1XDK

Crystal Structure of the RARbeta/RXRalpha Ligand Binding Domain Heterodimer in Complex with 9-cis Retinoic Acid and a Fragment of the TRAP220 Coactivator

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xdka_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoid-X receptor alpha (RXR-alpha)	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d1xdke_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoid-X receptor alpha (RXR-alpha)	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1xdkb_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoic acid receptor beta (RAR-beta)	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d1xdkf_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Retinoic acid receptor beta (RAR-beta)	house mouse (Mus musculus ) [TaxId: 10090 ],	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	8038700	3001442	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8038700	3001442	SCOP2B (2022-06-29)
B	SCOP2 Family	Nuclear receptor ligand-binding domain	8031458	4001384	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Nuclear receptor ligand-binding domain	8043836	3001442	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8043836	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	e1xdkA1	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	ECOD (1.6)
E	Hormone_recep	e1xdkE1	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	ECOD (1.6)
B	Hormone_recep_1	e1xdkB1	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)
F	Hormone_recep_1	e1xdkF1	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)

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)
E	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)
F	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
B, F	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, E	Retinoic acid receptor RXR-alpha	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding ion binding small molecule binding transcription factor binding transcription coregulator binding protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding ion binding small molecule binding transcription factor binding transcription coregulator binding protein binding protein-containing complex binding LBD domain binding protein domain specific binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity ligand-activated transcription factor activity DNA-binding transcription factor activity signaling receptor activity retinoic acid binding organic acid binding isoprenoid binding retinoid binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding identical protein binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear vitamin D receptor binding retinoic acid-responsive element binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear thyroid hormone receptor binding nuclear retinoic acid receptor binding nuclear steroid receptor activity DNA binding domain binding transcription coactivator binding chromatin binding chromatin DNA binding peptide binding RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding intronic transcription regulatory region sequence-specific DNA binding cation binding transition metal ion binding zinc ion binding metal ion binding enzyme binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth tissue development striated muscle tissue development muscle cell proliferation cellular process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation placenta development mesenchyme development regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death positive regulation of cellular process cellular developmental process cardiac muscle cell differentiation muscle cell differentiation cardiocyte differentiation muscle structure development cell differentiation striated muscle cell differentiation regulation of developmental process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process positive regulation of biomineral tissue development ossification biomineral tissue development regulation of multicellular organismal process regulation of multicellular organismal development bone mineralization positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling retinoic acid receptor signaling pathway cell communication signal transduction embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development heart morphogenesis anatomical structure morphogenesis animal organ morphogenesis multi-multicellular organism process reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process developmental process involved in reproduction maternal placenta development female pregnancy multi-organism reproductive process angiogenesis involved in coronary vascular morphogenesis blood vessel morphogenesis tube development coronary vasculature development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis coronary vasculature morphogenesis blood vessel development cellular biosynthetic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process peroxisome proliferator activated receptor signaling pathway mRNA transcription by RNA polymerase II mRNA transcription transcription by RNA polymerase II mRNA metabolic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound 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 macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process ventricular cardiac muscle cell differentiation ventricular cardiac muscle tissue morphogenesis ventricular cardiac muscle tissue development cardiac chamber development muscle organ development cardiac chamber morphogenesis muscle tissue morphogenesis tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis cardiac ventricle development muscle organ morphogenesis positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic 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 DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process positive regulation of cell communication thyroid hormone mediated signaling pathway response to organic substance positive regulation of signal transduction regulation of signal transduction hormone-mediated signaling pathway positive regulation of response to stimulus cellular response to endogenous stimulus response to hormone regulation of thyroid hormone mediated signaling pathway cellular response to organic substance cellular response to hormone stimulus regulation of signaling response to endogenous stimulus cellular response to chemical stimulus positive regulation of thyroid hormone mediated signaling pathway regulation of response to stimulus response to chemical regulation of cell communication positive regulation of signaling regulation of myelination nervous system development regulation of nervous system development myelination axon ensheathment ensheathment of neurons sensory organ development eye development