Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.30 kDa 
• Atom Count: 2364 
• Modelled Residue Count: 281 
• Deposited Residue Count: 287 
• Unique protein chains: 2

3CS8

Structural and Biochemical Basis for the Binding Selectivity of PPARg to PGC-1a

• PDB DOI: 10.2210/pdb3CS8/pdb

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


• Deposited: 2008-04-09 Released: 2008-06-03 
• Deposition Author(s): Li, Y., Martynowski, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.282 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Structural and biochemical basis for the binding selectivity of peroxisome proliferator-activated receptor gamma to PGC-1alpha.

Li, Y., Kovach, A., Suino-Powell, K., Martynowski, D., Xu, H.E.

(2008) J Biol Chem 283: 19132-19139

• PubMed: 18469005 
• DOI: 10.1074/jbc.M802040200
• Primary Citation of Related Structures:  
  3CS8


• PubMed Abstract: 
  

The functional interaction between the peroxisome proliferator-activated receptor gamma (PPARgamma) and its coactivator PGC-1alpha is crucial for the normal physiology of PPARgamma and its pharmacological response to antidiabetic treatment with rosiglitazone. Here we report the crystal structure of the PPARgamma ligand-binding domain bound to rosiglitazone and to a large PGC-1alpha fragment that contains two LXXLL-related motifs. The structure reveals critical contacts mediated through the first LXXLL motif of PGC-1alpha and the PPARgamma coactivator binding site. Through a combination of biochemical and structural studies, we demonstrate that the first LXXLL motif is the most potent among all nuclear receptor coactivator motifs tested, and only this motif of the two LXXLL-related motifs in PGC-1alpha is capable of binding to PPARgamma. Our studies reveal that the strong interaction of PGC-1alpha and PPARgamma is mediated through both hydrophobic and specific polar interactions. Mutations within the context of the full-length PGC-1alpha indicate that the first PGC-1alpha motif is necessary and sufficient for PGC-1alpha to coactivate PPARgamma in the presence or absence of rosiglitazone. These results provide a molecular basis for specific recruitment and functional interplay between PPARgamma and PGC-1alpha in glucose homeostasis and adipocyte differentiation.

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Organizational Affiliation: 

Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	275	Homo sapiens	Mutation(s): 0  Gene Names: PPARGC1A, LEM6, PGC1, PGC1A, PPARGC1, PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PGC-1alfa peptide	B	12	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
PHAROS:  Q9UBK2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BRL	F [auth A]	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) C18 H19 N3 O3 S YASAKCUCGLMORW-HNNXBMFYSA-N
SO4	C [auth A], D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
BRL	BindingDB:  3CS8	Ki: min: 8, max: 59 (nM) from 5 assay(s)
		Kd: min: 0.14, max: 48 (nM) from 3 assay(s)
		IC50: min: 1, max: 298 (nM) from 10 assay(s)
		EC50: min: 1, max: 1600 (nM) from 35 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.282 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.111	α = 90
b = 53.887	β = 104.83
c = 64.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-09 
• Released Date: 2008-06-03 
Deposition Author(s): Li, Y., Martynowski, D.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance