6AVI

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and Nonanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPAR gamma.

Shang, J.Brust, R.Mosure, S.A.Bass, J.Munoz-Tello, P.Lin, H.Hughes, T.S.Tang, M.Ge, Q.Kamekencka, T.M.Kojetin, D.J.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.43320
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) have revealed overlapping binding modes for synthetic and natural/endogenous ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a s ...

    Crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) have revealed overlapping binding modes for synthetic and natural/endogenous ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a synthetic ligand to the orthosteric pocket can push natural and endogenous PPARγ ligands (fatty acids) out of the orthosteric pocket towards an alternate ligand-binding site near the functionally important omega (Ω)-loop. X-ray crystallography, NMR spectroscopy, all-atom molecular dynamics simulations, and mutagenesis coupled to quantitative biochemical functional and cellular assays reveal that synthetic ligand and fatty acid cobinding can form a 'ligand link' to the Ω-loop and synergistically affect the structure and function of PPARγ. These findings contribute to a growing body of evidence indicating ligand binding to nuclear receptors can be more complex than the classical one-for-one orthosteric exchange of a natural or endogenous ligand with a synthetic ligand.


    Organizational Affiliation

    Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, United States.,Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
276Homo 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
KNA
Query on KNA

Download SDF File 
Download CCD File 
A, B
nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
 Ligand Interaction
GW9
Query on GW9

Download SDF File 
Download CCD File 
A, B
2-chloro-5-nitro-N-phenylbenzamide
C13 H9 Cl N2 O3
DNTSIBUQMRRYIU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.249 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.572α = 90.00
b = 61.743β = 102.15
c = 118.376γ = 90.00
Software Package:
Software NamePurpose
DIALSdata scaling
DIALSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01DK101871

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2019-01-09
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection