4DM8 | pdb_00004dm8

Crystal structure of RARb LBD in complex with 9cis retinoic acid

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8043757	3001442	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8043757	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		e4dm8B1	A: Alpha helical domain of ribonucleotide reductases	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: A2M_BRD	F:	ECOD (20:10:01)
A		e4dm8A1	A: Alpha helical domain of ribonucleotide reductases	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: A2M_BRD	F:	ECOD (20:10:01)

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)
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	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
C, D	Nuclear receptor coactivator 1	protein-containing complex binding binding protein binding protein dimerization activity protein-lysine-acetyltransferase activity protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity protein-containing complex binding binding protein binding protein dimerization activity protein-lysine-acetyltransferase activity protein N-acetyltransferase activity catalytic activity, acting on a protein acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear retinoid X receptor binding DNA-binding transcription factor binding nuclear estrogen receptor binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development placenta development chordate embryonic development embryonic morphogenesis labyrinthine layer development embryo development in utero embryonic development embryonic placenta morphogenesis labyrinthine layer morphogenesis anatomical structure morphogenesis embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development ovulation cycle rhythmic process estrous cycle multicellular organismal reproductive 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 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 cellular process apoptotic process programmed cell death positive regulation of cellular process cellular response to stimulus intracellular receptor signaling pathway signaling regulation of signal transduction regulation of thyroid hormone receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus regulation of intracellular signal transduction signal transduction cellular response to hormone stimulus regulation of signaling thyroid hormone receptor signaling pathway cellular response to chemical stimulus regulation of response to stimulus regulation of cell communication nuclear receptor-mediated signaling pathway head development brain development nervous system development cerebellum development central nervous system development metencephalon development hindbrain development behavior male mating behavior reproductive behavior mating behavior forebrain development pallium development cerebral cortex development telencephalon development nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway estrogen receptor signaling pathway cellular response to lipid peroxisome proliferator activated receptor signaling pathway mRNA transcription by RNA polymerase II RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression mRNA transcription mRNA metabolic process macromolecule biosynthetic 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 biosynthetic process metabolic process macromolecule metabolic process regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation regulation of biological quality response to Thyroglobulin triiodothyronine cellular response to Thyroglobulin triiodothyronine progesterone receptor signaling pathway cellular response to nitrogen compound response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound regulation of cellular response to insulin stimulus cellular response to oxygen-containing compound response to insulin cellular response to insulin stimulus positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process hippocampus development limbic system development regulation of transcription from RNA polymerase II promoter by galactose carbon catabolite regulation of transcription positive regulation of transcription by galactose cellular response to nutrient levels carbon catabolite regulation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription from RNA polymerase II promoter carbon catabolite activation of transcription response to nutrient levels regulation of transcription by galactose response to nutrient positive regulation of transcription from RNA polymerase II promoter by galactose cellular response to nutrient regulation of developmental process connective tissue development adipose tissue development positive regulation of adipose tissue development tissue development positive regulation of developmental process regulation of adipose tissue development positive regulation of multicellular organismal process regulation of multicellular organismal process hypothalamus development diencephalon development response to retinoic acid cellular developmental process regulation of cell differentiation positive regulation of neuron differentiation neurogenesis neuron differentiation positive regulation of cell differentiation cell differentiation generation of neurons regulation of neuron differentiation positive regulation of female receptivity female mating behavior regulation of female receptivity response to estradiol	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cell periphery plasma membrane membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific 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 molecular transducer activity signaling receptor activity ligand-modulated transcription factor 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 biological process regulation of multicellular organismal development 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 negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death digestive system development tube development embryo development digestive tract development embryonic organ development embryonic digestive tract development positive regulation of programmed cell death positive regulation of biological process positive regulation of apoptotic process positive regulation of cellular process cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling response to endogenous stimulus retinoic acid receptor signaling pathway hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical signal transduction nuclear receptor-mediated signaling pathway cellular response to hormone stimulus embryonic hindlimb morphogenesis limb development appendage development embryonic limb morphogenesis embryonic morphogenesis hindlimb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis heart development cardiac chamber morphogenesis heart morphogenesis circulatory system development cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis negative regulation of cell population proliferation regulation of stem cell proliferation cell population proliferation negative regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation 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 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 cartilage development regulation of chondrocyte differentiation negative regulation of cartilage development negative regulation of chondrocyte differentiation regulation of cell differentiation negative regulation of cell differentiation negative regulation of developmental process chondrocyte differentiation negative regulation of multicellular organismal 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 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 biosynthetic 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 regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule 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 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 cardiac muscle tissue development cardiac muscle cell differentiation muscle cell differentiation cardiocyte differentiation striated muscle tissue development muscle structure development striated muscle cell differentiation muscle tissue development positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
C, D	IPR028819	Nuclear receptor coactivator 1, basic helix-loop-helix	Domain
C, D	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
C, D	IPR017426	Nuclear receptor coactivator	Family
C, D	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
C, D	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
C, D	IPR035965	PAS domain superfamily	Homologous Superfamily
C, D	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
C, D	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
C, D	IPR056193	Nuclear receptor coactivator 1-3, bHLH 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
A, B	IPR003078	Retinoic acid receptor	Family
A, B	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B	IPR047158	Retinoic acid receptor, ligand-binding domain	Domain
A, B	IPR001723	Nuclear hormone receptor	Family
A, B	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B	IPR047159	Retinoic acid receptor, DNA-binding domain	Domain
A, B	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q15788	breast carcinoma breast cancer Mammary Neoplasms, Experimental prostate cancer endometriosis ovarian cancer psoriasis adenoma diffuse large B-cell lymphoma glioblastoma malignant glioma astrocytic tumor invasive ductal breast carcinoma osteosarcoma atypical teratoid rhabdoid tumor breast carcinoma breast cancer Mammary Neoplasms, Experimental prostate cancer endometriosis ovarian cancer psoriasis adenoma diffuse large B-cell lymphoma glioblastoma malignant glioma astrocytic tumor invasive ductal breast carcinoma osteosarcoma atypical teratoid rhabdoid tumor cancer large cell medulloblastoma myopathy
A, B	Pharos: P10826	microphthalmia, syndromic 12 Matthew-Wood syndrome squamous cell carcinoma endometriosis granular cell carcinoma sciatic neuropathy breast cancer lesion of sciatic nerve microphthalmia head and neck cancer adenocarcinoma tubular adenocarcinoma breast carcinoma cervical cancer dental caries microphthalmia, syndromic 12 Matthew-Wood syndrome squamous cell carcinoma endometriosis granular cell carcinoma sciatic neuropathy breast cancer lesion of sciatic nerve microphthalmia head and neck cancer adenocarcinoma tubular adenocarcinoma breast carcinoma cervical cancer dental caries Neuralgia-Neuritis, Sciatic Nerve primary biliary cholangitis gastric neoplasm head and neck neoplasm cancer lung carcinoma colorectal cancer malignant tumor of neck cribriform carcinoma of breast endometrial carcinoma open-angle glaucoma psoriasis acute promyelocytic leukemia hypertensive disorder chronic obstructive pulmonary disease cystic fibrosis neoplasm of neck ovarian cancer gastric cancer hereditary diffuse gastric adenocarcinoma attention deficit hyperactivity disorder, inattentive type intellectual disability lung benign neoplasm malignant mesothelioma coloboma cribriform carcinoma