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Yorodumi- PDB-8pwf: crystal structure of VDR in complex with Des-C-Ring and Aromatic-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pwf | ||||||
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Title | crystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 2 | ||||||
Components |
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Keywords | TRANSCRIPTION / nuclear receptor / VDR / agonist | ||||||
Function / homology | Function and homology information heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / locomotor rhythm ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / calcitriol binding / vitamin D binding / lithocholic acid binding / hematopoietic stem cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / heart looping / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / 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 / cellular response to hormone stimulus / Recycling of bile acids and salts / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ossification / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / cell differentiation / nuclear body / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | rochel, N. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Novel Des-C-Ring and Aromatic-D-Ring analogs Acting as Potent Agonists of the Vitamin D Receptor (VDR) Authors: Rochel, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pwf.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pwf.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pwf_validation.pdf.gz | 736.6 KB | Display | wwPDB validaton report |
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Full document | 8pwf_full_validation.pdf.gz | 741.3 KB | Display | |
Data in XML | 8pwf_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 8pwf_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/8pwf ftp://data.pdbj.org/pub/pdb/validation_reports/pw/8pwf | HTTPS FTP |
-Related structure data
Related structure data | 8pwdC 8pweC 8pwmC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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) / References: UniProt: Q9PTN2 |
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#2: Protein/peptide | Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596 |
#3: Chemical | ChemComp-FVB / ( Mass: 506.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32F6O3 / Feature type: SUBJECT OF INVESTIGATION |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: LiSO4 1.6M, Hepes 0.1M pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.74 Å / Num. obs: 15928 / % possible obs: 98.81 % / Redundancy: 20 % / Biso Wilson estimate: 67.86 Å2 / CC1/2: 1 / Net I/σ(I): 19.28 |
Reflection shell | Resolution: 2.3→2.382 Å / Num. unique obs: 1537 / CC1/2: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.74 Å / SU ML: 0.4201 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.381 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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