6MD4

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Rosiglitazone and Oleic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
275Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL

Download CCD File 
A
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.829α = 90
b = 61.834β = 102.34
c = 118.717γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata 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: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Author supporting evidence