6WMS | pdb_00006wms

Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID2 Peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8076674	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8076674	3001442	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)
B		e6wmsB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: GFP	F:	ECOD (20:10:01)
A		e6wmsA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: GFP	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00104	Ligand-binding domain of nuclear hormone receptor (Hormone_recep)	Ligand-binding domain of nuclear hormone receptor	This all helical domain is involved in binding the hormone in these receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F]	NCOR isoform c	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 histone deacetylase binding protein binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor 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 histone deacetylase binding protein binding enzyme binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear thyroid hormone receptor binding DNA-binding transcription factor binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of cellular process negative regulation of biological process RNA 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA 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 negative regulation of cellular process 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process negative regulation of small molecule metabolic process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process organic acid metabolic process regulation of small molecule metabolic process small molecule metabolic process fatty acid metabolic process negative regulation of fatty acid metabolic process carboxylic acid metabolic process regulation of ketone metabolic process regulation of fatty acid metabolic process monocarboxylic acid metabolic process negative regulation of lipid metabolic process lipid metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration negative regulation of glycolytic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process negative regulation of ATP metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process negative regulation of carbohydrate metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process negative regulation of purine nucleotide catabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process negative regulation of purine nucleotide metabolic process energy derivation by oxidation of organic compounds negative regulation of phosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process negative regulation of nucleotide catabolic process negative regulation of catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process negative regulation of phosphorus metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of JNK cascade regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication negative regulation of MAPK cascade organelle assembly microtubule cytoskeleton organization membraneless organelle assembly spindle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization chromosome segregation spindle organization cell cycle process negative regulation of miRNA transcription miRNA transcription regulation of miRNA metabolic process miRNA metabolic process negative regulation of miRNA metabolic process regulation of miRNA transcription behavior rhythmic process multicellular organismal process circadian behavior locomotory behavior rhythmic behavior circadian rhythm locomotor rhythm intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway androgen 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 regulation of androgen receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid negative regulation of androgen receptor signaling pathway nuclear receptor-mediated signaling pathway transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II chromatin organization	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol intracellular organelle mitotic spindle cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-bounded organelle cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol intracellular organelle mitotic spindle cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin chromosome protein-containing complex catalytic complex nuclear protein-containing complex histone deacetylase complex transcription regulator complex transcription repressor complex
A, B	Nuclear receptor Rev-ErbA beta variant 1	DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding 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 DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear receptor activity molecular transducer activity signaling receptor activity ligand-modulated transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA 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 negative regulation of cellular process 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process cellular developmental process cell differentiation regulation of lipid metabolic process lipid metabolic process rhythmic process circadian rhythm regulation of circadian rhythm cellular response to stimulus response to stimulus signaling response to endogenous stimulus hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical signal transduction cellular response to hormone stimulus chemical homeostasis homeostatic process lipid homeostasis regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response multicellular organismal process multicellular organismal-level homeostasis energy homeostasis skeletal muscle cell differentiation regulation of developmental process skeletal muscle tissue development animal organ development regulation of cell differentiation tissue development striated muscle tissue development muscle structure development skeletal muscle organ development regulation of skeletal muscle cell differentiation anatomical structure development muscle tissue development muscle organ development behavior circadian behavior rhythmic behavior positive regulation of DNA-templated transcription positive regulation of biological 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 RNA metabolic process positive regulation of RNA biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II intracellular receptor signaling pathway intracellular signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], D [auth F]	IPR017930	Myb domain	Domain
C [auth E], D [auth F]	IPR051571	Nuclear receptor corepressor	Family
C [auth E], D [auth F]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR031557	N-CoR, GPS2-interacting domain	Domain
C [auth E], D [auth F]	IPR017884	SANT domain	Domain
C [auth E], D [auth F]	IPR001005	SANT/Myb domain	Domain
A, B	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A, B	IPR001723	Nuclear hormone receptor	Family
A, B	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth E], D [auth F]	Pharos: O75376	glioblastoma transitional cell carcinoma breast cancer urinary bladder cancer liver cancer prostate cancer breast carcinoma endometriosis Hyperbilirubinemia, Neonatal giant cell glioblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary cutaneous T-cell lymphoma acute myeloid leukemia psoriasis glioblastoma transitional cell carcinoma breast cancer urinary bladder cancer liver cancer prostate cancer breast carcinoma endometriosis Hyperbilirubinemia, Neonatal giant cell glioblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary cutaneous T-cell lymphoma acute myeloid leukemia psoriasis malignant mesothelioma oligodendroglioma pancreatic ductal adenocarcinoma Pick disease astrocytic tumor subependymal giant cell astrocytoma urinary bladder neoplasm liver neoplasm mature T-cell and NK-cell non-Hodgkin lymphoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer breast adenocarcinoma malignant ependymoma
A, B	Pharos: Q14995	endometriosis osteosarcoma Pick disease ulcerative colitis adrenal cortex carcinoma atypical teratoid rhabdoid tumor chronic kidney disease ductal breast carcinoma in situ exocrine pancreatic carcinoma large cell medulloblastoma medulloblastoma ovarian cancer primitive neuroectodermal tumor amyotrophic lateral sclerosis breast cancer endometriosis osteosarcoma Pick disease ulcerative colitis adrenal cortex carcinoma atypical teratoid rhabdoid tumor chronic kidney disease ductal breast carcinoma in situ exocrine pancreatic carcinoma large cell medulloblastoma medulloblastoma ovarian cancer primitive neuroectodermal tumor amyotrophic lateral sclerosis breast cancer Crohn disease Endometrioma glioblastoma malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis astrocytic tumor breast carcinoma cystic fibrosis invasive ductal breast carcinoma malignant pancreatic neoplasm

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.