7XUZ | pdb_00007xuz

Crystal structure of a HDAC4-MEF2A-DNA ternary complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	SRF-like	8035395	3001928	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	SRF-like	8035395	3001928	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	SRF-like	8035395	3001928	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	SRF-like	8035395	3001928	SCOP2B (2022-06-29)
F [auth A]	SCOP2B Superfamily	HDAC4 glutamine-rich domain-like	8106680	3002863	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	HDAC4 glutamine-rich domain-like	8106680	3002863	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)
B [auth C]	G-alpha	e7xuzC01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: G-alpha	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], C [auth D], G, H	PF00319	SRF-type transcription factor (DNA-binding and dimerisation domain) (SRF-TF)	SRF-type transcription factor (DNA-binding and dimerisation domain)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth F], J	DNA (5'-D(TPCPTPTPAPTPAPAPAPTPAPGP*T)-3')	-	-	-
D [auth E], I	DNA (5'-D(PAPCPTPAPTPTPTPAPTPAP*A)-3')	-	-	-
B [auth C], C [auth D], G, H	myocyte-specific enhancer factor 2A isoform X4	histone deacetylase binding protein binding binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding histone deacetylase binding protein binding binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding protein heterodimerization activity protein dimerization activity transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific kinase binding protein kinase binding SMAD binding histone acetyltransferase binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular developmental process cell differentiation cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development cellular developmental process cell differentiation cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process apoptotic process cell death programmed cell death muscle structure development muscle organ development cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cellular component organization or biogenesis plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development mitochondrion distribution localization mitochondrion localization organelle localization RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion ventricular cardiac muscle cell differentiation cardiac muscle cell development cellular component assembly involved in morphogenesis membraneless organelle assembly muscle cell differentiation striated muscle tissue development cellular component biogenesis striated muscle cell development cellular anatomical entity morphogenesis cellular component assembly muscle cell development actin filament-based process cardiac cell development muscle tissue development actomyosin structure organization actin cytoskeleton organization organelle assembly cardiac muscle tissue development ventricular cardiac myofibril assembly cardiac muscle cell differentiation tissue development cardiocyte differentiation ventricular cardiac muscle cell development myofibril assembly organelle organization cardiac myofibril assembly anatomical structure formation involved in morphogenesis striated muscle cell differentiation supramolecular fiber organization cytoskeleton organization heart process system process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation muscle hypertrophy regulation of muscle adaptation positive regulation of cardiac muscle hypertrophy striated muscle hypertrophy regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy regulation of muscle hypertrophy muscle adaptation regulation of response to stimulus positive regulation of muscle hypertrophy cardiac muscle hypertrophy positive regulation of multicellular organismal process negative regulation of biological process regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process regulation of localization import into cell hexose transmembrane transport regulation of D-glucose import across plasma membrane transport carbohydrate import across plasma membrane carbohydrate transport positive regulation of D-glucose transmembrane transport hexose import across plasma membrane positive regulation of transmembrane transport positive regulation of D-glucose import across plasma membrane regulation of transport import across plasma membrane establishment of localization transmembrane transport regulation of transmembrane transport D-glucose import across plasma membrane positive regulation of transport D-glucose transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome
A [auth B], F [auth A]	Histone deacetylase 4	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding histone deacetylase binding protein binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding histone deacetylase binding protein binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity aminoacyltransferase activity ubiquitin-like protein transferase activity acyltransferase activity SUMO transferase activity transferase activity molecular adaptor activity transition metal ion binding zinc ion binding histone deacetylase activity histone modifying activity identical protein binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity, hydrolytic mechanism	regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal regulation of protein sumoylation regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process peptidyl-amino acid modification positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein sumoylation macromolecule modification metabolic process cellular process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development leukocyte differentiation ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration negative regulation of small molecule metabolic process negative regulation of glycolytic process oxoacid metabolic process negative regulation of biological process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process negative regulation of ATP metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process negative regulation of carbohydrate metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process negative regulation of metabolic process