1XIU

Crystal structure of the agonist-bound ligand-binding domain of Biomphalaria glabrata RXR

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xiua_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	(Biomphalaria glabrata ) [TaxId: 6526 ],	SCOPe (2.08)
B	d1xiub_	All alpha proteins	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	Nuclear receptor ligand-binding domain	automated matches	(Biomphalaria glabrata ) [TaxId: 6526 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Nuclear receptor ligand-binding domain	8071623	4001384	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nuclear receptor ligand-binding domain	8071624	3001442	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nuclear receptor ligand-binding domain	8071624	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	e1xiuA1	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	e1xiuB1	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)

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)
B	1.10.565.10	Mainly Alpha	Orthogonal Bundle	Retinoid X Receptor	Retinoid X Receptor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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	RXR-like protein	nuclear receptor activity nuclear steroid 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 vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding nuclear receptor activity nuclear steroid 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 vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding small molecule binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding retinoic acid-responsive element 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 cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation retinoic acid receptor signaling pathway hormone-mediated signaling pathway developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation 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 response to retinoic acid response to lipid response to oxygen-containing compound	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
C [auth E], D [auth F]	Nuclear receptor coactivator 1	transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein dimerization activity catalytic activity, acting on a protein N-acetyltransferase activity acyltransferase activity transferase activity peptide N-acetyltransferase activity transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding protein dimerization activity catalytic activity, acting on a protein N-acetyltransferase activity acyltransferase activity transferase activity peptide N-acetyltransferase activity histone acetyltransferase activity acetyltransferase activity peptide-lysine-N-acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound 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 response to organic cyclic 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 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 cellular response to stimulus intracellular receptor signaling pathway signaling hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus cellular response to organic cyclic compound estrogen receptor signaling pathway cellular response to chemical stimulus cellular response to lipid nuclear receptor-mediated signaling pathway 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 regulation of response to stimulus 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 positive regulation of nucleobase-containing compound metabolic process 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 regulation of signal transduction regulation of thyroid hormone receptor signaling pathway regulation of intracellular signal transduction regulation of signaling thyroid hormone receptor signaling pathway regulation of cell communication 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050274	Nuclear hormone receptor family NR2 subfamily	Family
A, B	IPR001723	Nuclear hormone receptor	Family
A, B	IPR000003	Retinoid X receptor/HNF4	Family
A, B	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A, B	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A, B	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A, B	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR010011	Nuclear receptor coactivator, DUF1518	Domain
C [auth E], D [auth F]	IPR028819	Nuclear receptor coactivator 1, basic helix-loop-helix	Domain
C [auth E], D [auth F]	IPR009110	Nuclear receptor coactivator, interlocking	Homologous Superfamily
C [auth E], D [auth F]	IPR017426	Nuclear receptor coactivator	Family
C [auth E], D [auth F]	IPR014935	Nuclear receptor coactivator, receptor-binding domain	Domain
C [auth E], D [auth F]	IPR014920	Nuclear receptor coactivator, Ncoa-type, interlocking	Domain
C [auth E], D [auth F]	IPR035965	PAS domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR037077	Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR013767	PAS fold	Domain
C [auth E], D [auth F]	IPR000014	PAS domain	Domain
C [auth E], D [auth F]	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth E], D [auth F]	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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.