PPAR gamma mutant complex

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Recurrent activating mutations of PPAR gamma associated with luminal bladder tumors.

Rochel, N.Krucker, C.Coutos-Thevenot, L.Osz, J.Zhang, R.Guyon, E.Zita, W.Vanthong, S.Hernandez, O.A.Bourguet, M.Badawy, K.A.Dufour, F.Peluso-Iltis, C.Heckler-Beji, S.Dejaegere, A.Kamoun, A.de Reynies, A.Neuzillet, Y.Rebouissou, S.Beraud, C.Lang, H.Massfelder, T.Allory, Y.Cianferani, S.Stote, R.H.Radvanyi, F.Bernard-Pierrot, I.

(2019) Nat Commun 10: 253-253

  • DOI: https://doi.org/10.1038/s41467-018-08157-y
  • Primary Citation of Related Structures:  
    6FZF, 6FZG, 6FZJ, 6FZP, 6FZY

  • PubMed Abstract: 

    The upregulation of PPARγ/RXRα transcriptional activity has emerged as a key event in luminal bladder tumors. It renders tumor cell growth PPARγ-dependent and modulates the tumor microenvironment to favor escape from immuno-surveillance. The activation of the pathway has been linked to PPARG gains/amplifications resulting in PPARγ overexpression and to recurrent activating point mutations of RXRα. Here, we report recurrent mutations of PPARγ that also activate the PPARγ/RXRα pathway, conferring PPARγ-dependency and supporting a crucial role of PPARγ in luminal bladder cancer. These mutations are found throughout the protein-including N-terminal, DNA-binding and ligand-binding domains-and most of them enhance protein activity. Structure-function studies of PPARγ variants with mutations in the ligand-binding domain allow identifying structural elements that underpin their gain-of-function. Our study reveals genomic alterations of PPARG that lead to pro-tumorigenic PPARγ/RXRα pathway activation in luminal bladder tumors and may open the way towards alternative options for treatment.

  • Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de La Santé et de La Recherche Médicale (INSERM), U1258/Centre National de Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404 Illkirch, France. rochel@igbmc.fr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma276Homo sapiensMutation(s): 1 
Gene Names: PPARGNR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDK

Download Ideal Coordinates CCD File 
B [auth A](2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid
C30 H29 N3 O4
Query on CL

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
EDK BindingDB:  6FZG Ki: min: 0.05, max: 1.48 (nM) from 4 assay(s)
EC50: min: 1.5, max: 389 (nM) from 13 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.375α = 90
b = 60.375β = 90
c = 162.174γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2019-02-13 
  • Deposition Author(s): Rochel, N.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description