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Yorodumi- PDB-4x1f: Crystal structure of the hPXR-LBD in complex with the synthetic e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x1f | |||||||||
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Title | Crystal structure of the hPXR-LBD in complex with the synthetic estrogen 17alpha-ethinylestradiol | |||||||||
Components | Nuclear receptor subfamily 1 group I member 2 | |||||||||
Keywords | GENE REGULATION / nuclear receptor / hormone receptor / pregnane X receptor / estrogen | |||||||||
Function / homology | Function and homology information xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Delfosse, V. / Huet, T. / Bourguet, W. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat Commun / Year: 2015 Title: Synergistic activation of human pregnane X receptor by binary cocktails of pharmaceutical and environmental compounds. Authors: Delfosse, V. / Dendele, B. / Huet, T. / Grimaldi, M. / Boulahtouf, A. / Gerbal-Chaloin, S. / Beucher, B. / Roecklin, D. / Muller, C. / Rahmani, R. / Cavailles, V. / Daujat-Chavanieu, M. / ...Authors: Delfosse, V. / Dendele, B. / Huet, T. / Grimaldi, M. / Boulahtouf, A. / Gerbal-Chaloin, S. / Beucher, B. / Roecklin, D. / Muller, C. / Rahmani, R. / Cavailles, V. / Daujat-Chavanieu, M. / Vivat, V. / Pascussi, J.M. / Balaguer, P. / Bourguet, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x1f.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x1f.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 4x1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x1f_validation.pdf.gz | 707.2 KB | Display | wwPDB validaton report |
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Full document | 4x1f_full_validation.pdf.gz | 709.4 KB | Display | |
Data in XML | 4x1f_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4x1f_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1f ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1f | HTTPS FTP |
-Related structure data
Related structure data | 4x1gC 4xaoC 1ilgS 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: 36280.867 Da / Num. of mol.: 1 / Fragment: UNP residues 130-434 Source method: isolated from a genetically manipulated source Details: Synthetic gene / Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469 | ||
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#2: Chemical | ChemComp-3WF / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 100 mM NaCl, 100 mM Imidazole, 10% Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 16, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.67 Å / Num. obs: 24998 / % possible obs: 100 % / Redundancy: 10.4 % / Rsym value: 0.08 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ILG Resolution: 2→45.67 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.67 Å
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Refine LS restraints |
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LS refinement shell |
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