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- PDB-7axa: Crystal structure of the hPXR-LBD in complex with clotrimazole -

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Basic information

Entry
Database: PDB / ID: 7axa
TitleCrystal structure of the hPXR-LBD in complex with clotrimazole
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsNUCLEAR PROTEIN / NUCLEAR RECEPTOR HORMONE RECEPTOR PREGNANE X RECEPTOR
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / intracellular receptor signaling pathway / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / intracellular receptor signaling pathway / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear body / 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 / nucleus
Similarity search - Function
: / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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 hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Similarity search - Domain/homology
1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsDelfosse, V. / Granell, M. / Blanc, P. / Bourguet, W.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INBS-04-01 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05 France
European Union (EU)825489 France
CitationJournal: 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
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)37,0922
Polymers36,7471
Non-polymers3451
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, A DIMERIC FORM REMAINS HYPOTHETICAL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
2
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)74,1854
Polymers73,4952
Non-polymers6902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area3170 Å2
ΔGint-41 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.350, 91.350, 86.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 36747.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469
#2: Chemical ChemComp-CL6 / 1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE / CLOTRIMAZOLE


Mass: 344.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H17ClN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 50 - 100 mM imidazole 8 - 14% isopropanol / PH range: 7.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.26→45.68 Å / Num. obs: 17442 / % possible obs: 98.6 % / Redundancy: 7.7 % / Biso Wilson estimate: 35.57 Å2 / Rrim(I) all: 0.061 / Net I/σ(I): 23.95
Reflection shellResolution: 2.26→2.32 Å / Mean I/σ(I) obs: 4.68 / Num. unique obs: 1184 / Rrim(I) all: 0.574

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Processing

Software
NameVersionClassification
PHENIXphasing
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ILG

1ilg


Resolution: 2.26→45.67 Å / SU ML: 0.2521 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8587
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 872 5 %RANDOM
Rwork0.1867 16565 --
obs0.1891 17437 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.31 Å2
Refinement stepCycle: LAST / Resolution: 2.26→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 25 170 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832311
X-RAY DIFFRACTIONf_angle_d0.9413142
X-RAY DIFFRACTIONf_chiral_restr0.0452343
X-RAY DIFFRACTIONf_plane_restr0.0059450
X-RAY DIFFRACTIONf_dihedral_angle_d21.2386894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.40.30221390.22922627X-RAY DIFFRACTION96.11
2.4-2.590.26731440.20512748X-RAY DIFFRACTION99.9
2.59-2.850.24371430.20772727X-RAY DIFFRACTION99.17
2.85-3.260.27041460.19822779X-RAY DIFFRACTION99.93
3.26-4.110.23841450.17452750X-RAY DIFFRACTION97.9
4.11-45.670.19561550.1732934X-RAY DIFFRACTION98.94

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