4S15 | pdb_00004s15

Crystal structure of the orphan nuclear receptor RORalpha ligand-binding domain in complex with 4alpha-caboxyl, 4beta-methyl-zymosterol (4ACD8)

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)
C [auth B]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8043672	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8043672	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)
C [auth B]	RNA_pol_Rpb2_6	e4s15B1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: RNA_pol_Rpb2_6	ECOD (v294.1)
A	Thymidylat_synt	e4s15A1	A: a/b three-layered sandwiches	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth 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
B [auth C], D	Nuclear receptor-interacting protein 1	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding signaling receptor binding histone deacetylase binding enzyme binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding nuclear glucocorticoid receptor binding DNA-binding transcription factor binding signaling receptor binding histone deacetylase binding enzyme 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription coactivator activity transcription regulator activity transcription coregulator activity transcription corepressor activity nuclear retinoic acid receptor binding nuclear retinoid X receptor binding nuclear estrogen receptor binding	rhythmic process circadian rhythm ovulation cycle process multicellular organismal process ovulation sexual reproduction reproductive process sex differentiation development of primary female sexual characteristics female gamete generation developmental process involved in reproduction gamete generation ovulation from ovarian follicle ovulation cycle rhythmic process circadian rhythm ovulation cycle process multicellular organismal process ovulation sexual reproduction reproductive process sex differentiation development of primary female sexual characteristics female gamete generation developmental process involved in reproduction gamete generation ovulation from ovarian follicle ovulation cycle multicellular organism development development of primary sexual characteristics anatomical structure development reproductive structure development system development developmental process gonad development reproductive system development female gonad development multicellular organismal reproductive process animal organ development ovarian follicle rupture female sex differentiation regulation of biosynthetic process regulation of biological process regulation of cellular process circadian regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process lipid storage nutrient storage cellular response to stimulus response to lipid response to stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to estradiol cellular response to estradiol stimulus 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 transcription by RNA polymerase II 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule cytoplasm cytosol chromatin chromosome protein-containing complex catalytic complex nuclear protein-containing complex histone deacetylase complex fibrillar center
A, C [auth B]	Nuclear receptor ROR-alpha	transcription factor binding transcription coregulator binding protein binding binding sequence-specific DNA binding DNA binding 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 signaling receptor activity ligand-modulated transcription factor activity transcription factor binding transcription coregulator binding protein binding binding sequence-specific DNA binding DNA binding 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 signaling receptor activity ligand-modulated transcription factor activity transcription corepressor binding double-stranded DNA 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 transcription coactivator binding sterol binding oxysterol binding steroid binding lipid binding beta-catenin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process chemical homeostasis homeostatic process triglyceride homeostasis acylglycerol homeostasis lipid homeostasis developmental process multicellular organismal process head development cell population proliferation animal organ development brain development nervous system development multicellular organism development central nervous system development cell proliferation in external granule layer cerebellar granule cell precursor proliferation anatomical structure development cell proliferation in hindbrain neural precursor cell proliferation hindbrain development system development regulation of biosynthetic process rhythmic process regulation of biological process regulation of cellular process circadian regulation of gene expression circadian rhythm biological regulation 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 regulation of macrophage activation regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation immune system process regulation of immune system process regulation of multicellular organismal process 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 muscle structure development cellular developmental process cell differentiation muscle cell differentiation regulation of steroid metabolic process steroid metabolic process regulation of lipid metabolic process lipid metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular 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 response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1 intracellular receptor signaling pathway signaling intracellular signal transduction cell communication signal transduction response to sterol response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to lipid cellular response to sterol cerebellar cortex morphogenesis hindbrain morphogenesis cerebellar Purkinje cell layer formation central nervous system neuron differentiation neurogenesis cerebellar Purkinje cell layer development cerebellar Purkinje cell differentiation neuron differentiation metencephalon development cerebellar Purkinje cell layer morphogenesis cerebellar cortex formation