3VT7 | pdb_00003vt7

Crystal structures of rat VDR-LBD with W282R mutation

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e3vt7A2	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: ACR_tran	F:	ECOD (20:10:01)

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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	COACTIVATOR PEPTIDE DRIP	protein binding binding signaling receptor binding peroxisome proliferator activated receptor binding chromatin binding promoter-specific chromatin binding DNA binding nucleic acid binding protein-containing complex binding LBD domain binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding binding signaling receptor binding peroxisome proliferator activated receptor binding chromatin binding promoter-specific chromatin binding DNA binding nucleic acid binding protein-containing complex binding LBD domain binding protein domain specific binding transcription 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 transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity nuclear retinoic acid receptor binding transcription corepressor activity transcription coregulator binding transcription coactivator binding nuclear estrogen receptor binding	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development 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 regulation of hormone levels phenol-containing compound metabolic process modified amino acid metabolic process metabolic process regulation of biological quality hormone metabolic process thyroid hormone generation thyroid hormone 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 regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process epithelium development retinal pigment epithelium development retina development in camera-type eye tissue development establishment of protein localization cellular localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization 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 embryonic hemopoiesis embryonic organ development 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 cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling intracellular signal transduction cell communication peroxisome proliferator activated receptor signaling pathway signal transduction nuclear receptor-mediated signaling pathway fat cell differentiation mRNA transcription by RNA polymerase II RNA metabolic process primary 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 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 response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to thyroid hormone stimulus cellular response to 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 sex differentiation 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 female sex differentiation morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium 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 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 biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process 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 heart development cardiac chamber morphogenesis cardiac muscle tissue development muscle tissue morphogenesis circulatory system development cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis heart trabecula morphogenesis cardiac ventricle development trabecula morphogenesis muscle organ morphogenesis thyroid hormone receptor signaling pathway hormone-mediated signaling pathway 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 response to lipid regulation of signal transduction response to vitamin cellular response to vitamin D response to vitamin D regulation of intracellular signal transduction 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 cellular response to lipid 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 response to peptide positive regulation of cytokine-mediated signaling pathway positive regulation of signaling response to steroid hormone nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway embryonic heart tube development placenta development chordate embryonic development in utero embryonic development embryonic placenta development embryo development ending in birth or egg hatching regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of transcription initiation by RNA polymerase II DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II stem cell differentiation hematopoietic stem cell differentiation hematopoietic progenitor cell differentiation regulation of hepatocyte proliferation positive regulation of cell population proliferation positive regulation of epithelial cell proliferation 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 mammary gland epithelial cell proliferation 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 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 regulation of intracellular estrogen receptor signaling pathway regulation of intracellular steroid hormone receptor signaling pathway positive regulation of intracellular signal transduction estrogen receptor signaling pathway positive regulation of intracellular steroid hormone receptor signaling pathway	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle mediator complex RNA polymerase II transcription regulator complex core mediator complex transcription regulator complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle mediator complex RNA polymerase II transcription regulator complex core mediator complex transcription regulator complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen nucleoplasm
A	Vitamin D3 receptor	vitamin binding binding vitamin D binding steroid binding lipid binding small molecule binding calcitriol binding D3 vitamins binding sequence-specific DNA binding DNA binding nucleic acid binding lithocholic acid binding organic acid binding bile acid binding vitamin binding binding vitamin D binding steroid binding lipid binding small molecule binding calcitriol binding D3 vitamins binding sequence-specific DNA binding DNA binding nucleic acid binding lithocholic acid binding organic acid binding bile acid binding ion binding anion binding carboxylic acid binding monocarboxylic acid binding nuclear receptor activity DNA-binding transcription factor activity, RNA polymerase II-specific molecular transducer activity transcription regulator activity DNA-binding transcription factor activity signaling receptor activity ligand-modulated transcription factor activity 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 steroid receptor activity 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 cation binding transition metal ion binding zinc ion binding metal ion binding bile acid nuclear receptor activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of calcium ion transport regulation of localization regulation of biological process transport regulation of transport regulation of monoatomic ion transport developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development regulation of calcium ion transport regulation of localization regulation of biological process transport regulation of transport regulation of monoatomic ion transport biological regulation establishment of localization metal ion transport calcium ion transport localization monoatomic ion transport regulation of metal ion transport monoatomic cation transport response to stimulus response to metal ion response to chemical response to calcium ion skeletal system development regulation of biosynthetic