3ADX

Human PPARgamma ligand-binding domain in complex with indomethacin and nitro-233


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The nuclear receptor PPARgamma individually responds to serotonin- and fatty acid-metabolites

Waku, T.Shiraki, T.Oyama, T.Maebara, K.Nakamori, R.Morikawa, K.

(2010) Embo J. 29: 3395-3407

  • DOI: 10.1038/emboj.2010.197
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The nuclear receptor, peroxisome proliferator-activated receptor γ (PPARγ), recognizes various synthetic and endogenous ligands by the ligand-binding domain. Fatty-acid metabolites reportedly activate PPARγ through conformational changes of the Ω loo ...

    The nuclear receptor, peroxisome proliferator-activated receptor γ (PPARγ), recognizes various synthetic and endogenous ligands by the ligand-binding domain. Fatty-acid metabolites reportedly activate PPARγ through conformational changes of the Ω loop. Here, we report that serotonin metabolites act as endogenous agonists for PPARγ to regulate macrophage function and adipogenesis by directly binding to helix H12. A cyclooxygenase inhibitor, indomethacin, is a mimetic agonist of these metabolites. Crystallographic analyses revealed that an indole acetate functions as a common moiety for the recognition by the sub-pocket near helix H12. Intriguingly, a serotonin metabolite and a fatty-acid metabolite each bind to distinct sub-pockets, and the PPARγ antagonist, T0070907, blocked the fatty-acid agonism, but not that of the serotonin metabolites. Mutational analyses on receptor-mediated transcription and coactivator binding revealed that each metabolite individually uses coregulator and/or heterodimer interfaces in a ligand-type-specific manner. Furthermore, the inhibition of the serotonin metabolism reduced the expression of the endogenous PPARγ-target gene. Collectively, these results suggest a novel agonism, in which PPARγ functions as a multiple sensor in response to distinct metabolites.


    Organizational Affiliation

    The Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Furuedai, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
287Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NRO
Query on NRO

Download SDF File 
Download CCD File 
A
3-[5-(2-nitropent-1-en-1-yl)furan-2-yl]benzoic acid
C16 H15 N O5
IRHZCQDCMUWUKV-RAXLEYEMSA-N
 Ligand Interaction
IMN
Query on IMN

Download SDF File 
Download CCD File 
A, B
INDOMETHACIN
C19 H16 Cl N O4
CGIGDMFJXJATDK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMNEC50: 50000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.051α = 90.00
b = 61.742β = 102.85
c = 118.480γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance