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- PDB-8r00: Crystal structure of the human PXR ligand-binding domain in compl... -

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Basic information

Entry
Database: PDB / ID: 8r00
TitleCrystal structure of the human PXR ligand-binding domain in complex with furanodienone
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsTRANSCRIPTION / Nuclear 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 / 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
: / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBourguet, W. / Carivenc, C. / Sirounian, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE34-0009-01 France
CitationJournal: Nat Commun / Year: 2025
Title: An abundant ginger compound furanodienone alleviates gut inflammation via the xenobiotic nuclear receptor PXR in mice.
Authors: Wang, X. / Zhang, G. / Bian, Z. / Chow, V. / Grimaldi, M. / Carivenc, C. / Sirounian, S. / Li, H. / Sladekova, L. / Motta, S. / Luperi, Y. / Gong, Y. / Costello, C. / Li, L. / Jachimowicz, M. ...Authors: Wang, X. / Zhang, G. / Bian, Z. / Chow, V. / Grimaldi, M. / Carivenc, C. / Sirounian, S. / Li, H. / Sladekova, L. / Motta, S. / Luperi, Y. / Gong, Y. / Costello, C. / Li, L. / Jachimowicz, M. / Guo, M. / Hu, S. / Wilson, D. / Balaguer, P. / Bourguet, W. / Mani, S. / Bonati, L. / Peng, H. / March, J. / Wang, H. / Wang, S. / Krause, H.M. / Liu, J.
History
DepositionOct 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 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)36,9782
Polymers36,7471
Non-polymers2301
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.826, 91.826, 85.731
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 BL21(DE3) (bacteria) / References: UniProt: O75469
#2: Chemical ChemComp-XFQ / furanodienone / 3,6,10-trimethyl-8,11-dihydro-7~{H}-cyclodeca[b]furan-4-one


Mass: 230.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 50-100 mM IMIDAZOLE, 8-14% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.95→85.73 Å / Num. obs: 27166 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.018 / Rrim(I) all: 0.052 / Net I/σ(I): 21.3 / Num. measured all: 207844
Reflection shellResolution: 1.95→2.06 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.586 / Num. measured all: 28977 / Num. unique obs: 3897 / CC1/2: 0.88 / Rpim(I) all: 0.219 / Rrim(I) all: 0.627 / Net I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.07 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1436 5.29 %
Rwork0.1948 --
obs0.196 27126 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 17 144 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092282
X-RAY DIFFRACTIONf_angle_d1.1253104
X-RAY DIFFRACTIONf_dihedral_angle_d20.433328
X-RAY DIFFRACTIONf_chiral_restr0.054341
X-RAY DIFFRACTIONf_plane_restr0.006407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.33451480.26412505X-RAY DIFFRACTION100
2.02-2.10.26361350.22642544X-RAY DIFFRACTION100
2.1-2.20.27231240.21282573X-RAY DIFFRACTION100
2.2-2.310.25971170.20732551X-RAY DIFFRACTION100
2.31-2.460.22581510.20832548X-RAY DIFFRACTION100
2.46-2.650.24291430.20782554X-RAY DIFFRACTION100
2.65-2.910.21731510.2052571X-RAY DIFFRACTION100
2.91-3.330.23941320.21032577X-RAY DIFFRACTION99
3.33-4.20.20651640.17652597X-RAY DIFFRACTION99
4.2-41.070.17571710.17622670X-RAY DIFFRACTION97

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