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- PDB-5xuq: Crystal structure of VDR-LBD complexed with an antagonist, 2-meth... -
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Basic information
Entry | Database: PDB / ID: 5xuq | ||||||
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Title | Crystal structure of VDR-LBD complexed with an antagonist, 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin D3 | ||||||
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![]() | TRANSCRIPTION / Vitamin D receptor antagonist helix 10/11 | ||||||
Function / homology | ![]() enucleate erythrocyte development / negative regulation of bone trabecula formation / positive regulation of type II interferon-mediated signaling pathway / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / SUMOylation of intracellular receptors ...enucleate erythrocyte development / negative regulation of bone trabecula formation / positive regulation of type II interferon-mediated signaling pathway / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / SUMOylation of intracellular receptors / G0 to G1 transition / thyroid hormone receptor signaling pathway / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / dense fibrillar component / core mediator complex / regulation of vitamin D receptor signaling pathway / positive regulation of parathyroid hormone secretion / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / nuclear retinoic acid receptor binding / mediator complex / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / negative regulation of ossification / cellular response to thyroid hormone stimulus / positive regulation of vitamin D receptor signaling pathway / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / peroxisome proliferator activated receptor binding / intestinal absorption / bile acid signaling pathway / lens development in camera-type eye / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / nuclear thyroid hormone receptor binding / megakaryocyte development / histone acetyltransferase binding / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / response to aldosterone / RSV-host interactions / LBD domain binding / epithelial cell proliferation involved in mammary gland duct elongation / fat cell differentiation / mammary gland branching involved in pregnancy / regulation of calcium ion transport / monocyte differentiation / decidualization / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / embryonic placenta development / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / cellular response to epidermal growth factor stimulus / T-tubule / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / positive regulation of erythrocyte differentiation / nuclear receptor coactivator activity / liver development / skeletal system development / promoter-specific chromatin binding / nuclear estrogen receptor binding / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / apoptotic signaling pathway / transcription coregulator activity / animal organ morphogenesis / Heme signaling / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / brain development Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kato, A. / Itoh, T. / Yamamoto, K. | ||||||
![]() | ![]() Title: Discovery of Potent Vitamin D Receptor Antagonist Authors: Kato, A. / Tabei, M. / Itoh, T. / Yamamoto, K. #1: ![]() Title: Crystal structure of VDR-LBD complexed with antagonist 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin D3 Authors: Kato, A. / Itoh, T. / Yamamoto, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.4 KB | Display | ![]() |
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Full document | ![]() | 746.3 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30595.037 Da / Num. of mol.: 1 / Fragment: UNP residues 116-423 / Mutation: deletion 165-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: UNP residues 640-652 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2 Production host: ![]() ![]() |
#3: Chemical | ChemComp-8FF / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→41.71 Å / Num. obs: 6482 / % possible obs: 99 % / Redundancy: 3.3 % / Net I/σ(I): 9.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.861 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→41.71 Å
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