6WC5 | pdb_00006wc5

Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA 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)
A	SCOP2B Superfamily	SRF-like	8036692	3001928	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SRF-like	8036692	3001928	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SRF-like	8036692	3001928	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SRF-like	8036692	3001928	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Homeodomain-like	8071006	3000001	SCOP2B (2022-06-29)
J [auth N]	SCOP2B Superfamily	Homeodomain-like	8071006	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	Pro_isomerase	e6wc5A1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
B	Urm1	e6wc5B1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Urm1	ECOD (develop294)
C	Pro_isomerase	e6wc5C1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
D	Pro_isomerase	e6wc5D1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)
I	Urm1	e6wc5I1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Urm1	ECOD (develop294)
J [auth N]	Pro_isomerase	e6wc5N1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00319	SRF-type transcription factor (DNA-binding and dimerisation domain) (SRF-TF)	SRF-type transcription factor (DNA-binding and dimerisation domain)		Domain
I, J [auth N]	PF00046	Homeodomain (Homeodomain)	Homeodomain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Myocyte-specific enhancer factor 2B	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity histone deacetylase binding protein binding binding enzyme 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 DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity histone deacetylase binding protein binding binding enzyme 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 protein dimerization activity 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 muscle structure development muscle organ development 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 muscle structure development muscle organ development regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription 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 primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	cellular anatomical structure cell junction 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 cellular anatomical structure cell junction 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
E, G	Myocardin enhancer DNA	-	-	-
F, H	Myocardin enhancer DNA	-	-	-
I, J [auth N]	Homeobox protein Nkx-2.5	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding identical protein binding protein homodimerization activity protein dimerization activity	heart process multicellular organismal process system process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation heart process multicellular organismal process system process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation developmental process heart development multicellular organism development anatomical structure development animal organ development circulatory system development system development cardiac chamber morphogenesis heart morphogenesis ventricular septum development anatomical structure morphogenesis cardiac septum development cardiac septum morphogenesis ventricular septum morphogenesis cardiac chamber development animal organ morphogenesis cardiac ventricle development epithelium development embryonic heart tube left/right pattern formation tube development pattern specification process embryo development tissue development embryonic heart tube development regionalization embryonic organ development left/right pattern formation heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth striated muscle tissue development muscle cell proliferation cellular process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation regulation of biosynthetic process regulation of cellular process 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 cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process involved in heart morphogenesis apoptotic process involved in morphogenesis cell death apoptotic process involved in development apoptotic process programmed cell death cellular developmental process cell differentiation epithelial cell differentiation hemopoiesis cell development embryo development ending in birth or egg hatching pharyngeal system development chordate embryonic development outflow tract septum morphogenesis outflow tract morphogenesis immune system development spleen development immune system process hematopoietic or lymphoid organ development RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of striated muscle cell apoptotic process cardiac muscle cell development muscle cell differentiation cardiac pacemaker cell development muscle structure development striated muscle cell development muscle cell development atrioventricular node development atrioventricular node cell development cardiac cell development cardiac conduction system development atrioventricular node cell differentiation cardiac muscle cell differentiation cardiocyte differentiation striated muscle cell differentiation cardiac pacemaker cell differentiation cardiac septum cell differentiation Purkinje myocyte development ventricular cardiac muscle tissue development Purkinje myocyte differentiation His-Purkinje system development His-Purkinje system cell differentiation adult heart development negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic 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 negative regulation of RNA metabolic process positive regulation of blood circulation positive regulation of heart contraction positive regulation of multicellular organismal process 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 regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process tube morphogenesis embryonic heart tube morphogenesis heart looping determination of bilateral symmetry epithelial tube morphogenesis determination of left/right symmetry specification of symmetry embryonic organ morphogenesis embryonic morphogenesis