1GA5

CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth A]	d1ga5a_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Orphan nuclear receptor reverb DNA-binding domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth B]	d1ga5b_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Orphan nuclear receptor reverb DNA-binding domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth E]	d1ga5e_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Orphan nuclear receptor reverb DNA-binding domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d1ga5f_	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Nuclear receptor	Orphan nuclear receptor reverb DNA-binding domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039050	3000068	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039050	3000068	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039050	3000068	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039050	3000068	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]	zf-C4	e1ga5A1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
F [auth B]	zf-C4	e1ga5B1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
G [auth E]	zf-C4	e1ga5E1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)
H [auth F]	zf-C4	e1ga5F1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: zf-C4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
F [auth B]	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
G [auth E]	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)
H [auth F]	3.30.50.10	Alpha Beta	2-Layer Sandwich	Erythroid Transcription Factor GATA-1	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B], G [auth E], H [auth F]	PF00105	Zinc finger, C4 type (two domains) (zf-C4)	Zinc finger, C4 type (two domains)	In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], C [auth G]	5'-D(CPAPAPCPTPAPGPGPTPCPAPCPTPAPGPGPTPCPAPG)-3'	-	-	-
B [auth D], D [auth H]	5'-D(CPTPGPAPCPCPTPAPGPTPGPAPCPCPTPAPGPTP(5IT)PG)-3'	-	-	-
E [auth A], F [auth B], G [auth E], H [auth F]	ORPHAN NUCLEAR RECEPTOR NR1D1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound 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 nuclear receptor activity molecular transducer activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound 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 nuclear receptor activity molecular transducer activity ligand-activated transcription factor activity signaling receptor activity transcription factor binding transcription coregulator binding transcription corepressor binding protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor 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 nuclear steroid receptor activity tetrapyrrole binding heme binding E-box binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway innate immune response-activating signaling pathway regulation of biological process immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus regulation of toll-like receptor 4 signaling pathway regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of signaling signaling positive regulation of biological process innate immune response activating cell surface receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress negative regulation of cellular process innate immune response response to external biotic stimulus negative regulation of toll-like receptor 4 signaling pathway cell surface pattern recognition receptor signaling pathway regulation of signaling positive regulation of innate immune response cell surface receptor signaling pathway negative regulation of response to stimulus defense response biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of immune system process immune system process toll-like receptor 4 signaling pathway regulation of cell communication cellular process cellular homeostasis chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis intracellular chemical homeostasis intracellular glucose homeostasis protein destabilization regulation of protein stability regulation of biological quality cell population proliferation regulation of cell population proliferation regulation of type B pancreatic cell proliferation type B pancreatic cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation catabolic process proteolysis involved in protein catabolic process proteolysis proteasomal protein catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process negative regulation of inflammatory response regulation of inflammatory response negative regulation of response to external stimulus regulation of neuroinflammatory response negative regulation of defense response inflammatory response negative regulation of neuroinflammatory response neuroinflammatory response regulation of biosynthetic process rhythmic process circadian regulation of gene expression cellular biosynthetic process cellular metabolic process circadian rhythm regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process developmental process fat cell differentiation regulation of developmental process cellular developmental process regulation of cell differentiation cell differentiation regulation of fat cell differentiation multicellular organismal process multicellular organismal-level homeostasis temperature homeostasis circadian temperature homeostasis RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process response to hormone response to endogenous stimulus response to chemical response to leptin circadian sleep/wake cycle rhythmic behavior regulation of circadian sleep/wake cycle regulation of circadian rhythm regulation of behavior behavior circadian behavior regulation of multicellular organismal process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of 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 positive regulation of cellular biosynthetic process response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1 positive regulation of bile acid biosynthetic process oxoacid metabolic process regulation of lipid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process cellular ketone metabolic process regulation of small molecule metabolic process positive regulation of lipid