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Yorodumi- PDB-3aun: Crystal structure of the rat vitamin D receptor ligand binding do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aun | ||||||
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Title | Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205 | ||||||
Components |
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Keywords | TRANSCRIPTION / Binding Sites / Biphenyl Compounds / Protein Binding / Tertiary / Rats / Receptors / Calcitriol / Vitamin D | ||||||
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 / LBD domain 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 / monocyte differentiation / 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 / embryonic placenta development / 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 / fat cell differentiation / mammary gland branching involved in pregnancy / regulation of calcium ion transport / nuclear retinoid X receptor binding / decidualization / general transcription initiation factor binding / cellular response to epidermal growth factor stimulus / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / positive regulation of transcription initiation by RNA polymerase II / peroxisome proliferator activated receptor signaling pathway / animal organ regeneration / heterochromatin / erythrocyte development / positive regulation of transcription elongation by RNA polymerase II / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / transcription coregulator activity / T-tubule / RORA activates gene expression / 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 / mRNA transcription by RNA polymerase II / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / apoptotic signaling pathway / animal organ morphogenesis / PPARA activates gene expression / Heme signaling / response to calcium ion / Nuclear Receptor transcription pathway / euchromatin / brain development Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Kakuda, S. / Takimoto-Kamimura, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Design, synthesis and X-ray crystallographic study of new nonsecosteroidal vitamin D receptor ligands Authors: Demizu, Y. / Takahashi, T. / Kaneko, F. / Sato, Y. / Okuda, H. / Ochiai, E. / Horie, K. / Takagi, K. / Kakuda, S. / Takimoto-Kamimura, M. / Kurihara, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aun.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aun.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 3aun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aun_validation.pdf.gz | 740.9 KB | Display | wwPDB validaton report |
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Full document | 3aun_full_validation.pdf.gz | 742.7 KB | Display | |
Data in XML | 3aun_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3aun_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3aun ftp://data.pdbj.org/pub/pdb/validation_reports/au/3aun | HTTPS FTP |
-Related structure data
Related structure data | 2zfxS 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: 30055.498 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Mutation: DEL(165-211) mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P13053 |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) / References: UniProt: Q15648 |
#3: Chemical | ChemComp-YR4 / ( |
#4: Water | ChemComp-HOH / |
Sequence details | CHAIN A IS DELETION MUTANT. REISDUES 165-211 WERE DELETED. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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Detector | Detector: CCD / Date: May 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 27038 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % |
Reflection shell | Resolution: 1.8→1.87 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zfx Resolution: 1.81→27.31 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 2.286 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.735 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→27.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.812→1.859 Å / Total num. of bins used: 20
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