visual system development camera-type eye development sensory system development epithelium development visceral serous pericardium development pericardium development response to retinoic acid response to lipid response to oxygen-containing compound response to corticosteroid response to steroid hormone response to glucocorticoid response to organic cyclic compound embryo implantation regulation of vitamin D receptor signaling pathway response to nutrient levels regulation of response to nutrient levels response to vitamin cellular response to vitamin D response to vitamin D response to nutrient cellular response to organic cyclic compound cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to vitamin cellular response to lipid positive regulation of vitamin D receptor signaling pathway cellular response to nutrient negative regulation of cell population proliferation regulation of cell population proliferation positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of translation post-transcriptional regulation of gene expression translational initiation protein metabolic process regulation of translational initiation by iron organonitrogen compound metabolic process regulation of translational initiation regulation of protein metabolic process positive regulation of translational initiation by iron translation positive regulation of gene expression regulation of translation positive regulation of translational initiation negative regulation of gene expression prostate gland development regulation of reproductive process gland development prostate gland epithelium morphogenesis gland morphogenesis reproductive structure development regulation of morphogenesis of an epithelium regulation of anatomical structure morphogenesis regulation of morphogenesis of a branching structure reproductive system development morphogenesis of an epithelium urogenital system development regulation of branching involved in prostate gland morphogenesis prostate gland morphogenesis morphogenesis of a branching structure branching involved in prostate gland morphogenesis morphogenesis of a branching epithelium secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development epithelial cell differentiation prostate glandular acinus development epithelial cell differentiation involved in prostate gland development glandular epithelial cell differentiation columnar/cuboidal epithelial cell differentiation	protein-containing complex transcription regulator complex intracellular organelle intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle receptor complex axon cell projection protein-containing complex transcription regulator complex intracellular organelle intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle receptor complex axon cell projection neuron projection plasma membrane bounded cell projection membrane-bounded organelle mitochondrion cytoplasm intracellular membrane-bounded organelle RNA polymerase II transcription regulator complex nucleus nuclear protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B, F	Retinoic acid receptor, beta	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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity heterocyclic compound binding small molecule binding protein-containing complex binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding nuclear retinoid X receptor binding DNA-binding transcription factor binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity ligand-activated transcription factor activity signaling receptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process growth animal organ development tissue development anatomical structure morphogenesis bone growth skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis cartilage development cellular developmental process cell differentiation cellular process regulation of multicellular organismal development regulation of biological process regulation of cellular process regulation of developmental process regulation of myelination biological regulation nervous system development regulation of nervous system development myelination axon ensheathment ensheathment of neurons regulation of multicellular organismal process neurogenesis cellular response to stimulus response to organic substance response to stimulus signaling response to endogenous stimulus hormone-mediated signaling pathway cell communication cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical signal transduction cellular response to organic substance cellular response to hormone stimulus cell population proliferation digestive system development tube development embryo development digestive tract development embryonic organ development embryonic digestive tract development apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process intracellular receptor signaling pathway retinoic acid receptor signaling pathway embryonic hindlimb morphogenesis limb development appendage development embryonic limb morphogenesis embryonic morphogenesis hindlimb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis negative regulation of cell population proliferation regulation of stem cell proliferation negative regulation of biological process negative regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation negative regulation of cellular process ureteric bud development mesonephric epithelium development epithelium development kidney epithelium development mesonephros development renal system development kidney development mesonephric tubule development neural precursor cell proliferation regulation of cartilage development negative regulation of cartilage development negative regulation of developmental process negative regulation of multicellular organismal process head development forebrain development brain development central nervous system development telencephalon development striatum development subpallium development glandular epithelial cell development cell development epithelial cell differentiation glandular epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development columnar/cuboidal epithelial cell differentiation regulation of chondrocyte differentiation negative regulation of chondrocyte differentiation regulation of cell differentiation negative regulation of cell differentiation chondrocyte differentiation negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process embryonic organ morphogenesis sensory organ development embryonic eye morphogenesis eye development visual system development eye morphogenesis sensory organ morphogenesis sensory system development multicellular organism growth ventricular cardiac muscle cell differentiation heart development cardiac muscle tissue development cardiac muscle cell