1MDY

CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth A]	d1mdya_	All alpha proteins	HLH-like	HLH, helix-loop-helix DNA-binding domain	HLH, helix-loop-helix DNA-binding domain	Myod B/HLH domain	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth B]	d1mdyb_	All alpha proteins	HLH-like	HLH, helix-loop-helix DNA-binding domain	HLH, helix-loop-helix DNA-binding domain	Myod B/HLH domain	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth C]	d1mdyc_	All alpha proteins	HLH-like	HLH, helix-loop-helix DNA-binding domain	HLH, helix-loop-helix DNA-binding domain	Myod B/HLH domain	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth D]	d1mdyd_	All alpha proteins	HLH-like	HLH, helix-loop-helix DNA-binding domain	HLH, helix-loop-helix DNA-binding domain	Myod B/HLH domain	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2 Family	HLH helix-loop-helix DNA-binding domain	8024865	4000913	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	HLH helix-loop-helix DNA-binding domain	8037244	3001962	SCOP2 (2022-06-29)
F [auth B]	SCOP2B Superfamily	HLH helix-loop-helix DNA-binding domain	8037244	3001962	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	HLH helix-loop-helix DNA-binding domain	8037244	3001962	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	HLH helix-loop-helix DNA-binding domain	8037244	3001962	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)
E [auth A]	PF00010	e1mdyA1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: PF00010	ECOD (1.6)
F [auth B]	PF00010	e1mdyB1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: PF00010	ECOD (1.6)
G [auth C]	PF00010	e1mdyC1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: PF00010	ECOD (1.6)
H [auth D]	PF00010	e1mdyD1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: PF00010	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (4.3.0)
F [auth B]	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (4.3.0)
G [auth C]	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (4.3.0)
H [auth D]	4.10.280.10	Few Secondary Structures	Irregular	MYOD Basic-Helix-Loop-Helix Domain, subunit B	Helix-loop-helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A]	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain	-	Domain
E [auth A]	PF01586	Myogenic Basic domain (Basic)	Myogenic Basic domain	-	Family
F [auth B], G [auth C], H [auth D]	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain	-	Domain
F [auth B], G [auth C], H [auth D]	PF01586	Myogenic Basic domain (Basic)	Myogenic Basic domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth F], C [auth G], D [auth H]	DNA (5'-D(TPCPAPAPCPAPGPCPTPGPTPTPGPA)-3')	-	-	-
E [auth A]	PROTEIN (MYOD BHLH DOMAIN)	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding bHLH transcription factor binding DNA-binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding identical protein binding protein homodimerization activity protein dimerization activity chromatin DNA binding E-box binding nuclear receptor binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation cellular process myoblast differentiation positive regulation of cellular process myotube cell development cell development muscle cell differentiation myotube differentiation muscle cell development striated muscle cell differentiation regulation of biosynthetic process cellular biosynthetic process 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 organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process heart development multicellular organismal process cardiac muscle tissue development cardiac muscle cell differentiation animal organ development tissue development cardiocyte differentiation striated muscle tissue development circulatory system development multicellular organism development muscle tissue development system development muscle organ development skeletal muscle cell differentiation skeletal muscle tissue development skeletal muscle organ development cell fate determination myoblast fate determination cell fate commitment myoblast fate commitment cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation striated muscle adaptation system process muscle adaptation skeletal muscle adaptation skeletal muscle fiber adaptation muscle system process myoblast fusion cell-cell fusion syncytium formation by plasma membrane fusion anatomical structure morphogenesis anatomical structure formation involved in morphogenesis syncytium formation positive regulation of cellular component organization regulation of cellular component organization regulation of syncytium formation by plasma membrane fusion cellular component organization cellular component organization or biogenesis positive regulation of myoblast fusion regulation of myoblast fusion positive regulation of syncytium formation by plasma membrane fusion positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process skeletal muscle fiber development positive regulation of muscle cell differentiation regulation of muscle cell differentiation alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing RNA processing regulation of mRNA processing RNA splicing regulation of RNA splicing mRNA metabolic process RNA splicing, via transesterification reactions regulation of alternative mRNA splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process positive regulation of snRNA transcription by RNA polymerase II snRNA metabolic process snRNA transcription by RNA polymerase II snRNA transcription regulation of snRNA transcription by RNA polymerase II cellular response to chemical stimulus cellular response to oxygen levels response to chemical response to oxygen levels response to abiotic stimulus positive regulation of skeletal muscle tissue regeneration tissue regeneration regulation of growth skeletal muscle tissue regeneration regulation of response to external stimulus developmental growth regeneration regulation of multicellular organismal process positive regulation of developmental growth regulation of multicellular organismal development regulation of developmental growth growth response to external stimulus positive regulation of growth regulation of response to stimulus regulation of skeletal muscle tissue regeneration response to organic substance response to cytokine cellular response to tumor necrosis factor cellular response to cytokine stimulus cellular response to organic substance response to tumor necrosis factor regulation of muscle tissue development positive regulation of skeletal muscle tissue development regulation of striated muscle cell differentiation regulation of skeletal muscle tissue development regulation of cell development regulation of skeletal muscle fiber development positive regulation of skeletal muscle fiber development regulation of myotube differentiation positive regulation of striated muscle cell differentiation positive regulation of cell development positive regulation of muscle tissue development myotube differentiation involved in skeletal muscle regeneration response to lipid cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to lipid response to estradiol cellular response to estradiol stimulus response to organic cyclic compound myoblast proliferation negative regulation of cell population proliferation cell population proliferation negative regulation of biological process regulation of myoblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of myoblast proliferation response to endogenous stimulus response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus cellular response to endogenous stimulus response to corticosteroid response to hormone response to steroid hormone cellular response to steroid hormone stimulus cellular response to hormone stimulus	protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex euchromatin