negative regulation of purine nucleotide catabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process negative regulation of purine nucleotide metabolic process energy derivation by oxidation of organic compounds negative regulation of phosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process negative regulation of cellular process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process negative regulation of nucleotide catabolic process negative regulation of catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process negative regulation of phosphorus metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process regulation of biosynthetic process epigenetic regulation of gene expression gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis response to peptide response to stimulus response to chemical response to cytokine response to interleukin-1 negative regulation of macromolecule metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of developmental process negative regulation of muscle cell differentiation regulation of cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation myotube differentiation muscle structure development negative regulation of myotube differentiation regulation of myotube differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of striated muscle cell differentiation regulation of muscle cell differentiation striated muscle cell differentiation cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation multicellular organism development nervous system development system development protein refolding regulation of protein refolding protein maturation protein folding regulation of protein folding negative regulation of protein folding negative regulation of protein refolding positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription defense response response to stress inflammatory response negative regulation of RNA biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process regulation of muscle adaptation system process regulation of system process regulation of muscle system process muscle system process response to muscle inactivity muscle adaptation response to denervation involved in regulation of muscle adaptation regulation of response to stimulus response to inactivity regulation of multicellular organismal process positive regulation of transcription by RNA polymerase II muscle hypertrophy striated muscle adaptation striated muscle hypertrophy cardiac muscle adaptation cardiac muscle hypertrophy cardiac muscle hypertrophy in response to stress muscle hypertrophy in response to stress cellular response to stimulus biological process involved in interspecies interaction between organisms signaling cytokine-mediated signaling pathway response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon innate immune response cellular response to cytokine stimulus signal transduction response to external biotic stimulus cell surface receptor signaling pathway immune response response to other organism defense response to symbiont response to external stimulus defense response to other organism type I interferon-mediated signaling pathway response to type I interferon	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol chromatin chromosome protein-containing complex catalytic complex nuclear protein-containing complex histone deacetylase complex transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], C [auth D], G, H	IPR022102	Holliday junction regulator protein family C-terminal	Domain
B [auth C], C [auth D], G, H	IPR033896	MADS MEF2-like, N-terminal	Domain
B [auth C], C [auth D], G, H	IPR036879	Transcription factor, MADS-box superfamily	Homologous Superfamily
B [auth C], C [auth D], G, H	IPR002100	Transcription factor, MADS-box	Domain
A [auth B], F [auth A]	IPR023801	Histone deacetylase domain	Domain
A [auth B], F [auth A]	IPR000286	Histone deacetylase HDAC	Family
A [auth B], F [auth A]	IPR024643	Histone deacetylase, glutamine rich N-terminal domain	Domain
A [auth B], F [auth A]	IPR046949	Histone deacetylase 4/5/7/9	Family
A [auth B], F [auth A]	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], C [auth D], G, H	Pharos: Q02078	coronary artery disease, autosomal dominant, 1 atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma myopathy ovarian cancer primitive neuroectodermal tumor subependymal giant cell astrocytoma breast cancer large cell medulloblastoma malignant glioma Nonorganic psychosis pancreatic intraductal papillary-mucinous carcinoma lung cancer medulloblastoma coronary artery disease, autosomal dominant, 1 atypical teratoid rhabdoid tumor glioblastoma malignant ependymoma myopathy ovarian cancer primitive neuroectodermal tumor subependymal giant cell astrocytoma breast cancer large cell medulloblastoma malignant glioma Nonorganic psychosis pancreatic intraductal papillary-mucinous carcinoma lung cancer medulloblastoma oligodendroglioma plasma cell myeloma rheumatoid arthritis
A [auth B], F [auth A]	Pharos: P56524	2q37 microdeletion syndrome brachydactyly intellectual disability malignant mesothelioma urinary bladder cancer cocaine abuse contact dermatitis Familial Primary Pulmonary Hypertension cocaine dependence lung cancer medulloblastoma osteosarcoma primary cutaneous T-cell lymphoma chronic obstructive pulmonary disease schizophrenia 2q37 microdeletion syndrome brachydactyly intellectual disability malignant mesothelioma urinary bladder cancer cocaine abuse contact dermatitis Familial Primary Pulmonary Hypertension cocaine dependence lung cancer medulloblastoma osteosarcoma primary cutaneous T-cell lymphoma chronic obstructive pulmonary disease schizophrenia facioscapulohumeral muscular dystrophy glioblastoma invasive ductal breast carcinoma malignant ependymoma ovarian cancer amyotrophic lateral sclerosis brachydactyly type E1 subependymal giant cell astrocytoma urinary bladder neoplasm idiopathic pulmonary arterial hypertension large cell medulloblastoma malignant glioma mature T-cell and NK-cell non-Hodgkin lymphoma myopathy plasma cell myeloma atypical teratoid rhabdoid tumor psoriasis tuberculosis gastric carcinoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.