6I62

Crystal structure of human ERRg LBD in complex with HPTE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Insights into the activation mechanism of human estrogen-related receptor gamma by environmental endocrine disruptors.

Thouennon, E.Delfosse, V.Bailly, R.Blanc, P.Boulahtouf, A.Grimaldi, M.Barducci, A.Bourguet, W.Balaguer, P.

(2019) Cell Mol Life Sci 76: 4769-4781

  • DOI: 10.1007/s00018-019-03129-x
  • Primary Citation of Related Structures:  
    6I64, 6I63, 6I66, 6I65, 6I67, 6I62, 6I61

  • PubMed Abstract: 
  • The estrogen-related receptor γ (ERRγ, NR3B3) is a constitutively active nuclear receptor which has been proposed to act as a mediator of the low-dose effects of a number of environmental endocrine-disrupting chemicals (EDCs) such as the xenoestrogen bisphenol-A (BPA) ...

    The estrogen-related receptor γ (ERRγ, NR3B3) is a constitutively active nuclear receptor which has been proposed to act as a mediator of the low-dose effects of a number of environmental endocrine-disrupting chemicals (EDCs) such as the xenoestrogen bisphenol-A (BPA). To better characterize the ability of exogenous compounds to bind and activate ERRγ, we used a combination of cell-based, biochemical, structural and computational approaches. A purposely created stable cell line allowed for the determination of the EC50s for over 30 environmental ERRγ ligands, including previously unknown ones. Interestingly, affinity constants (Kds) of the most potent compounds measured by isothermal titration calorimetry were in the 50-500 nM range, in agreement with their receptor activation potencies. Crystallographic analysis of the interaction between the ERRγ ligand-binding domain (LBD) and compounds of the bisphenol, alkylphenol and naphthol families revealed a partially shared binding mode and minimal alterations of the receptor conformation upon ligand binding. Further biophysical characterizations coupled to molecular dynamics simulations suggested a mechanism through which ERRγ ligands would exhibit their agonistic properties by preserving the transcriptionally active form of the receptor while rigidifying some loop regions with associated functions. This unique mechanism contrasts with the classical one involving a ligand-induced repositioning and stabilization of the C-terminal activation helix H12.


    Organizational Affiliation

    Institut de Recherche en Cancérologie de Montpellier (IRCM), Inserm, Univ Montpellier, ICM, Montpellier, France. patrick.balaguer@inserm.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen-related receptor gammaA237Homo sapiensMutation(s): 0 
Gene Names: ESRRGERR3ERRG2KIAA0832NR3B3
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens)
Explore P62508 
Go to UniProtKB:  P62508
PHAROS:  P62508
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
27N (Subject of Investigation/LOI)
Query on 27N

Download Ideal Coordinates CCD File 
B [auth A]4,4'-(2,2,2-trichloroethane-1,1-diyl)diphenol
C14 H11 Cl3 O2
IUGDILGOLSSKNE-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
27N Binding MOAD:  6I62 Kd: 157.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.198α = 90
b = 64.198β = 90
c = 136.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FrancePlan Cancer ASC16007FSA

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references