Biological Assembly 1  

 3D View: Structure | Electron Density | 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

• 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
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS:  P37231 GTEx:  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PGC-1alfa peptide	B	12	N/A	Mutation(s): 0
Find proteins for Q9UBK2 (Homo sapiens) Explore Q9UBK2  Go to UniProtKB:  Q9UBK2
NIH Common Fund Data Resources
PHAROS:  Q9UBK2 GTEx:  ENSG00000109819

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BRL	EC50:  10   nM  BindingDB
BRL	IC50:  76   nM  BindingDB
BRL	EC50:  1   nM  BindingDB
BRL	EC50:  30   nM  BindingDB
BRL	EC50:  260   nM  BindingDB
BRL	EC50:  240   nM  BindingDB
BRL	IC50:  112   nM  BindingDB
BRL	EC50:  396   nM  BindingDB
BRL	IC50:  103   nM  BindingDB
BRL	Ki:  8   nM  BindingDB
BRL	EC50:  332   nM  BindingDB
BRL	EC50:  300   nM  BindingDB
BRL	EC50:  20   nM  BindingDB
BRL	EC50:  316   nM  BindingDB
BRL	EC50:  326   nM  BindingDB
BRL	IC50:  159   nM  BindingDB
BRL	Kd:  1.2000000476837158   nM  BindingDB
BRL	EC50:  52   nM  BindingDB
BRL	IC50:  1   nM  BindingDB
BRL	EC50:  39   nM  BindingDB
BRL	EC50:  40   nM  BindingDB
BRL	Ki:  27   nM  BindingDB
BRL	EC50:  1100   nM  BindingDB
BRL	IC50:  292   nM  BindingDB
BRL	IC50:  298   nM  BindingDB
BRL	EC50:  4   nM  BindingDB
BRL	EC50:  100   nM  BindingDB
BRL	EC50:  1600   nM  BindingDB
BRL	EC50:  95   nM  BindingDB
BRL	Ki:  47   nM  BindingDB
BRL	EC50:  83   nM  BindingDB
BRL	EC50:  87   nM  BindingDB
BRL	EC50:  89   nM  BindingDB
BRL	Kd:  0.14000000059604645   nM  BindingDB
BRL	IC50:  38   nM  BindingDB
BRL	EC50:  8   nM  BindingDB
BRL	EC50:  117   nM  BindingDB
BRL	EC50:  120   nM  BindingDB
BRL	EC50:  114   nM  BindingDB

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