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- PDB-4x1g: Crystal structure of the hPXR-LBD in complex with the synthetic e... -

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Basic information

Entry
Database: PDB / ID: 4x1g
TitleCrystal structure of the hPXR-LBD in complex with the synthetic estrogen 17alpha-ethinylestradiol and the pesticide trans-nonachlor
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsGENE REGULATION / HORMONE RECEPTOR / ESTROGEN / 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 / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / 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
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 ...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
Ethinyl estradiol / Trans-nonachlor / ISOPROPYL ALCOHOL / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionNov 24, 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)37,2005
Polymers36,2811
Non-polymers9194
Water2,198122
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)74,40010
Polymers72,5622
Non-polymers1,8388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area2020 Å2
ΔGint-25 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.340, 91.340, 85.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-3WF / Ethinyl estradiol / Ethinylestradiol


Mass: 296.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24O2 / Comment: medication, hormone*YM
#3: Chemical ChemComp-3WG / Trans-nonachlor


Mass: 444.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H5Cl9
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 50 mM NaCl, 50 mM LiCl, 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: 2.25→40.85 Å / Num. obs: 17316 / % possible obs: 97.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.09 / Net I/σ(I): 12.4
Reflection shellResolution: 2.25→2.38 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 99

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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: 2.25→38.715 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 866 5 %Random selection
Rwork0.1741 ---
obs0.1763 17316 97.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 53 122 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082318
X-RAY DIFFRACTIONf_angle_d1.0673160
X-RAY DIFFRACTIONf_dihedral_angle_d13.682878
X-RAY DIFFRACTIONf_chiral_restr0.039357
X-RAY DIFFRACTIONf_plane_restr0.005397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.3910.28871430.20652715X-RAY DIFFRACTION99
2.391-2.57560.28491420.2112708X-RAY DIFFRACTION99
2.5756-2.83470.2471440.1962740X-RAY DIFFRACTION99
2.8347-3.24480.26031440.19142736X-RAY DIFFRACTION98
3.2448-4.08730.19471440.15252733X-RAY DIFFRACTION97
4.0873-38.72110.17581490.15812818X-RAY DIFFRACTION95

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