2PRG

LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma.

Nolte, R.T.Wisely, G.B.Westin, S.Cobb, J.E.Lambert, M.H.Kurokawa, R.Rosenfeld, M.G.Willson, T.M.Glass, C.K.Milburn, M.V.

(1998) Nature 395: 137-143

  • DOI: https://doi.org/10.1038/25931
  • Primary Citation of Related Structures:  
    1PRG, 2PRG

  • PubMed Abstract: 

    The peroxisome proliferator-activated receptor-gamma (PPAR-gamma) is a ligand-dependent transcription factor that is important in adipocyte differentiation and glucose homeostasis and which depends on interactions with co-activators, including steroid receptor co-activating factor-1 (SRC-1). Here we present the X-ray crystal structure of the human apo-PPAR-gamma ligand-binding domain (LBD), at 2.2 A resolution; this structure reveals a large binding pocket, which may explain the diversity of ligands for PPAR-gamma. We also describe the ternary complex containing the PPAR-gamma LBD, the antidiabetic ligand rosiglitazone (BRL49653), and 88 amino acids of human SRC-1 at 2.3 A resolution. Glutamate and lysine residues that are highly conserved in LBDs of nuclear receptors form a 'charge clamp' that contacts backbone atoms of the LXXLL helices of SRC-1. These results, together with the observation that two consecutive LXXLL motifs of SRC-1 make identical contacts with both subunits of a PPAR-gamma homodimer, suggest a general mechanism for the assembly of nuclear receptors with co-activators.


  • Organizational Affiliation

    Department of Structural Chemistry, Glaxo Wellcome Research and Development, Research Triangle Park, North Carolina 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
A, B
271Homo sapiensMutation(s): 0 
Gene Names: HUMAN PPAR GAMMA CDNA
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR RECEPTOR COACTIVATOR SRC-188Homo sapiensMutation(s): 0 
Gene Names: SRC-1 CDNA
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BRL BindingDB:  2PRG Ki: min: 8, max: 59 (nM) from 6 assay(s)
Kd: min: 1.2, max: 3300 (nM) from 3 assay(s)
IC50: min: 7.7, max: 6.00e+4 (nM) from 14 assay(s)
EC50: min: 1, max: 1600 (nM) from 45 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.21α = 90
b = 69.061β = 90
c = 177.966γ = 90
Software Package:
Software NamePurpose
CNSrefinement
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-19
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-01-15
    Changes: Advisory, Derived calculations
  • Version 1.4: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-05-22
    Changes: Data collection