+Open data
-Basic information
Entry | Database: PDB / ID: 7ax8 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the hPXR-LBD in apo form (P43212 SG) | ||||||||||||
Components | Nuclear receptor subfamily 1 group I member 2 | ||||||||||||
Keywords | NUCLEAR PROTEIN / NUCLEAR RECEPTOR HORMONE RECEPTOR PREGNANE X RECEPTOR | ||||||||||||
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 / positive regulation of gene expression / regulation of DNA-templated transcription / 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 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||||||||
Authors | Delfosse, V. / Huet, T. / Bourguet, W. | ||||||||||||
Funding support | France, 3items
| ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Mechanistic insights into the synergistic activation of the RXR-PXR heterodimer by endocrine disruptor mixtures. Authors: Delfosse, V. / Huet, T. / Harrus, D. / Granell, M. / Bourguet, M. / Gardia-Parege, C. / Chiavarina, B. / Grimaldi, M. / Le Mevel, S. / Blanc, P. / Huang, D. / Gruszczyk, J. / Demeneix, B. / ...Authors: Delfosse, V. / Huet, T. / Harrus, D. / Granell, M. / Bourguet, M. / Gardia-Parege, C. / Chiavarina, B. / Grimaldi, M. / Le Mevel, S. / Blanc, P. / Huang, D. / Gruszczyk, J. / Demeneix, B. / Cianferani, S. / Fini, J.B. / Balaguer, P. / Bourguet, W. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ax8.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ax8.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ax8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ax8_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ax8_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 7ax8_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7ax8_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/7ax8 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/7ax8 | HTTPS FTP |
-Related structure data
Related structure data | 7ax9C 7axaC 7axbC 7axcC 7axdC 7axeC 7axfC 7axgC 7axhC 7axiC 7axjC 7axkC 7axlC 1ilgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 36280.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pRSETA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469 |
---|---|
#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 50 - 100 mM imidazole 8 - 14% isopropanol / PH range: 7.0 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→51.765 Å / Num. obs: 20534 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.54 Å2 / Rrim(I) all: 0.078 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2006 / Rrim(I) all: 0.652 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ILG Resolution: 2.15→51.765 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.77 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.13 Å2 / Biso mean: 43.09 Å2 / Biso min: 21.22 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→51.765 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|