process regulation of cellular process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process system process digestion intestinal absorption digestive system process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular response to stimulus 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 cellular response to chemical stimulus response to hormone signal transduction nuclear receptor-mediated signaling pathway cellular response to hormone stimulus 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription response to bile acid response to lipid response to oxygen-containing compound anatomical structure morphogenesis cell morphogenesis mRNA transcription by RNA polymerase II mRNA transcription mRNA metabolic process transcription by RNA polymerase II regulation of body fluid levels secretion mammary gland development gland development body fluid secretion lactation regulation of biological quality negative regulation of cell population proliferation cell population proliferation regulation of keratinocyte proliferation negative regulation of biological process negative regulation of keratinocyte proliferation regulation of cell population proliferation negative regulation of cellular process regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation keratinocyte proliferation response to aldosterone response to ketone response to alcohol response to mineralocorticoid response to corticosteroid response to steroid hormone negative regulation of RNA biosynthetic 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 biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process transmembrane transport phosphate ion transmembrane transport phosphate ion transport inorganic anion transport cellular developmental process cell differentiation animal organ morphogenesis regulation of developmental process negative regulation of developmental process bone trabecula formation bone trabecula morphogenesis anatomical structure formation involved in morphogenesis regulation of bone trabecula formation skeletal system morphogenesis negative regulation of bone trabecula formation trabecula formation trabecula morphogenesis response to nutrient levels response to vitamin cellular response to vitamin D response to vitamin D response to nutrient cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to vitamin cellular response to lipid cellular response to nutrient branching involved in mammary gland duct morphogenesis multi-multicellular organism process mammary gland morphogenesis reproductive process maternal process involved in female pregnancy branching morphogenesis of an epithelial tube developmental process involved in reproduction tube morphogenesis gland morphogenesis mammary gland branching involved in pregnancy epithelial tube morphogenesis female pregnancy epithelium development tube development multicellular organismal reproductive process morphogenesis of an epithelium tissue development mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure multi-organism reproductive process morphogenesis of a branching epithelium positive regulation of cell communication regulation of parathyroid hormone secretion regulation of hormone secretion regulation of system process positive regulation of secretion by cell hormone secretion positive regulation of parathyroid hormone secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion signal release regulation of multicellular organismal process regulation of signaling regulation of hormone levels export from cell cell-cell signaling parathyroid hormone secretion regulation of secretion endocrine process endocrine hormone secretion positive regulation of transport regulation of cell communication hormone transport positive regulation of multicellular organismal process regulation of endocrine process positive regulation of signaling regulation of response to nutrient levels positive regulation of signal transduction regulation of signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus regulation of vitamin D receptor signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of vitamin D receptor signaling pathway regulation of phosphate transmembrane transport negative regulation of phosphate transmembrane transport negative regulation of transport regulation of phosphate transport negative regulation of transmembrane transport regulation of transmembrane transport placenta development maternal placenta development decidualization cell junction maintenance cellular component organization cell junction organization cellular component maintenance cellular component organization or biogenesis cell-cell junction maintenance cell-cell junction organization cell death apoptotic signaling pathway apoptotic process programmed cell death positive regulation of keratinocyte differentiation regulation of epidermal cell differentiation epidermis development regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal development epidermal cell differentiation positive regulation of epidermis development positive regulation of epithelial cell differentiation skin development keratinocyte differentiation regulation of epidermis development regulation of keratinocyte differentiation positive regulation of epidermal cell differentiation ossification negative regulation of multicellular organismal process regulation of ossification negative regulation of ossification bile acid signaling pathway nuclear receptor-mediated bile acid signaling pathway cellular response to nitrogen compound response to nitrogen compound cellular response to amyloid-beta response to amyloid-beta apoptotic process involved in morphogenesis regulation of programmed cell death positive regulation of apoptotic process involved in mammary gland involution apoptotic process involved in development positive regulation of apoptotic process involved in morphogenesis mammary gland involution positive regulation of programmed cell death positive regulation of apoptotic process involved in development apoptotic process involved in mammary gland involution regulation of apoptotic process regulation of apoptotic process involved in development positive regulation of apoptotic process tissue remodeling response to estradiol	cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin cell periphery cellular anatomical structure sarcolemma plasma membrane membrane T-tubule intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex receptor complex heterochromatin perinuclear region of cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix RNA polymerase II transcription regulator complex nuclear protein-containing complex transcription regulator complex membrane microdomain membrane raft plasma membrane raft plasma membrane region caveola nucleoplasm nucleolus dense fibrillar component euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR019680	Mediator complex, subunit Med1	Domain
B [auth C]	IPR051999	Mediator complex subunit 1	Family
A	IPR001628	Zinc finger, nuclear hormone receptor-type	Domain
A	IPR013088	Zinc finger, NHR/GATA-type	Homologous Superfamily
A	IPR042153	VDR, DNA-binding domain	Domain
A	IPR050234	Nuclear hormone receptor family NR1 subfamily	Family
A	IPR001723	Nuclear hormone receptor	Family
A	IPR000324	Vitamin D receptor	Family
A	IPR000536	Nuclear hormone receptor, ligand-binding domain	Domain
A	IPR035500	Nuclear hormone receptor-like domain superfamily	Homologous Superfamily

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