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Yorodumi- PDB-3w5r: Crystal structure of complexes of vitamin D receptor ligand bindi... -
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-Basic information
Entry | Database: PDB / ID: 3w5r | ||||||
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Title | Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives | ||||||
Components |
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Keywords | TRANSCRIPTION / ZINC-FINGER / NUCLEAR RECEPTOR-AGONIST COMPLEX / RECEPTOR / TRANSCRIPTION REGULATION / ACTIVATOR / DNA-BINDING / METAL-BINDING / PHOSPHOPROTEIN / NUCLEUS | ||||||
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 / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / 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 / lithocholic acid binding / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of ossification / positive regulation of hepatocyte proliferation / embryonic hindlimb morphogenesis / vitamin D receptor signaling pathway / peroxisome proliferator activated receptor binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / bile acid signaling pathway / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / histone acetyltransferase binding / cellular response to hepatocyte growth factor stimulus / response to aldosterone / RSV-host interactions / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / 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 / heterochromatin / erythrocyte development / 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 / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / liver development / nuclear receptor coactivator activity / skeletal system development / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / apoptotic signaling pathway / animal organ morphogenesis / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / euchromatin / brain development / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / PPARA activates gene expression Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Masuno, H. / Ikura, T. / Ito, N. | ||||||
Citation | Journal: J.Lipid Res. / Year: 2013 Title: Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives. Authors: Masuno, H. / Ikura, T. / Morizono, D. / Orita, I. / Yamada, S. / Shimizu, M. / Ito, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w5r.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w5r.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 3w5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w5r ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5r | HTTPS FTP |
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-Related structure data
Related structure data | 3w5pC 3w5qC 3w5tC 1rjkS 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: 30595.037 Da / Num. of mol.: 1 / Fragment: VDR-LBD, UNP RESIDUES 116-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Plasmid: PET14B / 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: SYNTHETIC PEPTIDE / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648 |
#3: Chemical | ChemComp-LOA / ( |
#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: 2.08 Å3/Da / Density % sol: 40.91 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 20, 2006 |
Radiation | Monochromator: TRIANGULAR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 13707 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1319 / Rsym value: 0.295 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RJK Resolution: 2.2→40.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 144664.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.0169 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→40.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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