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Yorodumi- PDB-8fpe: Crystal structure of pregnane X receptor ligand binding domain co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fpe | ||||||
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Title | Crystal structure of pregnane X receptor ligand binding domain complexed with T0901317 analog T0-BP | ||||||
Components | Nuclear receptor subfamily 1 group I member 2 | ||||||
Keywords | TRANSCRIPTION / nuclear receptor / transcription factor / metabolism / antibiotic | ||||||
Function / homology | Function and homology information xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / SUMOylation of intracellular receptors / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / SUMOylation of intracellular receptors / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / 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: 2.3 Å | ||||||
Authors | Huber, A.D. / Poudel, S. / Seetharaman, J. / Miller, D.J. / Lin, W. / Li, Y. / Chen, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein. Authors: Lin, W. / Huber, A.D. / Poudel, S. / Li, Y. / Seetharaman, J. / Miller, D.J. / Chen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fpe.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fpe.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/8fpe ftp://data.pdbj.org/pub/pdb/validation_reports/fp/8fpe | HTTPS FTP |
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-Related structure data
Related structure data | 8e3nC 8eqzC 1m13S S: Starting model for refinement 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: 36208.742 Da / Num. of mol.: 1 / Fragment: UNP residues 153-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Production host: Escherichia coli (E. coli) / References: UniProt: O75469 |
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#2: Chemical | ChemComp-Y5B / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50 mM imidazole pH 7, 12% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.76 Å / Num. obs: 16633 / % possible obs: 99.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 49.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1591 / CC1/2: 0.815 / Rpim(I) all: 0.331 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M13 Resolution: 2.3→35.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8927 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 55.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→35.54 Å
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Refine LS restraints |
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LS refinement shell |
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