3DZY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 

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Ligand Structure Quality Assessment 


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 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: RXRANR2B1
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Find proteins for P19793 (Homo sapiens)
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Go to UniProtKB:  P19793
PHAROS:  P19793
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gammaB [auth D]419Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
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Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NCOA2 PeptideF [auth E], E [auth G]13N/AMutation(s): 0 
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Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
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')C20N/A
    Protein Feature View
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    • Reference Sequence
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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
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      BRL (Subject of Investigation/LOI)
      Query on BRL

      Download Ideal Coordinates CCD File 
      J [auth D]2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
      C18 H19 N3 O3 S
      YASAKCUCGLMORW-HNNXBMFYSA-N
       Ligand Interaction
      9CR (Subject of Investigation/LOI)
      Query on 9CR

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

      Download Ideal Coordinates CCD File 
      H [auth A], I [auth A], K [auth D], L [auth D]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Binding Affinity Annotations 
      IDSourceBinding Affinity
      BRL BindingDB:  3DZY Ki: min: 8, max: 59 (nM) from 4 assay(s)
      Kd: min: 0.14, max: 1.2 (nM) from 2 assay(s)
      IC50: min: 1, max: 298 (nM) from 8 assay(s)
      EC50: min: 1, max: 1600 (nM) from 31 assay(s)
      9CR BindingDB:  3DZY Ki: min: 8, max: 583 (nM) from 4 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 12 assay(s)
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.213 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 63.803α = 90
      b = 146.514β = 115.59
      c = 67.223γ = 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