4H10 | pdb_00004h10

Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic Helix-Loop-Helix domains with E-box 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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	HLH, helix-loop-helix DNA-binding domain	8073244	4000913	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	HLH, helix-loop-helix DNA-binding domain	8073245	3001962	SCOP2 (2022-06-29)
A	SCOP2 Family	HLH, helix-loop-helix DNA-binding domain	8073246	4000913	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HLH, helix-loop-helix DNA-binding domain	8073247	3001962	SCOP2 (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	HLH	e4h10B1	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)
A	HLH	e4h10A1	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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain		Domain
A	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
D	E-box DNA antisense strand	-	-	-
C	E-box DNA sense strand	-	-	-
B	Circadian locomoter output cycles protein kaput	sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein binding protein dimerization activity sequence-specific double-stranded DNA binding double-stranded DNA binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity protein-lysine-acetyltransferase activity sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein binding protein dimerization activity sequence-specific double-stranded DNA binding double-stranded DNA binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific 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 chromatin DNA binding E-box binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response response to redox state response to light stimulus photoperiodism response to radiation response to abiotic stimulus cellular response to stimulus response to ionizing radiation cellular response to ionizing radiation cellular process cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus regulation of biosynthetic process rhythmic process regulation of cellular process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process multicellular organismal process hair cycle molting cycle regulation of hair cycle regulation of multicellular organismal process regulation of localization establishment of protein localization nitrogen compound transport regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling hormone secretion protein localization to extracellular region cell communication localization peptide secretion regulation of secretion by cell secretion by cell amide transport signal release intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of signaling regulation of transport secretion regulation of hormone levels regulation of peptide transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell cell-cell signaling regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB 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 DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cellular response to stress negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling DNA damage response signal transduction in response to DNA damage negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of type B pancreatic cell development epithelial cell differentiation regulation of cell development multicellular organism development pancreas development cell differentiation anatomical structure development endocrine pancreas development type B pancreatic cell differentiation system development epithelium development endocrine system development animal organ development type B pancreatic cell development tissue development epithelial cell development enteroendocrine cell differentiation regulation of circadian rhythm intracellular receptor signaling pathway response to lipid negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction hormone-mediated signaling pathway negative regulation of cell communication cellular response to endogenous stimulus negative regulation of intracellular steroid hormone receptor signaling pathway response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus negative regulation of response to stimulus response to endogenous stimulus nuclear receptor-mediated corticosteroid signaling pathway negative regulation of signal transduction cellular response to chemical stimulus response to chemical cellular response to lipid negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated signaling pathway regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process positive regulation of circadian rhythm protein acetylation macromolecule modification protein modification process protein acylation 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 cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle intracellular membrane-bounded organelle chromatoid body cytoplasmic ribonucleoprotein granule cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle intracellular membrane-bounded organelle chromatoid body cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen RNA polymerase II transcription regulator complex protein-containing complex CLOCK-BMAL transcription complex nuclear protein-containing complex transcription regulator complex
A	Aryl hydrocarbon receptor nuclear translocator-like protein 1	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 protein binding protein dimerization 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 protein binding protein dimerization activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding signaling receptor binding DNA-binding transcription factor binding aryl hydrocarbon receptor binding Hsp90 protein binding heat shock protein binding transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity 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 E-box binding	cellular response to stimulus regulation of biological process regulation of cellular process regulation of cellular senescence cellular response to stress response to stimulus response to stress biological regulation cellular process cellular senescence developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular response to stimulus regulation of biological process regulation of cellular process regulation of cellular senescence cellular response to stress response to stimulus response to stress biological regulation cellular process cellular senescence developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular developmental process cell development regulation of neurogenesis regulation of cell differentiation nervous system development regulation of cell development regulation of nervous system development multicellular organism development neurogenesis cell differentiation anatomical structure development regulation of