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 

wwPDB Validation   3D Report Full Report


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:  
    3E00, 3DZY, 3DZU

  • 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 ...

    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alpha A467Homo sapiensMutation(s): 0 
Gene Names: NR2B1RXRARXRalpha
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS:  P19793
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma D419Homo sapiensMutation(s): 0 
Gene Names: NR1C3PPARGPPARgamma
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
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PHAROS:  P37231
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NCOA2 Peptide EG13N/AMutation(s): 0 
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
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PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • 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')C20N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • 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')F20N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      9CR
      Query on 9CR

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

      Download Ideal Coordinates CCD File 
      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 
      A, D
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      9CREC50:  10   nM  BindingDB
      9CRIC50:  32   nM  BindingDB
      9CREC50:  195   nM  BindingDB
      9CREC50:  13   nM  BindingDB
      9CRIC50:  29   nM  BindingDB
      9CRKd:  32   nM  BindingDB
      9CRKd:  1560   nM  BindingDB
      9CRKd:  1810   nM  BindingDB
      9CREC50:  250   nM  BindingDB
      9CREC50:  6   nM  BindingDB
      9CREC50:  100   nM  BindingDB
      9CRKd:  3   nM  BindingDB
      9CRKd:  50   nM  BindingDB
      9CREC50:  120   nM  BindingDB
      9CREC50:  200   nM  BindingDB
      9CRKi:  12   nM  BindingDB
      9CRKd:  1.5   nM  BindingDB
      9CRKi:  8   nM  BindingDB
      9CRKd:  8   nM  BindingDB
      9CREC50:  316   nM  BindingDB
      9CRKd:  9   nM  BindingDB
      9CREC50:  110   nM  BindingDB
      9CREC50:  1.5   nM  BindingDB
      9CREC50:  120   nM  BindingDB
      9CRKi:  8.399999618530273   nM  BindingDB
      9CRIC50:  82   nM  BindingDB
      9CRKd:  13   nM  BindingDB
      9CRKd:  14   nM  BindingDB
      9CRKd:  240   nM  BindingDB
      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

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • 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