DR Ensembl; ENST00000355311.10; ENSP00000347463.4; ENSG00000108001.16. [Q9H4W6-1]
DR Ensembl; ENST00000368648.8; ENSP00000357637.3; ENSG00000108001.16. [Q9H4W6-2]
DR GeneID; 253738; -.
DR KEGG; hsa:253738; -.
DR UCSC; uc001lki.3; human. [Q9H4W6-1]
DR AGR; HGNC:19087; -.
DR DisGeNET; 253738; -.
DR GeneCards; EBF3; -.
DR GeneReviews; EBF3; -.
DR HGNC; HGNC:19087; EBF3.
DR HPA; ENSG00000108001; Tissue enhanced (adipose).
DR MalaCards; EBF3; -.
DR MIM; 607407; gene.
DR MIM; 617330; phenotype.
DR neXtProt; NX_Q9H4W6; -.
DR OpenTargets; ENSG00000108001; -.
DR PharmGKB; PA134972607; -.
DR VEuPathDB; HostDB:ENSG00000108001; -.
DR eggNOG; KOG3836; Eukaryota.
DR GeneTree; ENSGT00950000182859; -.
DR HOGENOM; CLU_016320_3_1_1; -.
DR InParanoid; Q9H4W6; -.
DR OrthoDB; 3641706at2759; -.
DR PhylomeDB; Q9H4W6; -.
DR TreeFam; TF313391; -.
DR PathwayCommons; Q9H4W6; -.
DR SignaLink; Q9H4W6; -.
DR SIGNOR; Q9H4W6; -.
DR BioGRID-ORCS; 253738; 15 hits in 1172 CRISPR screens.
DR ChiTaRS; EBF3; human.
DR EvolutionaryTrace; Q9H4W6; -.
DR GenomeRNAi; 253738; -.
DR Pharos; Q9H4W6; Tbio.
DR PRO; PR:Q9H4W6; -.
DR Proteomes; UP000005640; Chromosome 10.
DR RNAct; Q9H4W6; Protein.
DR Bgee; ENSG00000108001; Expressed in tibialis anterior and 136 other cell types or tissues.
DR ExpressionAtlas; Q9H4W6; baseline and differential.
DR Genevisible; Q9H4W6; HS.
DR GO; GO:0000785; C:chromatin; ISA:NTNU_SB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; ISA:NTNU_SB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0045893; P:positive regulation of DNA-templated transcription; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd11606; COE_DBD; 1.
DR CDD; cd01175; IPT_COE; 1.
DR Gene3D; 1.10.287.4280; -; 1.
DR Gene3D; 2.60.40.10; Immunoglobulins; 1.
DR Gene3D; 2.60.40.3180; Transcription factor COE1, DNA-binding domain; 1.
DR InterPro; IPR032200; COE_DBD.
DR InterPro; IPR038173; COE_DBD_sf.
DR InterPro; IPR032201; COE_HLH.
DR InterPro; IPR038006; COE_IPT.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR014756; Ig_E-set.
DR InterPro; IPR002909; IPT_dom.
DR InterPro; IPR003523; Transcription_factor_COE.
DR InterPro; IPR018350; Transcription_factor_COE_CS.
DR PANTHER; PTHR10747; TRANSCRIPTION FACTOR COE FAMILY MEMBER; 1.
DR PANTHER; PTHR10747:SF4; TRANSCRIPTION FACTOR COE3; 1.
DR Pfam; PF16422; COE1_DBD; 1.
DR Pfam; PF16423; COE1_HLH; 1.
DR Pfam; PF01833; TIG; 1.
DR SMART; SM00429; IPT; 1.
DR SUPFAM; SSF81296; E set domains; 1.
