3L0L | pdb_00003l0l

Crystal structure of orphan nuclear receptor RORgamma in complex with natural ligand

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)
A	d3l0la_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d3l0lb_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	automated matches	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)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8102465	3001442	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8102465	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)
A	Cu_amine_oxid	e3l0lA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: sensor domains	T: sensor domains	F: Cu_amine_oxid	ECOD (develop294)
C [auth B]	RVP	e3l0lB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
C [auth B]	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
A, C [auth B]	Nuclear receptor ROR-gamma	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 ligand-modulated transcription factor activity sterol binding oxysterol binding steroid binding lipid binding nuclear receptor activity molecular transducer activity signaling receptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process connective tissue development adipose tissue development animal organ development anatomical structure development tissue development multicellular organismal process cellular developmental process T-helper cell differentiation hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation developmental process connective tissue development adipose tissue development animal organ development anatomical structure development tissue development multicellular organismal process cellular developmental process T-helper cell differentiation hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation CD4-positive, alpha-beta T cell differentiation leukocyte activation alpha-beta T cell differentiation T cell activation immune system process cell differentiation CD4-positive, alpha-beta T cell activation alpha-beta T cell activation T cell differentiation cellular process leukocyte differentiation immune system development multicellular organism development lymph node development hematopoietic or lymphoid organ development system development regulatory T cell differentiation 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 positive regulation of circadian rhythm positive regulation of biological process regulation of circadian rhythm cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical cellular response to xenobiotic stimulus xenobiotic metabolic process response to xenobiotic stimulus fat cell differentiation regulation of developmental process regulation of cell differentiation regulation of fat cell differentiation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cell activation involved in immune response T cell activation involved in immune response alpha-beta T cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response immune response T cell differentiation involved in immune response adaptive immune response immune effector process T-helper 17 cell differentiation T-helper 17 type immune response regulation of steroid metabolic process steroid metabolic process regulation of lipid metabolic process lipid metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of thymocyte apoptotic process leukocyte apoptotic process regulation of programmed cell death lymphocyte apoptotic process thymocyte apoptotic process negative regulation of leukocyte apoptotic process regulation of T cell apoptotic process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of T cell apoptotic process negative regulation of apoptotic process regulation of thymocyte apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process Peyer's patch development mucosa-associated lymphoid tissue development mucosal tolerance induction tolerance induction dependent upon immune response tolerance induction in gut-associated lymphoid tissue tolerance induction in mucosal-associated lymphoid tissue immune response in gut-associated lymphoid tissue tolerance induction to nonself antigen mucosal immune response tolerance induction organ or tissue specific immune response 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome nuclear body
B [auth C], D [auth E]	SCR2-2	protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity 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 protein binding binding protein domain specific binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity 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 chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding protein dimerization activity signaling receptor binding aryl hydrocarbon receptor binding	regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process cellular process regulation of metabolic process lipid metabolic process regulation of primary metabolic process developmental process multicellular organismal process regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development positive regulation of biological process tissue development positive regulation of developmental process regulation of adipose tissue development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal process response to ketone response to lipid response to stimulus response to hormone response to steroid hormone response to chemical response to endogenous stimulus response to progesterone response to oxygen-containing compound cellular response to stimulus cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to hormone stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication 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 macromolecule metabolic process RNA 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 nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription intracellular receptor signaling pathway intracellular signal transduction peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm response to Thyroglobulin triiodothyronine cellular response to Thyroglobulin triiodothyronine negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular response to nitrogen compound response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, C [auth B]	IPR001723	Nuclear hormone receptor	Family
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]	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, C [auth B]	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
B [auth C], D [auth E]	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
B [auth C], D [auth E]	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
B [auth C], D [auth E]	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
B [auth C], D [auth E]	IPR017426	Nuclear receptor coactivator	Family
B [auth C], D [auth E]	IPR056193	Nuclear receptor coactivator 1-3, bHLH domain	Domain
B [auth C], D [auth E]	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
B [auth C], D [auth E]	IPR013767	PAS fold	Domain
B [auth C], D [auth E]	IPR000014	PAS domain	Domain
B [auth C], D [auth E]	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B [auth C], D [auth E]	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
B [auth C], D [auth E]	IPR035965	PAS domain superfamily	Homologous Superfamily
B [auth C], D [auth E]	IPR028822	Nuclear receptor coactivator 2, basic helix-loop-helix	Domain
B [auth C], D [auth E]	IPR032565	Nuclear receptor coactivator 2/3, DUF4927	Domain
B [auth C], D [auth E]	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: P51449	autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency Inflammation advanced sleep phase syndrome allergic rhinitis circadian rhythm sleep disorder, delayed sleep phase type inflammatory bowel disease attention deficit hyperactivity disorder, inattentive type heart disease myocardial infarction psoriasis ulcerative colitis
B [auth C], D [auth E]	Pharos: Q15596	breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma prostate cancer psoriasis ulcerative colitis adenoma endometriosis interstitial cystitis Mammary Neoplasms osteosarcoma testicular cancer atypical teratoid rhabdoid tumor Crohn disease Gaucher disease large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm testicular germ cell tumor breast cancer endogenous depression glioblastoma medulloblastoma plasma cell myeloma