Annotations: 8Q9P

Crystal Structure of the MADS-box/MEF2 Domain of MEF2D bound to dsDNA and HDAC5 deacetylase binding motif

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth A]	DNA_topoisoIV	e8q9pA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: DNA_topoisoIV	ECOD (v295)
C [auth B]	DNA_topoisoIV	e8q9pB1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: DNA_topoisoIV	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C [auth B]	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
B [auth A], C [auth B]	MEF2D protein	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein binding binding protein dimerization activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding	developmental process animal organ development anatomical structure development animal gross anatomical part developmental process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process developmental process animal organ development anatomical structure development animal gross anatomical part developmental process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process multicellular organism development multicellular organismal process nervous system development system development regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
E [auth L]	MADS box dsNA rev:TCTTATAAATAGTT	-	-	-
D [auth K]	MADS box dsDNA fw: AACTATTTATAAGA	-	-	-
A [auth X]	HDAC5 (histone deacetylase 5) binding motif peptide: TRP-GLY-SER-GLY-GLU-VAL-LYS-LEU-ARG-LEU-GLN-GLU-PHE-LEU-LEU-SER-LYS-SER	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding histone deacetylase binding enzyme 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 transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding histone deacetylase binding enzyme 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 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 kinase binding protein kinase C binding protein kinase binding cation binding ion binding metal ion binding small molecule 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 cellular process negative regulation of biological process RNA 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 regulation of cellular process negative regulation of biological process RNA 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 negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic 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 response to stimulus response to chemical response to xenobiotic stimulus developmental process regulation of developmental process cellular developmental process regulation of cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation myotube differentiation muscle structure development regulation of muscle cell differentiation cell differentiation regulation of myotube differentiation anatomical structure development striated muscle cell differentiation animal gross anatomical part developmental process multicellular organismal process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation immune system process leukocyte differentiation response to activity epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation system development negative regulation of gene expression negative regulation of gene expression, epigenetic negative regulation of muscle cell differentiation negative regulation of myotube differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of striated muscle cell differentiation negative regulation of locomotion regulation of cell motility cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration angiogenesis negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration tube morphogenesis regulation of cell migration regulation of endothelial cell migration blood vessel endothelial cell migration cell migration cell motility locomotion negative regulation of cell migration blood vessel development blood vessel morphogenesis tube development regulation of cell migration involved in sprouting angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis regulation of locomotion anatomical structure formation involved in morphogenesis negative regulation of cell motility negative regulation of cell migration involved in sprouting angiogenesis defense response response to stress inflammatory response cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound cellular response to endogenous stimulus response to hormone response to insulin cellular response to insulin stimulus cellular response to hormone stimulus transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of biological 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 cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to cocaine response to alkaloid	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 protein-containing complex catalytic complex nuclear protein-containing complex histone deacetylase complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth X]	: Q9UQL6	cocaine abuse cocaine dependence Familial Primary Pulmonary Hypertension breast cancer glioblastoma malignant ependymoma mature T-cell and NK-cell non-Hodgkin lymphoma plasma cell myeloma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor depressive disorder idiopathic pulmonary arterial hypertension malignant glioma primary cutaneous T-cell lymphoma bipolar disorder cocaine abuse cocaine dependence Familial Primary Pulmonary Hypertension breast cancer glioblastoma malignant ependymoma mature T-cell and NK-cell non-Hodgkin lymphoma plasma cell myeloma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor depressive disorder idiopathic pulmonary arterial hypertension malignant glioma primary cutaneous T-cell lymphoma bipolar disorder major depressive disorder malignant mesothelioma neurotic disorder

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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.