DR PROSITE; PS01345; COE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; Alternative splicing; Developmental protein;
KW Disease variant; DNA-binding; Intellectual disability; Metal-binding;
KW Nucleus; Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..596
FT /note="Transcription factor COE3"
FT /id="PRO_0000107832"
FT DOMAIN 263..346
FT /note="IPT/TIG"
FT ZN_FING 151..170
FT /note="C5-type"
FT /evidence="ECO:0000255"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 63..66
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 197..204
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 236..239
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 451..483
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 163
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 172
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT VAR_SEQ 252..260
FT /note="Missing (in isoform Short)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_001113"
FT VAR_SEQ 521..558
FT /note="IVPSSPTMAASSVTLPSNCSSTHGIFSFSPANVISAVK -> MK (in
FT isoform Short)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_001114"
FT VARIANT 66
FT /note="N -> D (in HADDS; significant loss of
FT transcriptional activator activity; localizes both in the
FT cytoplasm and the nucleus; decreased chromatin binding;
FT dbSNP:rs1057519518)"
FT /evidence="ECO:0000269|PubMed:28017373"
FT /id="VAR_078033"
FT VARIANT 141
FT /note="Y -> C (in HADDS; significant loss of
FT transcriptional activator activity; localizes both in the
FT cytoplasm and the nucleus; decreased chromatin-binding;
FT dbSNP:rs1057519519)"
FT /evidence="ECO:0000269|PubMed:28017373"
FT /id="VAR_078034"
FT VARIANT 159
FT /note="I -> IHEI (in HADDS; significant loss of
FT transcriptional activator activity; localizes both in the
FT cytoplasm and the nucleus; decreased chromatin-binding)"
FT /evidence="ECO:0000269|PubMed:28017373"
FT /id="VAR_078035"
FT VARIANT 163
FT /note="R -> L (in HADDS; partial loss of transcriptional
FT activator activity; dbSNP:rs1057519389)"
FT /evidence="ECO:0000269|PubMed:28017372"
FT /id="VAR_078036"
FT VARIANT 163
FT /note="R -> P (in HADDS; loss of transcriptional activator
FT activity; dbSNP:rs1057519389)"
FT /evidence="ECO:0000269|PubMed:28017370"
FT /id="VAR_078037"
FT VARIANT 163
FT /note="R -> Q (in HADDS; loss of transcriptional activator
FT activity; dbSNP:rs1057519389)"
FT /evidence="ECO:0000269|PubMed:28017372"
FT /id="VAR_078038"
FT VARIANT 171
FT /note="G -> D (in HADDS; significant loss of
FT transcriptional activator activity; localizes both in the
FT cytoplasm and the nucleus; decreased chromatin-binding;
FT dbSNP:rs1057519437)"
FT /evidence="ECO:0000269|PubMed:28017373"
FT /id="VAR_078039"
FT VARIANT 177
FT /note="P -> L (in HADDS; according to PubMed:28017373 shows
FT significant loss of transcriptional activator activity
FT while according to PubMed:28017370 shows partial loss of
FT transcriptional activator activity; localizes both in the
FT cytoplasm and the nucleus; decreased chromatin-binding;
FT dbSNP:rs869312668)"
FT /evidence="ECO:0000269|PubMed:28017370,
FT ECO:0000269|PubMed:28017373"
FT /id="VAR_078040"
FT VARIANT 193
FT /note="K -> N (in HADDS; significant loss of
FT transcriptional activator activity; dbSNP:rs1057519520)"
FT /evidence="ECO:0000269|PubMed:28017370"
FT /id="VAR_078041"
FT VARIANT 209
FT /note="R -> W (in HADDS; significant loss of
FT transcriptional activator activity; localizes both in the
FT cytoplasm and the nucleus; decreased chromatin-binding;
FT dbSNP:rs779003155)"
FT /evidence="ECO:0000269|PubMed:28017373"
FT /id="VAR_078042"
FT STRAND 264..274
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 280..287
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 293..296
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 299..301
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 310..314
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 322..330
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 333..335
FT /evidence="ECO:0007829|PDB:3MUJ"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:3N50"
FT STRAND 341..346
FT /evidence="ECO:0007829|PDB:3MUJ"
FT HELIX 353..363
FT /evidence="ECO:0007829|PDB:3MUJ"
FT HELIX 376..391
FT /evidence="ECO:0007829|PDB:3MUJ"
FT HELIX 396..412
FT /evidence="ECO:0007829|PDB:3N50"
SQ SEQUENCE 596 AA; 64864 MW; EE5C9D10CD3DED02 CRC64;
MFGIQENIPR GGTTMKEEPL GSGMNPVRSW MHTAGVVDAN TAAQSGVGLA RAHFEKQPPS
NLRKSNFFHF VLALYDRQGQ PVEIERTAFV DFVEKEKEPN NEKTNNGIHY KLQLLYSNGV
RTEQDLYVRL IDSMTKQAIV YEGQDKNPEM CRVLLTHEIM CSRCCDKKSC GNRNETPSDP
VIIDRFFLKF FLKCNQNCLK NAGNPRDMRR FQVVVSTTVN VDGHVLAVSD NMFVHNNSKH
GRRARRLDPS EGTAPSYLEN ATPCIKAISP SEGWTTGGAT VIIIGDNFFD GLQVVFGTML
VWSELITPHA IRVQTPPRHI PGVVEVTLSY KSKQFCKGAP GRFVYTALNE PTIDYGFQRL
QKVIPRHPGD PERLPKEVLL KRAADLVEAL YGMPHNNQEI ILKRAADIAE ALYSVPRNHN
QIPTLGNNPA HTGMMGVNSF SSQLAVNVSE TSQANDQVGY SRNTSSVSPR GYVPSSTPQQ
SNYNTVSTSM NGYGSGAMAS LGVPGSPGFL NGSSANSPYG IVPSSPTMAA SSVTLPSNCS
STHGIFSFSP ANVISAVKQK SAFAPVVRPQ ASPPPSCTSA NGNGLQAMSG LVVPPM
//
