Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.98 kDa 
• Atom Count: 4382 
• Residue Count: 502 
• Unique protein chains: 1

4EM9

Human PPAR gamma in complex with nonanoic acids

• DOI: 10.2210/pdb4EM9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-11 Released: 2013-03-06 
• Deposition Author(s): Liberato, M.V., Nascimento, A.S., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Literature

Medium chain fatty acids are selective peroxisome proliferator activated receptor (PPAR) Gamma activators and pan-PPAR partial agonists

Liberato, M.V., Nascimento, A.S., Ayers, S.D., Lin, J.Z., Cvoro, A., Silveira, R.L., Martinez, L., Souza, P.C., Saidemberg, D., Deng, T., Amato, A.A., Togashi, M., Hsueh, W.A., Phillips, K., Palma, M.S., Neves, F.A., Skaf, M.S., Webb, P., Polikarpov, I.

(2012) PLoS One 7: e36297-e36297

• PubMed: 22649490 
• DOI: 10.1371/journal.pone.0036297
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Thiazolidinediones (TZDs) act through peroxisome proliferator activated receptor (PPAR) γ to increase insulin sensitivity in type 2 diabetes (T2DM), but deleterious effects of these ligands mean that selective modulators with improved clinical profiles are needed. We obtained a crystal structure of PPARγ ligand binding domain (LBD) and found that the ligand binding pocket (LBP) is occupied by bacterial medium chain fatty acids (MCFAs). We verified that MCFAs (C8-C10) bind the PPARγ LBD in vitro and showed that they are low-potency partial agonists that display assay-specific actions relative to TZDs; they act as very weak partial agonists in transfections with PPARγ LBD, stronger partial agonists with full length PPARγ and exhibit full blockade of PPARγ phosphorylation by cyclin-dependent kinase 5 (cdk5), linked to reversal of adipose tissue insulin resistance. MCFAs that bind PPARγ also antagonize TZD-dependent adipogenesis in vitro. X-ray structure B-factor analysis and molecular dynamics (MD) simulations suggest that MCFAs weakly stabilize C-terminal activation helix (H) 12 relative to TZDs and this effect is highly dependent on chain length. By contrast, MCFAs preferentially stabilize the H2-H3/β-sheet region and the helix (H) 11-H12 loop relative to TZDs and we propose that MCFA assay-specific actions are linked to their unique binding mode and suggest that it may be possible to identify selective PPARγ modulators with useful clinical profiles among natural products.

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Organizational Affiliation: 

São Carlos Physics Institute, University of São Paulo, São Carlos, Sao Paulo, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator-activated receptor gamma	A, B	275	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231 GTEx  ENSG00000132170

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TCE	B	3,3',3''-phosphanetriyltripropanoic acid C9 H15 O6 P PZBFGYYEXUXCOF-UHFFFAOYSA-N
KNA	A, B	nonanoic acid C9 H18 O2 FBUKVWPVBMHYJY-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.731	α = 90
b = 62.255	β = 101.94
c = 118.649	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-11 
• Released Date: 2013-03-06 
Deposition Author(s): Liberato, M.V., Nascimento, A.S., Polikarpov, I.

Revision History 

• Version 1.0: 2013-03-06
  Type: Initial release