multicellular organismal process system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation response to redox state regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process hair cycle molting cycle regulation of hair cycle regulation of localization establishment of protein localization nitrogen compound transport regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling hormone secretion protein localization to extracellular region cell communication localization peptide secretion regulation of secretion by cell secretion by cell amide transport signal release intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of signaling regulation of transport secretion regulation of hormone levels regulation of peptide transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell cell-cell signaling regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion 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 signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication intracellular signal transduction negative regulation of TOR signaling regulation of intracellular signal transduction negative regulation of cellular process signal transduction TOR signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process protein acylation positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process protein modification process positive regulation of cellular process positive regulation of protein acetylation regulation of protein metabolic process regulation of protein acetylation protein acetylation macromolecule modification positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of type B pancreatic cell development epithelial cell differentiation pancreas development endocrine pancreas development type B pancreatic cell differentiation epithelium development endocrine system development animal organ development type B pancreatic cell development tissue development epithelial cell development enteroendocrine cell differentiation fat cell differentiation negative regulation of developmental process negative regulation of fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation cellular response to oxidative stress cellular response to chemical stress oxidative stress-induced premature senescence response to oxidative stress cellular response to chemical stimulus stress-induced premature senescence response to chemical multicellular organismal-level homeostasis homeostatic process energy homeostasis intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway cellular response to endogenous stimulus negative regulation of intracellular steroid hormone receptor signaling pathway response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus nuclear receptor-mediated corticosteroid signaling pathway cellular response to lipid negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated signaling pathway regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process positive regulation of circadian rhythm regulation of circadian rhythm skeletal muscle cell differentiation skeletal muscle tissue development striated muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development regulation of skeletal muscle cell differentiation positive regulation of cell differentiation positive regulation of skeletal muscle cell differentiation muscle tissue development muscle organ development positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway positive regulation of signaling cell cycle regulation of cell cycle negative regulation of cold-induced thermogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis negative regulation of multicellular organismal process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle intracellular membrane-bounded organelle chromatoid body cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle intracellular membrane-bounded organelle chromatoid body cytoplasmic ribonucleoprotein granule ribonucleoprotein granule cytoplasm supramolecular complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen RNA polymerase II transcription regulator complex protein-containing complex CLOCK-BMAL transcription complex nuclear protein-containing complex transcription regulator complex aryl hydrocarbon receptor complex intracellular protein-containing complex receptor complex nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR047230	Circadian locomoter output cycles protein kaput-like	Family
B	IPR001067	Nuclear translocator	Family
B	IPR035965	PAS domain superfamily	Homologous Superfamily
B	IPR001610	PAC motif	Repeat
B	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR013767	PAS fold	Domain
B	IPR000014	PAS domain	Domain
B	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
A	IPR001067	Nuclear translocator	Family
A	IPR035965	PAS domain superfamily	Homologous Superfamily
A	IPR001610	PAC motif	Repeat
A	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR050933	Circadian Clock Transcription Factors	Family
A	IPR013767	PAS fold	Domain
A	IPR000014	PAS domain	Domain
A	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: O15516	seasonal affective disorder osteosarcoma psoriasis alcohol withdrawal delirium atypical teratoid rhabdoid tumor cocaine use glioblastoma juvenile dermatomyositis major depressive disorder ovarian cancer rheumatoid arthritis bipolar disorder depressive disorder heart disease large cell medulloblastoma seasonal affective disorder osteosarcoma psoriasis alcohol withdrawal delirium atypical teratoid rhabdoid tumor cocaine use glioblastoma juvenile dermatomyositis major depressive disorder ovarian cancer rheumatoid arthritis bipolar disorder depressive disorder heart disease large cell medulloblastoma malignant glioma myopathy pancreatic ductal adenocarcinoma schizophrenia amyotrophic lateral sclerosis cocaine dependence diabetes mellitus hereditary spastic paraplegia lung cancer
A	Pharos: O00327	chronic myelogenous leukemia, BCR-ABL1 positive seasonal affective disorder female infertility hyperargininemia ovarian cancer primitive neuroectodermal tumor Sterility, Postpartum atypical teratoid rhabdoid tumor coronary artery disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma acne bipolar disorder depressive disorder chronic myelogenous leukemia, BCR-ABL1 positive seasonal affective disorder female infertility hyperargininemia ovarian cancer primitive neuroectodermal tumor Sterility, Postpartum atypical teratoid rhabdoid tumor coronary artery disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma acne bipolar disorder depressive disorder heart disease lung cancer metabolic syndrome X myocardial ischemia pilocytic astrocytoma sleep-wake disorder adrenal cortex carcinoma medulloblastoma

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.