differentiation muscle cell differentiation cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development striated muscle cell differentiation muscle tissue development positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic 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 DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C, D, G, H	Thyroid Receptor Associated Protein 220	protein binding binding signaling receptor binding peroxisome proliferator activated receptor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein-containing complex binding protein binding binding signaling receptor binding peroxisome proliferator activated receptor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein-containing complex binding chromatin binding promoter-specific chromatin binding DNA binding organic cyclic compound binding nucleic acid binding LBD domain binding protein domain specific binding transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding general transcription initiation factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear vitamin D receptor binding nuclear thyroid hormone receptor binding sequence-specific DNA 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 nuclear retinoic acid receptor binding transcription corepressor activity transcription coregulator binding transcription coactivator binding chromatin DNA binding histone acetyltransferase binding enzyme binding nuclear estrogen receptor binding	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation head development central nervous system development animal organ development brain development erythrocyte development homeostatic process hemopoiesis cell development enucleate erythrocyte development erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation immune system process myeloid cell development homeostasis of number of cells myeloid cell homeostasis enucleate erythrocyte differentiation erythrocyte homeostasis heart development circulatory system development organonitrogen compound metabolic process regulation of hormone levels organic hydroxy compound metabolic process cellular metabolic process hormone metabolic process cellular modified amino acid metabolic process thyroid hormone metabolic process organic cyclic compound metabolic process organic substance metabolic process phenol-containing compound metabolic process metabolic process regulation of biological quality thyroid hormone generation cellular biosynthetic process transcription preinitiation complex assembly RNA metabolic process cellular component organization cellular component biogenesis protein-DNA complex organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process cellular component assembly transcription by RNA polymerase II protein-containing complex assembly organic substance biosynthetic process cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter protein-containing complex organization protein-DNA complex assembly primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process biosynthetic process organic cyclic compound biosynthetic process RNA polymerase II preinitiation complex assembly macromolecule metabolic process positive regulation of G0 to G1 transition regulation of cell cycle process positive regulation of biological process G0 to G1 transition positive regulation of cell cycle regulation of G0 to G1 transition positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process sensory organ development eye development visual system development camera-type eye development sensory system development lens development in camera-type eye 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 regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process epithelium development retinal pigment epithelium development retina development in camera-type eye tissue development cellular response to stimulus response to organic substance response to stimulus response to lipid response to endogenous stimulus cellular response to organic cyclic compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to organic substance cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport organic substance transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle establishment of localization in cell protein import into nucleus intracellular protein transport embryonic hindlimb morphogenesis limb development appendage development embryonic limb morphogenesis embryonic morphogenesis hindlimb morphogenesis embryonic appendage morphogenesis embryo development anatomical structure morphogenesis appendage morphogenesis limb morphogenesis embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development embryonic hemopoiesis embryonic organ development regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription cell morphogenesis regulation of cell development positive regulation of developmental process positive regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development regulation of myeloid cell differentiation regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis intracellular receptor signaling pathway signaling cell communication peroxisome proliferator activated receptor signaling pathway signal transduction fat cell differentiation mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process regulation of body fluid levels secretion mammary gland development gland development body fluid secretion lactation negative regulation of cell population proliferation cell population proliferation regulation of keratinocyte proliferation negative regulation of keratinocyte proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation keratinocyte proliferation response to thyroid hormone cellular response to thyroid hormone stimulus myeloid leukocyte differentiation mononuclear cell differentiation monocyte differentiation leukocyte differentiation branching involved in mammary gland duct morphogenesis development of secondary female sexual characteristics mammary gland morphogenesis reproductive process branching morphogenesis of an epithelial tube mammary gland branching involved in thelarche developmental process involved in reproduction tube morphogenesis gland morphogenesis animal organ morphogenesis thelarche epithelial tube morphogenesis development of secondary sexual characteristics tube development morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound 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 macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process hormone-mediated signaling pathway steroid hormone mediated signaling pathway nuclear receptor signaling pathway intracellular steroid hormone receptor signaling pathway 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 DNA-templated transcription positive