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- PDB-7axi: Crystal structure of the hPXR-LBD in complex with estradiol and c... -

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Basic information

Entry
Database: PDB / ID: 7axi
TitleCrystal structure of the hPXR-LBD in complex with estradiol and cis-chlordane
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
ESTRADIOL / ISOPROPYL ALCOHOL / (-)cis-chlordane / (+)cis-chlordane / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHuet, T. / Delfosse, V. / 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)37,5516
Polymers36,2811
Non-polymers1,2705
Water2,144119
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)75,10212
Polymers72,5622
Non-polymers2,54010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area3660 Å2
ΔGint-23 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.904, 91.904, 85.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pRESTA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75469

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Non-polymers , 6 types, 124 molecules

#2: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-S6E / (-)cis-chlordane / (1~{S},2~{R},3~{S},4~{R},6~{R},7~{R})-1,3,4,7,8,9,10,10-octakis(chloranyl)tricyclo[5.2.1.0^{2,6}]dec-8-ene / (1S,2R,3aR,7aR)-1,2,4,5,6,7,8,8-octachloro-2,3,3a,4,7,7a-hexahydro-1H-4,7-methanoindene


Mass: 409.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6Cl8 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-S6H / (+)cis-chlordane / (1~{R},2~{S},3~{R},4~{S},6~{S},7~{S})-1,3,4,7,8,9,10,10-octakis(chloranyl)tricyclo[5.2.1.0^{2,6}]dec-8-ene / (1R,2S,3aS,4S,7R,7aS)-1,2,4,5,6,7,8,8-octachloro-2,3,3a,4,7,7a-hexahydro-1H-4,7-methanoindene


Mass: 409.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6Cl8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.67 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.15→45.952 Å / Num. obs: 20581 / % possible obs: 100 % / Redundancy: 6.8 % / Rrim(I) all: 0.082 / Net I/σ(I): 14.8
Reflection shellResolution: 2.15→2.27 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2927 / Rrim(I) all: 0.472

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ILG

1ilg


Resolution: 2.15→45.952 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 1953 5.12 %random
Rwork0.1732 36175 --
obs0.1747 20532 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.23 Å2 / Biso mean: 35.7588 Å2 / Biso min: 14.83 Å2
Refinement stepCycle: final / Resolution: 2.15→45.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 68 119 2326
Biso mean--54.78 40.7 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082316
X-RAY DIFFRACTIONf_angle_d0.9863174
X-RAY DIFFRACTIONf_chiral_restr0.049361
X-RAY DIFFRACTIONf_plane_restr0.005394
X-RAY DIFFRACTIONf_dihedral_angle_d15.8631391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1501-2.20390.33251550.24872592
2.2039-2.26350.26651460.2162538
2.2635-2.33010.25641490.20872594
2.3301-2.40530.27231360.19532592
2.4053-2.49120.20191450.20262561
2.4912-2.5910.23641340.19972621
2.591-2.70890.24731460.18232559
2.7089-2.85170.22831360.18392608
2.8517-3.03030.21811190.18062570
3.0303-3.26420.22371670.18122567
3.2642-3.59260.21971440.15762584
3.5926-4.11220.15841340.1532581
4.1122-5.17980.13811260.1412600
5.1798-45.9520.16991160.1682608

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