Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA

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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-γ 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-γ and RXR-α as a heterodimer bound to DNA, ligands and coactivator peptides. PPAR-γ and RXR-α form a non-symmetric complex, allowing the ligand-binding domain (LBD) of PPAR-γ to contact multiple domains in both proteins. Three interfaces link PPAR-γ and RXR-α, including some that are DNA dependent. The PPAR-γ 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.

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Figure 1: Overall structure of the PPAR-γ–RXR-α complex on PPRE.
Figure 2: DNA-binding features of the complex.
Figure 3: Domain–domain interactions involving the PPAR-γ LBD.
Figure 4: Effect of different ligands on the PPAR-γ–RXR-α complex.
Figure 5: The dynamic features of the receptors.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures are deposited in the Protein Data Bank under accession numbers 3DZY, 3DZU and 3E00.

Change history

  • 20 November 2008

    In the AOP version of this paper, the Protein Data Bank accession number 3E00 was erroneously listed as 3EOO. This was corrected for print on 20 November 2008.


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We thank K. S. Molnar, S. J. Tuske and S. J. Coales for providing assistance with the H/D-Ex studies; M. Chruszcz and W. Minor for assistance with diffraction data processing and analysis; P. Rogers for analysis of mutant receptor expression; and P. Griffin for providing BVT.13.

Author Contributions V.C. expressed, purified and crystallized the samples, and with P.H. collected data and solved the structure. Y.H. performed the H/D-Ex work. S.R. provided the expression systems. Y.W. and T.P.B. performed the electrophoretic mobility shift assay and transcription reporter assays. F.R. supervised the work and wrote the manuscript.

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Chandra, V., Huang, P., Hamuro, Y. et al. Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA. Nature 456, 350–356 (2008) doi:10.1038/nature07413

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