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- PDB-4xao: Crystal structure of the hPXR-LBD obtained in presence of the pes... -

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Basic information

Entry
Database: PDB / ID: 4xao
TitleCrystal structure of the hPXR-LBD obtained in presence of the pesticide trans-nonachlor
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsGENE REGULATION / HORMONE RECEPTOR / PESTICIDE
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
: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsDelfosse, V. / Huet, T. / Bourguet, W.
Funding support France, 2items
OrganizationGrant numberCountry
ANR CESA France
Plan Cancer Inserm France
CitationJournal: 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
DepositionDec 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Jul 4, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4593
Polymers36,2811
Non-polymers1782
Water1,20767
1
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules

A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9186
Polymers72,5622
Non-polymers3574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area2390 Å2
ΔGint-19 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.300, 92.300, 86.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR


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
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 100 mM Imidazole, 10% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 16, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.58→41.28 Å / Num. obs: 12258 / % possible obs: 96.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 35.9 Å2 / Rsym value: 0.11 / Net I/σ(I): 14.66
Reflection shellResolution: 2.58→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.08 / % possible all: 78.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: 1.8.4_1496)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ILG

1ilg


Resolution: 2.58→41.28 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.56 / Stereochemistry target values: ML
Details: The protein PXR has been crystallized in presence of the pesticide trans-nonachlor. The ligand seems present in the ligand binding pocket but the density is not enough defined to model it. ...Details: The protein PXR has been crystallized in presence of the pesticide trans-nonachlor. The ligand seems present in the ligand binding pocket but the density is not enough defined to model it. Other data from native mass spectrometry indicate that the ligand could bind PXR.
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 981 8 %Random selection
Rwork0.1892 ---
obs0.1931 12258 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.6 Å2
Refinement stepCycle: LAST / Resolution: 2.58→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 12 67 2234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022233
X-RAY DIFFRACTIONf_angle_d0.5693025
X-RAY DIFFRACTIONf_dihedral_angle_d14.387812
X-RAY DIFFRACTIONf_chiral_restr0.022337
X-RAY DIFFRACTIONf_plane_restr0.003388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.71130.29051330.21111536X-RAY DIFFRACTION98
2.7113-2.88110.281380.21171586X-RAY DIFFRACTION100
2.8811-3.10350.23911380.21481583X-RAY DIFFRACTION100
3.1035-3.41570.30351390.21511598X-RAY DIFFRACTION100
3.4157-3.90960.23711400.18231605X-RAY DIFFRACTION100
3.9096-4.92440.18361410.15991629X-RAY DIFFRACTION100

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