F [auth B], G [auth C], H [auth D]	PROTEIN (MYOD BHLH DOMAIN)	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding bHLH transcription factor binding DNA-binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding identical protein binding protein homodimerization activity protein dimerization activity chromatin DNA binding E-box binding nuclear receptor binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation cellular process myoblast differentiation positive regulation of cellular process myotube cell development cell development muscle cell differentiation myotube differentiation muscle cell development striated muscle cell differentiation regulation of biosynthetic process cellular biosynthetic process 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 organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process heart development multicellular organismal process cardiac muscle tissue development cardiac muscle cell differentiation animal organ development tissue development cardiocyte differentiation striated muscle tissue development circulatory system development multicellular organism development muscle tissue development system development muscle organ development skeletal muscle cell differentiation skeletal muscle tissue development skeletal muscle organ development cell fate determination myoblast fate determination cell fate commitment myoblast fate commitment cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to starvation striated muscle adaptation system process muscle adaptation skeletal muscle adaptation skeletal muscle fiber adaptation muscle system process myoblast fusion cell-cell fusion syncytium formation by plasma membrane fusion anatomical structure morphogenesis anatomical structure formation involved in morphogenesis syncytium formation positive regulation of cellular component organization regulation of cellular component organization regulation of syncytium formation by plasma membrane fusion cellular component organization cellular component organization or biogenesis positive regulation of myoblast fusion regulation of myoblast fusion positive regulation of syncytium formation by plasma membrane fusion positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process skeletal muscle fiber development positive regulation of muscle cell differentiation regulation of muscle cell differentiation alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome mRNA processing RNA processing regulation of mRNA processing RNA splicing regulation of RNA splicing mRNA metabolic process RNA splicing, via transesterification reactions regulation of alternative mRNA splicing, via spliceosome mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process positive regulation of snRNA transcription by RNA polymerase II snRNA metabolic process snRNA transcription by RNA polymerase II snRNA transcription regulation of snRNA transcription by RNA polymerase II cellular response to chemical stimulus cellular response to oxygen levels response to chemical response to oxygen levels response to abiotic stimulus positive regulation of skeletal muscle tissue regeneration tissue regeneration regulation of growth skeletal muscle tissue regeneration regulation of response to external stimulus developmental growth regeneration regulation of multicellular organismal process positive regulation of developmental growth regulation of multicellular organismal development regulation of developmental growth growth response to external stimulus positive regulation of growth regulation of response to stimulus regulation of skeletal muscle tissue regeneration response to organic substance response to cytokine cellular response to tumor necrosis factor cellular response to cytokine stimulus cellular response to organic substance response to tumor necrosis factor regulation of muscle tissue development positive regulation of skeletal muscle tissue development regulation of striated muscle cell differentiation regulation of skeletal muscle tissue development regulation of cell development regulation of skeletal muscle fiber development positive regulation of skeletal muscle fiber development regulation of myotube differentiation positive regulation of striated muscle cell differentiation positive regulation of cell development positive regulation of muscle tissue development myotube differentiation involved in skeletal muscle regeneration response to lipid cellular response to organic cyclic compound response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to lipid response to estradiol cellular response to estradiol stimulus response to organic cyclic compound myoblast proliferation negative regulation of cell population proliferation cell population proliferation negative regulation of biological process regulation of myoblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of myoblast proliferation response to endogenous stimulus response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus cellular response to endogenous stimulus response to corticosteroid response to hormone response to steroid hormone cellular response to steroid hormone stimulus cellular response to hormone stimulus	protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A]	IPR022032	Myogenic determination factor 5	Domain
E [auth A]	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
E [auth A]	IPR002546	Myogenic muscle-specific protein, N-terminal	Domain
E [auth A]	IPR039704	Myogenic factor	Family
E [auth A]	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
F [auth B], G [auth C], H [auth D]	IPR022032	Myogenic determination factor 5	Domain
F [auth B], G [auth C], H [auth D]	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
F [auth B], G [auth C], H [auth D]	IPR002546	Myogenic muscle-specific protein, N-terminal	Domain
F [auth B], G [auth C], H [auth D]	IPR039704	Myogenic factor	Family
F [auth B], G [auth C], H [auth D]	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain

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 R01GM133198.