3E00

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with GW9662, 9-cis Retinoic Acid and NCOA2 Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.214 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA.

Chandra, V.Huang, P.Hamuro, Y.Raghuram, S.Wang, Y.Burris, T.P.Rastinejad, F.

(2008) Nature 456: 350-356

  • DOI: 10.1038/nature07413
  • Primary Citation of Related Structures:  
    3DZU, 3DZY, 3E00

  • PubMed Abstract: 
  • Nuclear receptors are multi-domain transcription factors that bind to DNA elements from which they regulate gene expression. The peroxisome proliferator-activated receptors (PPARs) form heterodimers with the retinoid X receptor (RXR), and PPAR-gamma has been intensively studied as a drug target because of its link to insulin sensitization ...

    Nuclear receptors are multi-domain transcription factors that bind to DNA elements from which they regulate gene expression. The peroxisome proliferator-activated receptors (PPARs) form heterodimers with the retinoid X receptor (RXR), and PPAR-gamma has been intensively studied as a drug target because of its link to insulin sensitization. Previous structural studies have focused on isolated DNA or ligand-binding segments, with no demonstration of how multiple domains cooperate to modulate receptor properties. Here we present structures of intact PPAR-gamma and RXR-alpha as a heterodimer bound to DNA, ligands and coactivator peptides. PPAR-gamma and RXR-alpha form a non-symmetric complex, allowing the ligand-binding domain (LBD) of PPAR-gamma to contact multiple domains in both proteins. Three interfaces link PPAR-gamma and RXR-alpha, including some that are DNA dependent. The PPAR-gamma LBD cooperates with both DNA-binding domains (DBDs) to enhance response-element binding. The A/B segments are highly dynamic, lacking folded substructures despite their gene-activation properties.


    Organizational Affiliation

    Department of Pharmacology, and Center for Molecular Design, University of Virginia Health System, 1300 Jefferson Park Avenue, Charlottesville, Virginia 22908-0735, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaA467Homo sapiensMutation(s): 0 
Gene Names: NR2B1RXRARXRalpha
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaB [auth D]419Homo sapiensMutation(s): 0 
Gene Names: NR1C3PPARGPPARgamma
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
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NCOA2 PeptideF [auth E],
E [auth G]
13N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3')C 20N/A
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3')D [auth F]20N/A
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CR
Query on 9CR

Download Ideal Coordinates CCD File 
I [auth A](9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
 Ligand Interaction
GW9
Query on GW9

Download Ideal Coordinates CCD File 
L [auth D]2-chloro-5-nitro-N-phenylbenzamide
C13 H9 Cl N2 O3
DNTSIBUQMRRYIU-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth D],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9CR BindingDB:  3E00 Ki: min: 8, max: 583 (nM) from 5 assay(s)
Kd: min: 1.5, max: 1810 (nM) from 11 assay(s)
IC50: min: 29, max: 82 (nM) from 3 assay(s)
EC50: min: 1.5, max: 316 (nM) from 13 assay(s)
GW9 BindingDB:  3E00 EC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.585α = 90
b = 146.775β = 115.52
c = 67.23γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-16
    Changes: Database references
  • Version 1.3: 2016-11-16
    Changes: Non-polymer description
  • Version 1.4: 2017-10-25
    Changes: Refinement description