regulation of RNA biosynthetic process thyroid hormone mediated signaling pathway steroid metabolic process lipid biosynthetic process androgen metabolic process androgen biosynthetic process steroid biosynthetic process hormone biosynthetic process steroid hormone biosynthetic process lipid metabolic process ventricular cardiac muscle tissue morphogenesis heart morphogenesis striated muscle tissue development muscle structure development ventricular cardiac muscle tissue development ventricular trabecula myocardium morphogenesis cardiac chamber development muscle tissue development muscle organ development cardiac chamber morphogenesis cardiac muscle tissue development muscle tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis heart trabecula morphogenesis cardiac ventricle development trabecula morphogenesis muscle organ morphogenesis hepaticobiliary system development liver development epidermal cell differentiation epidermis development epithelial cell differentiation skin development keratinocyte differentiation megakaryocyte differentiation megakaryocyte development regulation of vitamin D receptor signaling pathway response to nutrient levels regulation of response to nutrient levels regulation of signal transduction response to vitamin cellular response to vitamin D response to vitamin D regulation of signaling response to nutrient response to oxygen-containing compound cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to vitamin regulation of response to stimulus regulation of cell communication cellular response to nutrient blood vessel morphogenesis angiogenesis vasculature development anatomical structure formation involved in morphogenesis blood vessel development negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death multi-multicellular organism process maternal process involved in female pregnancy mammary gland branching involved in pregnancy female pregnancy multicellular organismal reproductive process multi-organism reproductive process positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction response to type II interferon response to cytokine regulation of type II interferon-mediated signaling pathway response to biotic stimulus cellular response to type II interferon interferon-mediated signaling pathway positive regulation of immune response positive regulation of response to type II interferon cellular response to cytokine stimulus positive regulation of immune system process immune response response to other organism regulation of innate immune response type II interferon-mediated signaling pathway response to external stimulus regulation of response to cytokine stimulus defense response to other organism positive regulation of defense response regulation of immune response regulation of response to type II interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms positive regulation of type II interferon-mediated signaling pathway regulation of response to external stimulus positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus response to stress regulation of response to stress innate immune response response to external biotic stimulus cell surface receptor signaling pathway positive regulation of innate immune response defense response regulation of cytokine-mediated signaling pathway defense response to symbiont positive regulation of cytokine-mediated signaling pathway positive regulation of signaling embryonic heart tube development placenta development embryonic placenta development mammary gland epithelial cell proliferation positive regulation of cell population proliferation regulation of DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of transcription initiation by RNA polymerase II regulation of transcription initiation by RNA polymerase II stem cell differentiation hematopoietic stem cell differentiation hematopoietic progenitor cell differentiation regulation of hepatocyte proliferation liver morphogenesis positive regulation of epithelial cell proliferation epithelial cell proliferation involved in liver morphogenesis hepatocyte proliferation positive regulation of hepatocyte proliferation branch elongation involved in mammary gland duct branching developmental growth epithelial cell proliferation involved in mammary gland duct elongation axis elongation branch elongation of an epithelium growth developmental growth involved in morphogenesis positive regulation of keratinocyte differentiation regulation of epidermal cell differentiation regulation of epithelial cell differentiation positive regulation of epidermis development positive regulation of epithelial cell differentiation positive regulation of multicellular organismal process regulation of epidermis development regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation animal organ regeneration regeneration regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation DNA-templated transcription elongation response to hepatocyte growth factor cellular response to growth factor stimulus cellular response to hepatocyte growth factor stimulus response to growth factor cellular response to epidermal growth factor stimulus response to epidermal growth factor positive regulation of intracellular estrogen receptor signaling pathway intracellular estrogen receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway regulation of intracellular steroid hormone receptor signaling pathway positive regulation of intracellular steroid hormone receptor signaling pathway	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity mediator complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity mediator complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle RNA polymerase II transcription regulator complex core mediator complex transcription regulator complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, E	IPR021780	Nuclear/hormone receptor activator site AF-1	Domain
A, E	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, E	IPR000003	Retinoid X receptor/HNF4	Family
A, E	IPR001723	Nuclear hormone receptor	Family
A, E	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, E	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
B, F	IPR003078	Retinoic acid receptor	Family
B, F	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
B, F	IPR047158	Retinoic acid receptor, ligand-binding domain	Domain
B, F	IPR001723	Nuclear hormone receptor	Family
B, F	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
B, F	IPR047159	Retinoic acid receptor, DNA-binding domain	Domain
B, F	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
B, F	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
C, D, G, H	IPR019680	Mediator complex, subunit Med1	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.