7AXL

Crystal structure of the hPXR-LBD in complex with estradiol and heptachlor endo-epoxide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report



Literature

Mechanistic insights into the synergistic activation of the RXR-PXR heterodimer by endocrine disruptor mixtures.

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.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2020551118
  • Primary Citation of Related Structures:  
    7AXG, 7AXF, 7AXI, 7AXH, 7AXK, 7AXJ, 7AXL, 7AXA, 7AXC, 7AXB

  • PubMed Abstract: 

    • Humans are chronically exposed to mixtures of xenobiotics referred to as endocrine-disrupting chemicals (EDCs). A vast body of literature links exposure to these chemicals with increased incidences of reproductive, metabolic, or neurological disorder ...

    Humans are chronically exposed to mixtures of xenobiotics referred to as endocrine-disrupting chemicals (EDCs). A vast body of literature links exposure to these chemicals with increased incidences of reproductive, metabolic, or neurological disorders. Moreover, recent data demonstrate that, when used in combination, chemicals have outcomes that cannot be predicted from their individual behavior. In its heterodimeric form with the retinoid X receptor (RXR), the pregnane X receptor (PXR) plays an essential role in controlling the mammalian xenobiotic response and mediates both beneficial and detrimental effects. Our previous work shed light on a mechanism by which a binary mixture of xenobiotics activates PXR in a synergistic fashion. Structural analysis revealed that mutual stabilization of the compounds within the ligand-binding pocket of PXR accounts for the enhancement of their binding affinity. In order to identify and characterize additional active mixtures, we combined a set of cell-based, biophysical, structural, and in vivo approaches. Our study reveals features that confirm the binding promiscuity of this receptor and its ability to accommodate bipartite ligands. We reveal previously unidentified binding mechanisms involving dynamic structural transitions and covalent coupling and report four binary mixtures eliciting graded synergistic activities. Last, we demonstrate that the robust activity obtained with two synergizing PXR ligands can be enhanced further in the presence of RXR environmental ligands. Our study reveals insights as to how low-dose EDC mixtures may alter physiology through interaction with RXR-PXR and potentially several other nuclear receptor heterodimers.

    Organizational Affiliation: 

    Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France; fini@mnhn.fr patrick.balaguer@inserm.fr bourguet@cbs.cnrs.fr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2A320Homo sapiensMutation(s): 0 
Gene Names: NR1I2, PXR
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
NIH Common Fund Data Resources
PHAROS  O75469
GTEx  ENSG00000144852
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S65
Query on S65
Download Ideal Coordinates CCD File 
A
heptachlor endo-epoxide
C10 H5 Cl7 O
ZXFXBSWRVIQKOD-WOBUKFROSA-N		 Ligand Interaction
EST
Query on EST
Download Ideal Coordinates CCD File 
A
ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.177α = 90
b = 91.177β = 90
c = 85.396γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-10-INBS-04-01
Agence Nationale de la Recherche (ANR)FranceANR-10-INBS-05
European Union (EU)France825489

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release