4X1G

Crystal structure of the hPXR-LBD in complex with the synthetic estrogen 17alpha-ethinylestradiol and the pesticide trans-nonachlor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synergistic activation of human pregnane X receptor by binary cocktails of pharmaceutical and environmental compounds.

Delfosse, V.Dendele, B.Huet, T.Grimaldi, M.Boulahtouf, A.Gerbal-Chaloin, S.Beucher, B.Roecklin, D.Muller, C.Rahmani, R.Cavailles, V.Daujat-Chavanieu, M.Vivat, V.Pascussi, J.M.Balaguer, P.Bourguet, W.

(2015) Nat Commun 6: 8089-8089

  • DOI: 10.1038/ncomms9089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Humans are chronically exposed to multiple exogenous substances, including environmental pollutants, drugs and dietary components. Many of these compounds are suspected to impact human health, and their combination in complex mixtures could exacerbat ...

    Humans are chronically exposed to multiple exogenous substances, including environmental pollutants, drugs and dietary components. Many of these compounds are suspected to impact human health, and their combination in complex mixtures could exacerbate their harmful effects. Here we demonstrate that a pharmaceutical oestrogen and a persistent organochlorine pesticide, both exhibiting low efficacy when studied separately, cooperatively bind to the pregnane X receptor, leading to synergistic activation. Biophysical analysis shows that each ligand enhances the binding affinity of the other, so the binary mixture induces a substantial biological response at doses at which each chemical individually is inactive. High-resolution crystal structures reveal the structural basis for the observed cooperativity. Our results suggest that the formation of 'supramolecular ligands' within the ligand-binding pocket of nuclear receptors contributes to the synergistic toxic effect of chemical mixtures, which may have broad implications for the fields of endocrine disruption, toxicology and chemical risk assessment.


    Organizational Affiliation

    Inserm U1054, Montpellier 34090, France.,Inserm, U1194, Montpellier 34298, France.,Inserm U661, Montpellier 34094, France.,CNRS UMR5203, Institut de Génomique Fonctionnelle, Montpellier 34094, France.,CHU de Montpellier, Institut de Recherche en Biothérapie, Montpellier 34295, France.,INRA UMR 1331, TOXALIM, Sophia-Antipolis 06903, France.,ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France.,IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier 34298, France.,NovAliX, Illkirch 67400, France.,CNRS UMR5048, Centre de Biochimie Structurale, Montpellier 34090, France.,Université de Montpellier, Montpellier 34090, France.,Inserm U1040, Montpellier 34295, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 1 group I member 2
A
316Homo sapiensMutation(s): 0 
Gene Names: NR1I2 (PXR)
Find proteins for O75469 (Homo sapiens)
Go to Gene View: NR1I2
Go to UniProtKB:  O75469
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3WF
Query on 3WF

Download SDF File 
Download CCD File 
A
Ethinyl estradiol
C20 H24 O2
BFPYWIDHMRZLRN-SLHNCBLASA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
3WG
Query on 3WG

Download SDF File 
Download CCD File 
A
Trans-nonachlor
C10 H5 Cl9
OCHOKXCPKDPNQU-DFACZZRHSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3WFKd: 11500 nM BINDINGMOAD
3WGKi: 3010 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.340α = 90.00
b = 91.340β = 90.00
c = 85.490γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ANR CESAFrance--
Plan Cancer InsermFrance--

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references
  • Version 1.2: 2018-07-04
    Type: Data collection, Structure summary