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

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Basic information

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


intermediate filament cytoskeleton / xenobiotic transport / 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 ...intermediate filament cytoskeleton / xenobiotic transport / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / 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 / 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 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
Similarity search - Domain/homology
ESTRADIOL / heptachlor endo-epoxide / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)37,5274
Polymers36,7471
Non-polymers7803
Water1,60389
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)75,0558
Polymers73,4952
Non-polymers1,5606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area3300 Å2
ΔGint-25 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.177, 91.177, 85.396
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
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

21A-689-

HOH

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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-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-S65 / heptachlor endo-epoxide / (1aR,1bR,5aS,6R,6aR)-2,3,4,5,6,7,7-heptachloro-1a,1b,5,5a,6,6a-hexahydro-2H-2,5-methanoindeno[1,2-b]oxirene


Mass: 389.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H5Cl7O / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.41 Å3/Da / Density % sol: 49.07 %
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: SLS / Beamline: X06SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.5→45.95 Å / Num. obs: 13015 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 45.97 Å2 / Rrim(I) all: 0.095 / Net I/σ(I): 27.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 24 % / Mean I/σ(I) obs: 5.7 / Num. unique obs: 1446 / Rrim(I) all: 0.648 / % possible all: 100

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Processing

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

1ilg


Resolution: 2.5→45.59 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 972 7.49 %random
Rwork0.1995 12000 --
obs0.2019 12972 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 46 89 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312309
X-RAY DIFFRACTIONf_angle_d0.68493151
X-RAY DIFFRACTIONf_chiral_restr0.0383355
X-RAY DIFFRACTIONf_plane_restr0.0035396
X-RAY DIFFRACTIONf_dihedral_angle_d19.7229859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.23391240.22361683X-RAY DIFFRACTION99.94
2.63-2.80.26451600.22311653X-RAY DIFFRACTION100
2.8-3.010.29571280.23991689X-RAY DIFFRACTION100
3.01-3.320.24911520.23241678X-RAY DIFFRACTION100
3.32-3.80.27551370.1921718X-RAY DIFFRACTION100
3.8-4.780.19041050.16941765X-RAY DIFFRACTION100
4.78-45.590.20411660.19641814X-RAY DIFFRACTION99.8

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