metabolic process small molecule metabolic process regulation of cellular ketone metabolic process bile acid biosynthetic process positive regulation of bile acid metabolic process regulation of bile acid biosynthetic process positive regulation of steroid biosynthetic process monocarboxylic acid metabolic process regulation of steroid biosynthetic process steroid metabolic process organic hydroxy compound metabolic process lipid biosynthetic process regulation of bile acid metabolic process steroid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process regulation of steroid metabolic process carboxylic acid metabolic process bile acid metabolic process positive regulation of lipid biosynthetic process organic hydroxy compound biosynthetic process positive regulation of steroid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process lipid metabolic process astrocyte differentiation negative regulation of astrocyte activation regulation of cell activation regulation of neurogenesis astrocyte activation glial cell development regulation of astrocyte differentiation regulation of cell development multicellular organism development gliogenesis anatomical structure development system development nervous system development negative regulation of gliogenesis negative regulation of glial cell differentiation central nervous system development glial cell activation negative regulation of multicellular organismal process cell development regulation of gliogenesis regulation of nervous system development neurogenesis negative regulation of neurogenesis astrocyte development negative regulation of nervous system development negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of developmental process cell activation regulation of glial cell differentiation negative regulation of astrocyte differentiation negative regulation of cell activation negative regulation of cell development glial cell differentiation regulation of astrocyte activation negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction regulation of macrophage activation regulation of leukocyte activation myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response negative regulation of microglial cell activation microglial cell activation regulation of microglial cell activation negative regulation of leukocyte activation negative regulation of macrophage activation hormone-mediated signaling pathway cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to hormone stimulus response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium cellular response to lipid response to molecule of bacterial origin sterol homeostasis cholesterol homeostasis lipid homeostasis protein localization regulation of localization establishment of protein localization nitrogen compound transport localization cellular macromolecule localization establishment of localization in cell regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus response to glucose insulin secretion involved in cellular response to glucose stimulus cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport hormone secretion protein localization to extracellular region peptide secretion secretion by cell regulation of secretion by cell response to monosaccharide response to carbohydrate amide transport signal release cellular response to hexose stimulus cellular response to monosaccharide stimulus secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell cellular response to glucose stimulus regulation of protein transport peptide transport response to hexose protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport insulin secretion cellular response to tumor necrosis factor response to tumor necrosis factor negative regulation of cold-induced thermogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis carbohydrate metabolic process glucan biosynthetic process polysaccharide biosynthetic process energy derivation by oxidation of organic compounds carbohydrate biosynthetic process glycogen metabolic process generation of precursor metabolites and energy glycogen biosynthetic process polysaccharide metabolic process glucan metabolic process energy reserve metabolic process	somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection intracellular anatomical structure cytoplasm intracellular organelle organelle intracellular non-membrane-bounded organelle chromatin chromosome somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection intracellular anatomical structure cytoplasm intracellular organelle organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle neuron spine synapse dendritic spine postsynapse cell junction membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth E], H [auth F]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
E [auth A], F [auth B], G [auth E], H [auth F]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
E [auth A], F [auth B], G [auth E], H [auth F]	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
E [auth A], F [auth B], G [auth E], H [auth F]	IPR001723	Nuclear hormone receptor	Family
E [auth A], F [auth B], G [auth E], H [auth F]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
E [auth A], F [auth B], G [auth E], H [auth F]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth A], F [auth B], G [auth E], H [auth F]	Pharos: P20393	subependymal giant cell astrocytoma adrenal cortex carcinoma bipolar disorder cutaneous lupus erythematosus Fatty Liver malignant ependymoma primitive neuroectodermal tumor spina bifida tuberculosis atopic eczema breast carcinoma depressive disorder fatty liver disease medulloblastoma psoriasis subependymal giant cell astrocytoma adrenal cortex carcinoma bipolar disorder cutaneous lupus erythematosus Fatty Liver malignant ependymoma primitive neuroectodermal tumor spina bifida tuberculosis atopic eczema breast carcinoma depressive disorder fatty liver disease medulloblastoma psoriasis atypical teratoid rhabdoid tumor chronic obstructive pulmonary disease ductal breast carcinoma in situ invasive ductal breast carcinoma osteosarcoma seasonal affective disorder

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.