5NTI | pdb_00005nti

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds

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)
B	d5ntib_	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)
D	d5ntid_	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	d5ntic_	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)
A	d5ntia_	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)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8102465	3001442	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8102465	3001442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8102465	3001442	SCOP2B (2022-06-29)
A	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)
B	ANAPC3, SRP_TPR_like	e5ntiB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: ANAPC3, SRP_TPR_like	ECOD (v294.1)
D	ANAPC3, SRP_TPR_like	e5ntiD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: ANAPC3, SRP_TPR_like	ECOD (v294.1)
C	ANAPC3, SRP_TPR_like	e5ntiC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: ANAPC3, SRP_TPR_like	ECOD (v294.1)
A	ANAPC3, SRP_TPR_like	e5ntiA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: ANAPC3, SRP_TPR_like	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
D	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
C	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, B, C, D	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, B, C, D	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
E [auth P], F [auth Q], G [auth R], H [auth S]	ASN-SER-HIS-GLN-LYS-VAL-THR-LEU-LEU-GLN-LEU-LEU-LEU-GLY-HIS-LYS-ASN-GLU-GLU-ASN	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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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
E [auth P], F [auth Q], G [auth R], H [auth S]	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

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.