4A69

Structure of HDAC3 bound to corepressor and inositol tetraphosphate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d4a69c_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Myb/SANT domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4a69d_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Myb/SANT domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	HDAC-like	8088481	4000427	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8088482	3000260	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8088482	3000260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8057554	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8057554	3000001	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Hist_deacetyl	e4a69A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
B	Hist_deacetyl	e4a69B1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Hist_deacetyl	ECOD (1.6)
C	Myb_DNA-binding_4	e4a69C2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Myb_DNA-binding_4	ECOD (1.6)
D	Myb_DNA-binding_4	e4a69D1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Myb_DNA-binding_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
B	3.40.800.20	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
C	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
D	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00850	Histone deacetylase domain (Hist_deacetyl)	Histone deacetylase domain	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...	Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].	Domain
C, D	PF00249	Myb-like DNA-binding domain (Myb_DNA-binding)	Myb-like DNA-binding domain	This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HISTONE DEACETYLASE 3,	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity catalytic activity histone deacetylase activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding NF-kappaB binding histone deacetylase binding enzyme binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity catalytic activity histone deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides histone modifying activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds transcription coregulator binding transcription corepressor binding chromatin binding protein de-2-hydroxyisobutyrylase activity cyclin binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein decrotonylase activity histone decrotonylase activity DNA binding organic cyclic compound binding nucleic acid binding chromatin DNA binding	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process negative regulation of muscle cell differentiation regulation of cell differentiation regulation of striated muscle cell differentiation regulation of cardiac muscle cell differentiation muscle cell differentiation striated muscle tissue development muscle structure development multicellular organism development cell differentiation negative regulation of cardiac muscle cell differentiation multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process negative regulation of muscle cell differentiation regulation of cell differentiation regulation of striated muscle cell differentiation regulation of cardiac muscle cell differentiation muscle cell differentiation striated muscle tissue development muscle structure development multicellular organism development cell differentiation negative regulation of cardiac muscle cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation regulation of multicellular organismal process muscle tissue development negative regulation of cardiocyte differentiation system development developmental process heart development regulation of biological process cardiac muscle tissue development negative regulation of developmental process negative regulation of striated muscle cell differentiation biological regulation animal organ development cardiac muscle cell differentiation tissue development cardiocyte differentiation circulatory system development regulation of muscle cell differentiation regulation of cardiocyte differentiation cellular process striated muscle cell differentiation negative regulation of multicellular organismal process establishment of skin barrier epithelium development skin development skin epidermis development epidermis development cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus cellular component organization cellular response to stress DNA damage response chromatin organization response to stress chromatin remodeling cellular component organization or biogenesis positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of signaling cellular biosynthetic process regulation of biosynthetic process epigenetic regulation of gene expression cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process protein localization regulation of localization cellular localization establishment of protein localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization establishment of localization in cell protein import into nucleus positive regulation of intracellular transport regulation of intracellular transport regulation of transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization positive regulation of transport establishment of protein localization to organelle regulation of cellular localization protein transport macromolecule localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport rhythmic process circadian regulation of gene expression circadian rhythm embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development regulation of multicellular organism growth regulation of growth regulation of developmental growth developmental growth growth multicellular organism growth regulation of protein stability regulation of biological quality establishment of organelle localization microtubule cytoskeleton organization spindle localization establishment or maintenance of cell polarity mitotic cell cycle establishment of mitotic spindle localization establishment of spindle localization establishment of spindle orientation organelle localization cell cycle microtubule cytoskeleton organization involved in mitosis cell cycle process establishment of cell polarity organelle organization mitotic cell cycle process establishment of mitotic spindle orientation microtubule-based process cytoskeleton organization response to fluid shear stress cellular response to fluid shear stress protein deacylation macromolecule modification primary metabolic process protein metabolic process macromolecule deacylation protein modification process protein deacetylation membrane organization cornified envelope assembly membrane biogenesis membrane assembly cellular component biogenesis cellular component assembly plasma membrane organization endomembrane system organization RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of mitotic cell cycle regulation of cell cycle regulation of circadian rhythm negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication negative regulation of JNK cascade JNK cascade intracellular signaling cassette negative regulation of response to stimulus regulation of JNK cascade regulation of MAPK cascade negative regulation of signal transduction MAPK cascade negative regulation of MAPK cascade organelle assembly non-membrane-bounded organelle assembly spindle assembly chromosome segregation spindle organization homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of phosphate metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of phosphorus metabolic process regulation of phosphorylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane mitotic spindle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane mitotic spindle cytoskeleton spindle intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex catalytic complex nuclear protein-containing complex histone deacetylase complex transcription regulator complex transcription repressor complex
C, D	NUCLEAR RECEPTOR COREPRESSOR 2	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding signaling receptor binding Notch binding histone deacetylase binding enzyme binding chromatin binding DNA binding organic cyclic compound binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding signaling receptor binding Notch binding histone deacetylase binding enzyme binding chromatin binding DNA binding organic cyclic compound binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity nuclear retinoic acid receptor binding nuclear retinoid X receptor binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development negative regulation of miRNA transcription regulation of miRNA metabolic process miRNA metabolic process miRNA transcription negative regulation of miRNA metabolic process regulation of miRNA transcription regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation regulation of biological quality cellular response to stimulus intracellular receptor signaling pathway response to stimulus response to lipid signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction hormone-mediated signaling pathway intracellular signal transduction negative regulation of cell communication cell communication negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway signal transduction androgen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus response to organic cyclic compound steroid hormone receptor signaling pathway cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus response to endogenous stimulus cellular response to organic cyclic compound negative regulation of signal transduction regulation of androgen receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus response to chemical cellular response to lipid negative regulation of androgen receptor signaling pathway regulation of cell communication nuclear receptor-mediated signaling pathway transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II response to estradiol response to oxygen-containing compound regulation of cellular ketone metabolic process cellular ketone metabolic process regulation of small molecule metabolic process small molecule metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix membrane nucleoplasm intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle protein-containing complex transcription regulator complex transcription repressor complex nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000286	Histone deacetylase family	Family
A, B	IPR023801	Histone deacetylase domain	Domain
A, B	IPR003084	Histone deacetylase	Family
A, B	IPR050284	Histone deacetylase and polyamine deacetylase	Family
A, B	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A, B	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
C, D	IPR017930	Myb domain	Domain
C, D	IPR051571	Nuclear receptor corepressor	Family
C, D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C, D	IPR031557	N-CoR, GPS2-interacting domain	Domain
C, D	IPR017884	SANT domain	Domain
C, D	IPR001005	SANT/Myb domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O15379	heart disease acute T cell leukemia malignant mesothelioma primary cutaneous T-cell lymphoma adult T-cell leukemia/lymphoma mature T-cell and NK-cell non-Hodgkin lymphoma schizophrenia plasma cell myeloma
C, D	Pharos: Q9Y618	Liver Cirrhosis, Experimental astrocytic tumor hypertensive disorder mature T-cell and NK-cell non-Hodgkin lymphoma ovarian cancer psoriasis bipolar disorder juvenile dermatomyositis myocardial infarction pancreatic ductal adenocarcinoma heart disease osteoarthritis primary cutaneous T-cell lymphoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.