2Q59

Crystal Structure of PPARgamma LBD bound to full agonist MRL20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Partial Agonists Activate PPARgamma Using a Helix 12 Independent Mechanism

Bruning, J.B.Chalmers, M.J.Prasad, S.Busby, S.A.Kamenecka, T.M.He, Y.Nettles, K.W.Griffin, P.R.

(2007) Structure 15: 1258-1271

  • DOI: 10.1016/j.str.2007.07.014
  • Primary Citation of Related Structures:  
  • Also Cited By: 3D6D

  • PubMed Abstract: 
  • Binding to helix 12 of the ligand-binding domain of PPARgamma is required for full agonist activity. Previously, the degree of stabilization of the activation function 2 (AF-2) surface was thought to correlate with the degree of agonism and transacti ...

    Binding to helix 12 of the ligand-binding domain of PPARgamma is required for full agonist activity. Previously, the degree of stabilization of the activation function 2 (AF-2) surface was thought to correlate with the degree of agonism and transactivation. To examine this mechanism, we probed structural dynamics of PPARgamma with agonists that induced graded transcriptional responses. Here we present crystal structures and amide H/D exchange (HDX) kinetics for six of these complexes. Amide HDX revealed each ligand induced unique changes to the dynamics of the ligand-binding domain (LBD). Full agonists stabilized helix 12, whereas intermediate and partial agonists did not at all, and rather differentially stabilized other regions of the binding pocket. The gradient of PPARgamma transactivation cannot be accounted for solely through changes to the dynamics of AF-2. Thus, our understanding of allosteric signaling must be extended beyond the idea of a dynamic helix 12 acting as a molecular switch.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, 5353 Parkside Drive, Jupiter, FL 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome Proliferator-Activated Receptor gamma
A
274Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisome Proliferator-Activated Receptor gamma
B
274Homo 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
240
Query on 240

Download SDF File 
Download CCD File 
A, B
(2S)-2-(2-{[1-(4-METHOXYBENZOYL)-2-METHYL-5-(TRIFLUOROMETHOXY)-1H-INDOL-3-YL]METHYL}PHENOXY)PROPANOIC ACID
MRL20
C28 H24 F3 N O6
BWTOBMCYVACNJZ-KRWDZBQOSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
240IC50: 1 - 2 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.161α = 90.00
b = 63.939β = 103.43
c = 119.187γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description