6AUG

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with SR16832


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.207 

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
  • Structures With Same Primary Citation

  • 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

    Department of Molecular Medicine, 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: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXG
Query on BXG

Download CCD File 
A, B
2-chloro-N-(6-methoxyquinolin-4-yl)-5-nitrobenzamide
C17 H12 Cl N3 O4
CVTZAGCRUDYUGB-UHFFFAOYSA-N
 Ligand Interaction
KNA
Query on KNA

Download CCD File 
A
nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.61α = 90
b = 62.08β = 102.34
c = 118.45γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2019-01-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence