Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Oleic Acid

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: experimental
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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: https://doi.org/10.7554/eLife.43320
  • Primary Citation of Related Structures:  
    5UGM, 6AUG, 6AVI, 6MCZ, 6MD0, 6MD1, 6MD2, 6MD4

  • 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 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

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma
A, B
275Homo sapiensMutation(s): 0 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
OLA BindingDB:  6MD0 IC50: 4100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.93α = 90
b = 62.17β = 102.2
c = 119.32γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK101871

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description