2QL2

Crystal Structure of the basic-helix-loop-helix domains of the heterodimer E47/NeuroD1 bound to DNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	HLH, helix-loop-helix DNA-binding domain	8076579	4000913	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HLH, helix-loop-helix DNA-binding domain	8076580	3001962	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8076580	3001962	SCOP2B (2022-06-29)
B	SCOP2 Family	HLH, helix-loop-helix DNA-binding domain	8076575	4000913	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	HLH, helix-loop-helix DNA-binding domain	8076576	3001962	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	HLH, helix-loop-helix DNA-binding domain	8076576	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)
A	HLH	e2ql2A1	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: HLH	ECOD (1.6)
C	HLH	e2ql2C1	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: HLH	ECOD (1.6)
B	HLH	e2ql2B1	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: HLH	ECOD (1.6)
D	HLH	e2ql2D1	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: HLH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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
A, C	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain	-	Domain
B, D	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Transcription factor E2-alpha	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid 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 DNA-binding transcription activator activity, RNA polymerase II-specific sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid 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 DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding protein binding bHLH transcription factor binding DNA-binding transcription factor binding identical protein 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 chromatin binding protein heterodimerization activity protein dimerization activity protein homodimerization activity E-box binding	response to stimulus response to chemical response to xenobiotic stimulus regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development response to stimulus response to chemical response to xenobiotic stimulus regulation of protein stability biological regulation regulation of biological quality protein stabilization developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development B cell lineage commitment mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process cell fate commitment leukocyte differentiation regulation of biosynthetic process regulation of biological 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 positive regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function 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 molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription T cell differentiation in thymus T cell activation T cell differentiation multicellular organism development nervous system development system development homeostatic process erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis positive regulation of cell population proliferation positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation leukocyte proliferation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation positive regulation of multicellular organismal process regulation of lymphocyte activation natural killer cell activation natural killer cell differentiation positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell cycle regulation of cell cycle positive regulation of cell cycle anatomical structure morphogenesis embryonic morphogenesis embryo development gastrulation regulation of developmental process regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process neurogenesis neuron differentiation positive regulation of cell differentiation generation of neurons regulation of neuron differentiation regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition immune system development immunoglobulin production somatic cell DNA recombination V(D)J recombination somatic recombination of immunoglobulin gene segments somatic diversification of immune receptors production of molecular mediator of immune response DNA recombination DNA metabolic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus animal organ development hematopoietic or lymphoid organ development tissue development Peyer's patch development mucosa-associated lymphoid tissue development biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle protein-DNA complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome membraneless organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, D	Neurogenic differentiation factor 1	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding 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 organic cyclic compound binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding 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 organic cyclic compound 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 E-box 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	developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development hindbrain development system development embryonic organ morphogenesis embryonic morphogenesis embryo development developmental process multicellular organismal process head development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development hindbrain development system development embryonic organ morphogenesis embryonic morphogenesis embryo development anatomical structure morphogenesis animal organ morphogenesis embryonic organ development sensory organ development eye development visual system development camera-type eye development sensory system development 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 transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process ear development inner ear development cellular response to stimulus response to stimulus homeostatic process response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis response to monosaccharide response to carbohydrate chemical homeostasis response to glucose response to chemical glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport establishment of localization positive regulation of DNA-binding transcription factor activity regulation of cellular process regulation of primary metabolic process positive regulation of molecular function regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of molecular function regulation of gene expression regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process epithelium development cellular developmental process tissue development epithelial cell differentiation glandular epithelial cell differentiation cell differentiation enteroendocrine cell differentiation columnar/cuboidal epithelial cell differentiation system process epithelial structure maintenance digestive system process regulation of system process intestinal epithelial structure maintenance tissue homeostasis regulation of digestive system process maintenance of gastrointestinal epithelium digestion regulation of intestinal epithelial structure maintenance multicellular organismal-level homeostasis anatomical structure homeostasis regulation of multicellular organismal process cerebellum development metencephalon development regulation of developmental process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell surface receptor signaling pathway via STAT signaling negative regulation of signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of cellular process regulation of receptor signaling pathway via JAK-STAT signal transduction negative regulation of receptor signaling pathway via JAK-STAT regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication negative regulation of receptor signaling pathway via STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT pancreas development endocrine system development endocrine pancreas development positive regulation of neuron differentiation neurogenesis neuron differentiation generation of neurons regulation of neuron differentiation regulation of epithelial cell apoptotic process negative regulation of programmed cell death regulation of type B pancreatic cell apoptotic process epithelial cell apoptotic process type B pancreatic cell apoptotic process negative regulation of type B pancreatic cell apoptotic process negative regulation of apoptotic process negative regulation of epithelial cell apoptotic process signal transduction involved in regulation of gene expression cell fate commitment positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process forebrain development dentate gyrus development pallium development telencephalon development hippocampus development limbic system development epithelial cell fate commitment pancreatic A cell fate commitment pancreatic A cell differentiation retina development in camera-type eye neural retina development amacrine cell differentiation regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II anterior/posterior pattern specification pattern specification process regionalization protein localization establishment of protein localization nitrogen compound transport hormone secretion protein localization to extracellular region peptide secretion secretion by cell amide transport signal release cellular macromolecule localization regulation of biological quality secretion regulation of hormone levels establishment of protein localization to extracellular region cell-cell signaling export from cell protein secretion peptide transport protein transport peptide hormone secretion macromolecule localization hormone transport insulin secretion pancreatic PP cell differentiation pancreatic PP cell fate commitment	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm
F, H	DNA (5'-D(DAPDGPDGPDAPDCPDCPDAPDGPDAPDTPDGPDGPDCPDCPDTPDA)-3')	-	-	-
E, G	DNA (5'-D(DTPDAPDGPDGPDCPDCPDAPDTPDCPDTPDGPDGPDTPDCPDCPDT)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR051098	Neuronal Differentiation E-box Binding Transcription Factors	Family
A, C	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A, C	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B, D	IPR016637	Neurogenic differentiation factor NeuroD	Family
B, D	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B, D	IPR022575	Neurogenic differentiation factor, domain of unknown function	Domain
B, D	IPR050359	Basic helix-loop-helix transcription factors	Family
B, D	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily

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.