6FZF

PPAR mutant complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

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: 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 ...

    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: 

    Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR144, 75005, Paris, France. isabelle.bernard-pierrot@curie.fr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaA, B279Homo sapiensMutation(s): 1 
Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma coactivator 1-alphaC, D14Homo sapiensMutation(s): 0 
Gene Names: PPARGC1A, LEM6, PGC1, PGC1A, PPARGC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens)
Explore Q9UBK2 
Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBK2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDK
Query on EDK
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		(2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid
C30 H29 N3 O4
QTQMRBZOBKYXCG-MHZLTWQESA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EDK BindingDB:  6FZF 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.644α = 90
b = 123.684β = 95.31
c = 54.466γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2018-03-14 
  • 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