7APO

Crystal structure of RARalpha ligand binding domain in complex with a fragment of the TIF2 coactivator

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)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038701	3001442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038701	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	Hormone_recep_1	e7apoA1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep_1	ECOD (1.6)
B	Hormone_recep_1	e7apoB1	A: alpha arrays	X: Nuclear receptor ligand-binding domain (From Topology)	H: Nuclear receptor ligand-binding domain (From Topology)	T: Nuclear receptor ligand-binding domain	F: Hormone_recep_1	ECOD (1.6)

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
A, B	Retinoic acid receptor alpha	protein binding binding protein kinase B binding kinase binding enzyme binding protein kinase binding histone deacetylase binding retinoic acid binding organic acid binding isoprenoid binding retinoid binding ion binding anion binding lipid binding protein binding binding protein kinase B binding kinase binding enzyme binding protein kinase binding histone deacetylase binding retinoic acid binding organic acid binding isoprenoid binding retinoid binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding small molecule binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding protein domain specific binding signaling receptor binding retinoic acid-responsive element binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding cytoskeletal protein binding alpha-actinin binding actinin binding transcription regulator activity DNA-binding transcription factor activity heterocyclic compound binding transcription factor binding transcription coregulator binding transcription coactivator binding chromatin binding chromatin DNA binding RNA binding mRNA 5'-UTR binding mRNA binding DNA-binding transcription repressor activity DNA-binding transcription factor activity, RNA polymerase II-specific nuclear receptor activity molecular transducer activity ligand-activated transcription factor activity signaling receptor activity protein kinase A binding translation regulator activity mRNA regulatory element binding translation repressor activity translation regulator activity, nucleic acid binding translation repressor activity cation binding transition metal ion binding zinc ion binding metal ion binding	multicellular organismal process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of interleukin-5 production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process interleukin-5 production multicellular organismal process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of interleukin-5 production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process interleukin-5 production positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation 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 positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of interleukin-5 production positive regulation of cellular biosynthetic process regulation of tumor necrosis factor production negative regulation of biological process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production tumor necrosis factor production negative regulation of cellular biosynthetic process negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of multicellular organismal process interleukin-13 production positive regulation of interleukin-13 production regulation of interleukin-13 production cellular response to stimulus response to lipid response to stimulus response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid response to chemical cellular response to lipid intracellular receptor signaling pathway signaling response to endogenous stimulus retinoic acid receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone signal transduction nuclear receptor-mediated signaling pathway cellular response to hormone stimulus embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure limb development appendage development protein phosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process mRNA transcription by RNA polymerase II RNA metabolic process nucleobase-containing compound biosynthetic process mRNA transcription mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II regulation of type II interferon production type II interferon production negative regulation of type II interferon production response to estrogen cellular response to estrogen stimulus glandular epithelial cell development cellular developmental process cell development epithelial cell differentiation glandular epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development cell differentiation columnar/cuboidal epithelial cell differentiation regulation of primary metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process multicellular organism growth developmental growth growth ventricular cardiac muscle cell differentiation heart development cardiac muscle tissue development cardiac muscle cell differentiation animal organ development muscle cell differentiation cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development striated muscle cell differentiation muscle tissue development localization import into cell transport phagocytosis apoptotic cell clearance endocytosis establishment of localization vesicle-mediated transport cell cycle regulation of cell cycle positive regulation of cell cycle sexual reproduction reproductive process multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation germ cell development response to peptide response to cytokine cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of miRNA transcription regulation of miRNA metabolic process miRNA metabolic process miRNA transcription negative regulation of miRNA metabolic process regulation of miRNA transcription regulation of cartilage development regulation of multicellular organismal development regulation of developmental process connective tissue development negative regulation of cartilage development negative regulation of developmental process skeletal system development cartilage development sex differentiation epithelial cell fate commitment Sertoli cell differentiation male gonad development male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics reproductive structure development gonad development reproductive system development Sertoli cell fate commitment cell fate commitment response to estradiol response to organic cyclic compound endochondral bone morphogenesis organ growth growth plate cartilage development endochondral bone growth animal organ morphogenesis bone development bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis trachea cartilage development trachea development respiratory system development prostate gland development gland development urogenital system development chondroblast differentiation regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death response to nutrient levels response to nutrient response to vitamin A response to vitamin regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation positive regulation of T cell differentiation alpha-beta T cell differentiation involved in immune response regulation of cell development type 2 immune response positive regulation of immune response T cell activation regulation of type 2 immune response regulation of T-helper cell differentiation alpha-beta T cell activation regulation of immune system process positive regulation of CD4-positive, alpha-beta T cell differentiation immune response T-helper cell differentiation positive regulation of cell development immune effector process regulation of response to stimulus regulation of leukocyte cell-cell adhesion positive regulation of alpha-beta T cell differentiation positive regulation of leukocyte cell-cell adhesion CD4-positive, alpha-beta T cell differentiation positive regulation of T-helper cell differentiation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation alpha-beta T cell differentiation T cell activation involved in immune response positive regulation of cell differentiation leukocyte activation involved in immune response regulation of T-helper 