+Open data
-Basic information
Entry | Database: PDB / ID: 5ow7 | ||||||
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Title | VDR complex | ||||||
Components |
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Keywords | TRANSCRIPTION / Nuclear Receptor / Complex / Vitamin D receptor | ||||||
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 mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...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 mediated 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 / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / calcium ion homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / ossification / BMAL1:CLOCK,NPAS2 activates circadian gene expression / nuclear receptor coactivator activity / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / mRNA transcription by RNA polymerase II / Heme signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / male gonad development / nuclear receptor activity / 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 / chromatin / regulation of DNA-templated transcription / 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: 2.1 Å | ||||||
Authors | Rochel, N. / Li, W. | ||||||
Funding support | France, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Investigation of 20S-hydroxyvitamin D3 analogs and their 1 alpha-OH derivatives as potent vitamin D receptor agonists with anti-inflammatory activities. Authors: Lin, Z. / Marepally, S.R. / Goh, E.S.Y. / Cheng, C.Y.S. / Janjetovic, Z. / Kim, T.K. / Miller, D.D. / Postlethwaite, A.E. / Slominski, A.T. / Tuckey, R.C. / Peluso-Iltis, C. / Rochel, N. / Li, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ow7.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ow7.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ow7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/5ow7 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/5ow7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ow9C 5owdC 2hc4S S: Starting model for refinement C: citing same article (ref.) |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vdra, nr1i1a, vdr / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: Q9PTN2 |
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#2: Protein/peptide | Mass: 1776.072 Da / Num. of mol.: 1 / Fragment: UNP residues 686-700 / Source method: obtained synthetically / Details: RHKILHRLLQEGSPS / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase |
#3: Chemical | ChemComp-AYK / ( |
#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: 2.28 Å3/Da / Density % sol: 46.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→21.8 Å / Num. obs: 20462 / % possible obs: 99 % / Redundancy: 1.2 % / Biso Wilson estimate: 32.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.75 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 2.95 / Num. unique obs: 1968 / CC1/2: 1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HC4 Resolution: 2.1→21.8 Å / Cor.coef. Fo:Fc: 0.9091 / Cor.coef. Fo:Fc free: 0.8934 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.191 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.157
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Displacement parameters | Biso mean: 42.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.258 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→21.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.21 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -30.7731 Å / Origin y: 25.6266 Å / Origin z: -1.2335 Å
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Refinement TLS group | Selection details: { A|* } |