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- PDB-8r81: Crystal structure of the hPXR-LBD in complex with compound JMV6845 -

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Basic information

Entry
Database: PDB / ID: 8r81
TitleCrystal structure of the hPXR-LBD in complex with compound JMV6845
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsGENE REGULATION / Nuclear receptor / transcription factor / PROTAC / xenobiotic 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 / 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 / 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
ISOPROPYL ALCOHOL / : / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDelfosse, V. / Huet, T. / Bourguet, W.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-035 France
CitationJournal: To Be Published
Title: Crystal structure of the hPXR-LBD in complex with compound JMV6845
Authors: Delfosse, V. / Huet, T. / Bourguet, W.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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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)37,3054
Polymers36,7471
Non-polymers5583
Water1,29772
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)74,6108
Polymers73,4952
Non-polymers1,1156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.849, 90.849, 86.682
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: 36747.465 Da / Num. of mol.: 1
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
#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-Y8B / 2,4,6-trimethyl-~{N}-[1-(phenylmethyl)benzimidazol-5-yl]benzenesulfonamide


Mass: 405.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50-100 mM Imidazole 8-16% 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-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.45→45.42 Å / Num. obs: 13906 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.031 / Rrim(I) all: 0.11 / Net I/σ(I): 18.1
Reflection shellResolution: 2.45→2.58 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1985 / CC1/2: 0.951 / Rpim(I) all: 0.143 / Rrim(I) all: 0.527 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→40.63 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 694 5.01 %RANDOM
Rwork0.1718 ---
obs0.1742 13861 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 39 72 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072247
X-RAY DIFFRACTIONf_angle_d0.9323044
X-RAY DIFFRACTIONf_dihedral_angle_d19.043301
X-RAY DIFFRACTIONf_chiral_restr0.046336
X-RAY DIFFRACTIONf_plane_restr0.006387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.640.28311410.20552556X-RAY DIFFRACTION100
2.64-2.90.24891490.18252576X-RAY DIFFRACTION100
2.9-3.320.20271350.18372598X-RAY DIFFRACTION100
3.33-4.190.20181270.15812653X-RAY DIFFRACTION100

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