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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1038/25931
  • Primary Citation of Related Structures:  
    2PRG, 1PRG

  • 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) ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMAA, B271Homo sapiensMutation(s): 0 
Gene Names: HUMAN PPAR GAMMA CDNA, PPARG, NR1C3
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
GTEx  ENSG00000132170
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEAR RECEPTOR COACTIVATOR SRC-1C88Homo sapiensMutation(s): 0 
Gene Names: SRC-1 CDNA, NCOA1, BHLHE74, SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS  Q15788
GTEx  ENSG00000084676
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL
Download Ideal Coordinates CCD File 
A, B
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BRLEC50:  52   nM  BindingDB
DRJEC50:  70   nM  BindingDB
BRLKd:  0.14000000059604645   nM  BindingDB
BRLEC50:  4   nM  BindingDB
BRLIC50:  159   nM  BindingDB
BRLKd:  1.2000000476837158   nM  BindingDB
BRLEC50:  1100   nM  BindingDB
BRLEC50:  87   nM  BindingDB
BRLEC50:  89   nM  BindingDB
BRLEC50:  83   nM  BindingDB
BRLEC50:  95   nM  BindingDB
BRLIC50:  103   nM  BindingDB
BRLKi:  8   nM  BindingDB
BRLIC50:  112   nM  BindingDB
BRLEC50:  100   nM  BindingDB
BRLEC50:  120   nM  BindingDB
BRLEC50:  114   nM  BindingDB
BRLEC50:  117   nM  BindingDB
BRLIC50:  76   nM  BindingDB
BRLEC50:  8   nM  BindingDB
BRLEC50:  10   nM  BindingDB
DRJKi:  88   nM  BindingDB
BRLEC50:  30   nM  BindingDB
BRLEC50:  240   nM  BindingDB
BRLIC50:  38   nM  BindingDB
BRLEC50:  1   nM  BindingDB
BRLEC50:  260   nM  BindingDB
DRJKd:  684.7999877929688   nM  BindingDB
BRLEC50:  20   nM  BindingDB
BRLEC50:  316   nM  BindingDB
BRLEC50:  326   nM  BindingDB
BRLKi:  47   nM  BindingDB
BRLEC50:  300   nM  BindingDB
BRLEC50:  332   nM  BindingDB
DRJEC50:  73.30000305175781   nM  BindingDB
BRLEC50:  396   nM  BindingDB
BRLIC50:  292   nM  BindingDB
BRLIC50:  298   nM  BindingDB
BRLKi:  27   nM  BindingDB
DRJKd:  270   nM  BindingDB
BRLEC50:  39   nM  BindingDB
BRLEC50:  40   nM  BindingDB
BRLIC50:  1   nM  BindingDB
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

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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