2 cell differentiation positive regulation of immune effector process regulation of cell-cell adhesion hemopoiesis regulation of cell adhesion cell activation positive regulation of T-helper 2 cell differentiation regulation of CD4-positive, alpha-beta T cell activation immune system process regulation of lymphocyte activation regulation of immune effector process regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation involved in immune response positive regulation of developmental process positive regulation of cell activation positive regulation of leukocyte activation T cell differentiation positive regulation of immune system process positive regulation of T cell activation positive regulation of alpha-beta T cell activation regulation of immune response leukocyte differentiation regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of response to stimulus positive regulation of CD4-positive, alpha-beta T cell activation cell adhesion cell-cell adhesion alpha-beta T cell activation involved in immune response positive regulation of hemopoiesis CD4-positive, alpha-beta T cell activation T-helper 2 cell differentiation lymphocyte activation involved in immune response regulation of lymphocyte differentiation positive regulation of cell adhesion regulation of T cell activation T cell differentiation involved in immune response positive regulation of type 2 immune response regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation positive regulation of DNA-templated transcription 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 head development face development hepaticobiliary system development liver development forebrain development brain development pallium development central nervous system development telencephalon development hippocampus development limbic system development regulation of myelination regulation of nervous system development myelination axon ensheathment ensheathment of neurons multi-multicellular organism process female pregnancy multi-organism reproductive process myeloid leukocyte differentiation regulation of granulocyte differentiation negative regulation of cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation regulation of myeloid cell differentiation regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development negative regulation of granulocyte differentiation granulocyte differentiation myeloid cell differentiation negative regulation of immune system process biological process involved in interspecies interaction between organisms response to other organism cellular response to lipopolysaccharide response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide response to biotic stimulus cellular response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to alcohol response to ethanol ureteric bud development mesonephric epithelium development kidney epithelium development mesonephros development renal system development kidney development mesonephric tubule development positive regulation of neuron differentiation neurogenesis neuron differentiation generation of neurons regulation of neuron differentiation negative regulation of cell population proliferation regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality sensory organ development eye development visual system development embryonic camera-type eye development camera-type eye development embryonic organ development sensory system development regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of molecular function regulation of molecular function regulation of binding positive regulation of binding regulation of hematopoietic progenitor cell differentiation hematopoietic progenitor cell differentiation	intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen cell periphery plasma membrane membrane protein-containing complex transcription regulator complex somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection chromatin chromosome perinuclear region of cytoplasm RNA polymerase II transcription regulator complex nuclear protein-containing complex nucleoplasm
C, D	Nuclear receptor coactivator 2	protein binding binding protein domain specific 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein binding binding protein domain specific 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 organic cyclic compound 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 nuclear receptor coactivator activity protein dimerization activity signaling receptor binding aryl hydrocarbon receptor binding	regulation of biological process regulation of lipid metabolic process biological regulation primary metabolic process metabolic 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 regulation of biological process regulation of lipid metabolic process biological regulation primary metabolic process metabolic 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 response to organic cyclic compound cellular response to stimulus cellular response to endogenous stimulus cellular response to chemical stimulus cellular process cellular response to hormone stimulus regulation of biosynthetic process rhythmic process regulation of cellular 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 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 signaling intracellular signal transduction cell communication peroxisome proliferator activated receptor signaling pathway signal transduction 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 biological process negative regulation of cellular metabolic 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 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 cellular biosynthetic 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 regulation of response to stimulus response to insulin cellular response to insulin stimulus 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 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 cellular anatomical entity intracellular organelle 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 cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B	IPR047158	Retinoic acid receptor, ligand-binding domain	Domain
A, B	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B	IPR001723	Nuclear hormone receptor	Family
A, B	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B	IPR003078	Retinoic acid receptor	Family
A, B	IPR047159	Retinoic acid receptor, DNA-binding domain	Domain
A, B	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
C, D	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
C, D	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
C, D	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
C, D	IPR017426	Nuclear receptor coactivator	Family
C, D	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
C, D	IPR013767	PAS fold	Domain
C, D	IPR000014	PAS domain	Domain
C, D	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
C, D	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
C, D	IPR035965	PAS domain superfamily	Homologous Superfamily
C, D	IPR028822	Nuclear receptor coactivator 2, basic helix-loop-helix	Domain
C, D	IPR032565	Nuclear receptor coactivator 2/3, DUF4927	Domain
C, D	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P10276	acute promyelocytic leukemia breast fibroadenoma Neoplasms, Second Primary cancer sciatic neuropathy benign breast phyllodes tumor breast carcinoma lesion of sciatic nerve psoriasis malignant ependymoma atypical teratoid rhabdoid tumor osteosarcoma breast cancer pituitary cancer schizophrenia acute promyelocytic leukemia breast fibroadenoma Neoplasms, Second Primary cancer sciatic neuropathy benign breast phyllodes tumor breast carcinoma lesion of sciatic nerve psoriasis malignant ependymoma atypical teratoid rhabdoid tumor osteosarcoma breast cancer pituitary cancer schizophrenia gastric cancer Sjogren syndrome hematologic disease tuberculosis malignant breast phyllodes tumor malignant glioma acute myeloid leukemia phyllodes tumor primitive neuroectodermal tumor gastric carcinoma hepatocellular carcinoma type 2 diabetes mellitus medulloblastoma myeloid leukemia pilocytic astrocytoma glioblastoma
C, D	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