morphogenesis of an epithelium determination of heart left/right asymmetry tissue morphogenesis ventricular cardiac muscle tissue morphogenesis ventricular trabecula myocardium morphogenesis muscle organ development muscle tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis heart trabecula morphogenesis trabecula morphogenesis muscle organ morphogenesis regulation of developmental process regulation of cell differentiation positive regulation of developmental process regulation of cardioblast differentiation positive regulation of cell differentiation positive regulation of cardiocyte differentiation regulation of stem cell differentiation positive regulation of cardioblast differentiation positive regulation of stem cell differentiation cardioblast differentiation stem cell differentiation regulation of cardiocyte differentiation bundle of His development cardiac muscle cell fate commitment muscle cell fate commitment cardiac cell fate commitment cardiac pacemaker cell fate commitment atrioventricular node cell fate commitment cell fate commitment cardiac atrium morphogenesis cardiac atrium development atrial septum morphogenesis atrial septum development thyroid gland development endocrine system development gland development atrial cardiac muscle cell differentiation atrial cardiac muscle cell development proepicardium development mesenchyme development septum transversum development positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation heart trabecula formation anatomical structure formation involved in morphogenesis trabecula formation negative regulation of muscle cell differentiation regulation of striated muscle cell differentiation myotube differentiation 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 regulation of cardiac muscle contraction cardiac muscle contraction muscle contraction muscle system process regulation of muscle system process striated muscle contraction regulation of striated muscle contraction regulation of muscle contraction septum secundum development heart valve development aortic valve development heart valve morphogenesis semi-lunar valve development aortic valve morphogenesis regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of transcription initiation by RNA polymerase II DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II ventricular cardiac muscle cell differentiation ventricular cardiac muscle cell development cellular component assembly involved in morphogenesis membraneless organelle assembly cellular component organization cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly actin filament-based process cellular component organization or biogenesis actomyosin structure organization actin cytoskeleton organization organelle assembly ventricular cardiac myofibril assembly myofibril assembly organelle organization cardiac myofibril assembly supramolecular fiber organization cytoskeleton organization venous blood vessel development pulmonary myocardium development vasculature development blood vessel development positive regulation of neuron differentiation neurogenesis neuron differentiation nervous system development generation of neurons regulation of neuron differentiation blood vessel morphogenesis vasculogenesis regulation of localization transport regulation of transport regulation of monoatomic ion transport regulation of sodium ion transport establishment of localization metal ion transport positive regulation of sodium ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport sodium ion transport atrial cardiac muscle tissue development regulation of growth regulation of cardiac muscle tissue growth regulation of organ growth regulation of heart growth regulation of cardiac muscle cell proliferation regulation of multicellular organismal development regulation of developmental growth cardiac ventricle formation cardiac chamber formation right ventricular cardiac muscle tissue morphogenesis cardiac right ventricle morphogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle Nkx-2.5 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR033896	MADS MEF2-like, N-terminal	Domain
A, B, C, D	IPR036879	Transcription factor, MADS-box superfamily	Homologous Superfamily
A, B, C, D	IPR002100	Transcription factor, MADS-box	Domain
I, J [auth N]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
I, J [auth N]	IPR020479	Homeodomain, metazoa	Domain
I, J [auth N]	IPR001356	Homeodomain	Domain
I, J [auth N]	IPR050394	Homeobox NK-like transcription regulators	Family
I, J [auth N]	IPR017970	Homeobox, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q02080	bipolar I disorder endogenous depression non-alcoholic fatty liver disease
I, J [auth N]	Pharos: P52952	tetralogy of fallot hypoplastic left heart syndrome hypothyroidism, congenital, nongoitrous, 5 atrial fibrillation atrial septal defect 7 congenital hypothyroidism conotruncal heart malformations double outlet right ventricle ventricular septal defect 3 hypoplastic left heart syndrome 2 ventricular septal defect familial atrial fibrillation Cardiomegaly dilated cardiomyopathy myotonic dystrophy type 1 tetralogy of fallot hypoplastic left heart syndrome hypothyroidism, congenital, nongoitrous, 5 atrial fibrillation atrial septal defect 7 congenital hypothyroidism conotruncal heart malformations double outlet right ventricle ventricular septal defect 3 hypoplastic left heart syndrome 2 ventricular septal defect familial atrial fibrillation Cardiomegaly dilated cardiomyopathy myotonic dystrophy type 1 aortic valve disease 1 atrial fibrillation, familial, 1 myotonic dystrophy osteosarcoma congenital myotonic dystrophy thyroid ectopia familial isolated congenital asplenia Holt-Oram syndrome aortic valve calcification athyreosis intellectual disability atrial septal defect progressive familial heart block, type 1A dilated cardiomyopathy 1A heart disease hypertrophic pyloric stenosis aortic valve disease hypothyroidism open-angle glaucoma cerebrovascular disorder right atrial isomerism

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.