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Yorodumi- PDB-3dr1: Side-chain fluorine atoms of non-steroidal vitamin D3 analogs sta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dr1 | ||||||
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Title | Side-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix 12 of vitamin D receptor | ||||||
Components |
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Keywords | GENE REGULATION/TRANSFERASE / GENE REGULATION / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription / Transcription regulation / Zinc / Zinc-finger / Activator / Acyltransferase / Alternative splicing / Chromosomal rearrangement / Phosphoprotein / Polymorphism / Proto-oncogene / Transferase / Ubl conjugation / GENE REGULATION-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / lithocholic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hematopoietic stem cell proliferation / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / heart looping / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / calcium ion homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ossification / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / hippocampus development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sato, Y. / Rochel, N. / Moras, D. | ||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Superagonistic fluorinated vitamin D3 analogs stabilize helix 12 of the vitamin D receptor. Authors: Eelen, G. / Valle, N. / Sato, Y. / Rochel, N. / Verlinden, L. / De Clercq, P. / Moras, D. / Bouillon, R. / Munoz, A. / Verstuyf, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dr1.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dr1.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3dr1 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3dr1 | HTTPS FTP |
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-Related structure data
Related structure data | 2hc4S 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: 34060.672 Da / Num. of mol.: 1 / Fragment: Ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21de3 / References: UniProt: Q9PTN2 |
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#2: Protein/peptide | Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-C5D / ( |
#5: 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: 2.34 Å3/Da / Density % sol: 47.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Li sulfate 1.6M, Mg sulfate 50mM, Bis Tris 0.1M , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2007 |
Radiation | Monochromator: Si(311) or Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 10290 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 13.4 % / Biso Wilson estimate: 56.8 Å2 / Rsym value: 0.111 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 13.4 / Num. unique all: 990 / Rsym value: 0.299 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HC4 Resolution: 2.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1
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Displacement parameters | Biso mean: 48.8 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å
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