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Yorodumi- PDB-3w0i: Crystal Structure of Rat VDR Ligand Binding Domain in Complex wit... -
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-Basic information
Entry | Database: PDB / ID: 3w0i | ||||||
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Title | Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands | ||||||
Components |
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Keywords | TRANSCRIPTION / GENE REGULATION | ||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Shimizu, T. / Asano, L. / Kuwabara, N. / Ito, I. / Waku, T. / Yanagisawa, J. / Miyachi, H. | ||||||
Citation | Journal: Febs Lett. / Year: 2013 Title: Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands. Authors: Asano, L. / Ito, I. / Kuwabara, N. / Waku, T. / Yanagisawa, J. / Miyachi, H. / Shimizu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w0i.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w0i.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3w0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w0i_validation.pdf.gz | 715.6 KB | Display | wwPDB validaton report |
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Full document | 3w0i_full_validation.pdf.gz | 719 KB | Display | |
Data in XML | 3w0i_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3w0i_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/3w0i ftp://data.pdbj.org/pub/pdb/validation_reports/w0/3w0i | HTTPS FTP |
-Related structure data
Related structure data | 3w0gC 3w0hC 3w0jC 1rk3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28755.025 Da / Num. of mol.: 1 Fragment: LIGAND BINDING DOMAIN, UNP residues 121-159, 218-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nr1i1, Vdr / Production host: Escherichia coli (E. coli) / References: UniProt: P13053 |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: DRIP 205 NR2 BOX PEPTIDE, UNP residues 640-652 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648 |
#3: Chemical | ChemComp-O11 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M MOPS (pH7.0), 16-18% PEG 4000, 0.2M sodium formate, 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 22, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.17 Å / Num. all: 11841 / Num. obs: 11692 / % possible obs: 98.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.98 Å / % possible all: 98.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RK3 Resolution: 1.9→41.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.427 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.397 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 44.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→41.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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