cerebellum morphogenesis generation of neurons cerebellar cortex development anatomical structure morphogenesis cerebellum development anatomical structure formation involved in morphogenesis cell differentiation in hindbrain fat cell differentiation regulation of developmental process negative regulation of developmental process negative regulation of biological process regulation of cell differentiation negative regulation of fat cell differentiation negative regulation of cellular process negative regulation of cell differentiation regulation of fat cell differentiation nucleoside phosphate metabolic process ribose phosphate metabolic process cyclic purine nucleotide metabolic process carbohydrate derivative metabolic process nucleotide metabolic process cyclic nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process cGMP metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process purine ribonucleotide metabolic process phosphorus metabolic process regulation of cytokine production cytokine production regulation of vascular endothelial growth factor production vascular endothelial growth factor production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production positive regulation of cytokine production blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis blood vessel development negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cell surface receptor signaling pathway smoothened signaling pathway regulation of smoothened signaling pathway regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response sterol homeostasis cholesterol homeostasis cellular response to tumor necrosis factor response to tumor necrosis factor positive regulation of circadian rhythm regulation of circadian rhythm cellular response to xenobiotic stimulus xenobiotic metabolic process response to xenobiotic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response alpha-beta T cell activation T cell differentiation lymphocyte activation involved in immune response T-helper cell differentiation immune response hemopoiesis T cell differentiation involved in immune response adaptive immune response immune effector process T-helper 17 cell differentiation leukocyte differentiation T-helper 17 type immune response monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process nitric oxide metabolic process nitric oxide biosynthetic process reactive nitrogen species metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR031408	Nuclear receptor-interacting protein 1, repression domain 4	Domain
B [auth C], D	IPR026649	Nuclear receptor-interacting protein 1	Family
B [auth C], D	IPR031407	Nuclear receptor-interacting protein 1, repression domain 3	Family
B [auth C], D	IPR031406	Nuclear receptor-interacting protein 1, repression domain 2	Domain
B [auth C], D	IPR031405	Nuclear receptor-interacting protein 1, repression domain 1	Domain
A, C [auth B]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, C [auth B]	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, C [auth B]	IPR044101	Retinoid-related orphan receptors, DNA-binding domain	Domain
A, C [auth B]	IPR003079	Nuclear receptor ROR	Family
A, C [auth B]	IPR001723	Nuclear hormone receptor	Family
A, C [auth B]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, C [auth B]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C], D	Pharos: P48552	breast carcinoma myocardial infarction schizophrenia congestive heart failure endometrial carcinoma Heart Failure, Right-Sided juvenile dermatomyositis lung cancer malignant mesothelioma adenoma atypical teratoid rhabdoid tumor osteosarcoma cystic fibrosis primitive neuroectodermal tumor gastroesophageal reflux disease breast carcinoma myocardial infarction schizophrenia congestive heart failure endometrial carcinoma Heart Failure, Right-Sided juvenile dermatomyositis lung cancer malignant mesothelioma adenoma atypical teratoid rhabdoid tumor osteosarcoma cystic fibrosis primitive neuroectodermal tumor gastroesophageal reflux disease hepatocellular carcinoma large cell medulloblastoma lymphoplasmacytic lymphoma amyotrophic lateral sclerosis medulloblastoma B-cell chronic lymphocytic leukemia myopathy ovarian cancer endometrial cancer rheumatoid arthritis gastric cancer ulcerative colitis glioblastoma heart failure hereditary spastic paraplegia malignant glioma astrocytic tumor breast cancer oligodendroglioma Crohn disease Pick disease sarcoidosis gastric carcinoma Hashimoto thyroiditis
A, C [auth B]	Pharos: P35398	hydrolethalus syndrome subependymal giant cell astrocytoma juvenile dermatomyositis lymphoplasmacytic lymphoma malignant glioma allergic rhinitis MALT lymphoma atopic eczema myopathy Autistic Disorder pancreatic ductal adenocarcinoma breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia depressive disorder peripheral neuropathy hydrolethalus syndrome subependymal giant cell astrocytoma juvenile dermatomyositis lymphoplasmacytic lymphoma malignant glioma allergic rhinitis MALT lymphoma atopic eczema myopathy Autistic Disorder pancreatic ductal adenocarcinoma breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia depressive disorder peripheral neuropathy esophageal adenocarcinoma pituitary cancer glioblastoma seasonal affective disorder intellectual developmental disorder with or without epilepsy or cerebellar ataxia ulcerative colitis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma amyotrophic lateral sclerosis medulloblastoma atypical teratoid rhabdoid tumor non-small cell lung carcinoma bipolar disorder pancreatic intraductal papillary-mucinous carcinoma cutaneous lupus erythematosus periodontitis dermatomyositis Pick disease gastric cancer primitive neuroectodermal tumor hereditary diffuse gastric adenocarcinoma spina bifida invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma asthma autism ovarian cancer breast cancer pancreatic intraductal papillary-mucinous neoplasm cystic fibrosis peripheral nervous system disease epilepsy pilocytic astrocytoma gastric neoplasm psoriasis

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.