6C5Q

PPARg LBD bound to SR10171


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.404 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

PPAR gamma in Complex with an Antagonist and Inverse Agonist: a Tumble and Trap Mechanism of the Activation Helix.

Frkic, R.L.Marshall, A.C.Blayo, A.L.Pukala, T.L.Kamenecka, T.M.Griffin, P.R.Bruning, J.B.

(2018) iScience 5: 69-79

  • DOI: 10.1016/j.isci.2018.06.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peroxisome proliferator activated receptor γ (PPARγ) is a nuclear receptor and target for antidiabetics that increase insulin sensitivity. Owing to the side effects of PPARγ full agonists, research has recently focused on non-activating ligands of PP ...

    Peroxisome proliferator activated receptor γ (PPARγ) is a nuclear receptor and target for antidiabetics that increase insulin sensitivity. Owing to the side effects of PPARγ full agonists, research has recently focused on non-activating ligands of PPARγ, which increase insulin sensitivity with decreased side effects. Here, we present the crystal structures of inverse agonist SR10171 and a chemically related antagonist SR11023 bound to the PPARγ ligand-binding domain, revealing an allosteric switch in the activation helix, helix 12 (H12), forming an antagonist conformation in the receptor. H12 interacts with the antagonists to become fixed in an alternative location. Native mass spectrometry indicates that this prevents contacts with coactivator peptides and allows binding of corepressor peptides. Antagonists of related nuclear receptors act to sterically prevent the active configuration of H12, whereas these antagonists of PPARγ alternatively trap H12 in an inactive configuration, which we have termed the tumble and trap mechanism.


    Organizational Affiliation

    Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
281Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EKS
Query on EKS

Download SDF File 
Download CCD File 
A
2-{3-[(5-{[(1S)-1-(4-tert-butylphenyl)ethyl]carbamoyl}-2,3-dimethyl-1H-indol-1-yl)methyl]phenoxy}-2-methylpropanoic acid
C34 H40 N2 O4
DLXSTRGKTJFVEB-QFIPXVFZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.404 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 65.190α = 90.00
b = 65.190β = 90.00
c = 368.450γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references