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Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings

Abstract

Nuclear hormone receptors (NHRs) control numerous physiological processes through the regulation of gene expression. The present study provides a structural basis for understanding the role of DNA in the spatial organization of NHR heterodimers in complexes with coactivators such as Med1 and SRC-1. We have used SAXS, SANS and FRET to determine the solution structures of three heterodimer NHR complexes (RXR–RAR, PPAR–RXR and RXR–VDR) coupled with the NHR interacting domains of coactivators bound to their cognate direct repeat elements. The structures show an extended asymmetric shape and point to the important role played by the hinge domains in establishing and maintaining the integrity of the structures. The results reveal two additional features: the conserved position of the ligand-binding domains at the 5′ ends of the target DNAs and the binding of only one coactivator molecule per heterodimer, to RXR's partner.

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Figure 1: Solution structure of the RXR–RAR–DR5 and RXR–VDR–DR3 complexes.
Figure 2: Solution structures of RAR–RXR and PPAR–RXR complexes to DR1.
Figure 3: Validation of the models.
Figure 4: One molecule of Med1 domain binds to RAR in the RXR–RAR–DR5 complex.
Figure 5: Functional implication of the conserved relative positions of the RXR's partner and the bound coactivator.

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Acknowledgements

We thank G. Zaccai for fruitful discussions about the SANS experiments, C. Birck for help in analytical ultracentrifugation and I. Kolb-Cheynel for the production of PPAR in insect cells. We thank the Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) for assistance, the Structural Biology and Genomics and the Bioinformatics platforms of the IGBMC. We are grateful to I. Davidson and O. Pourquié for constructive comments on the manuscript. This study was supported by the Centre National de Recherche Scientifique, the Institut National de Santé et de Recherche Médicale, Université de Strasbourg, the European Commission Structural Proteomics in Europe SPINE2-Complexes (LSHG-CT-2006-031220 to D.M.) under the integrated program, Quality of Life and Management of Living Resources, by Agence National de la Recherche to N.R. and D.M., and the European Union I3 grant for access to the EMBL beamline. D.I.S. and M.R. acknowledge financial support from the European Union Framework 6 Programme (Design Study SAXIER, RIDS 011934). F.C. was an Association pour la Recherche sur le Cancer (ARC) fellowship recipient.

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F.C., C.P.-I. and N.R. purified proteins; F.C. and N.R. conducted SAXS and analytical ultracentrifugation experiments; N.R. conducted SANS experiments; M.M. and M.H. produced deuterated protein; P.C. and M.R. helped during SANS and SAXS data collection; J.G. and Y.M. conducted and analyzed FRET experiments; E.M. built the initial VDR–RXR model; N.R. and D.I.S. analyzed SAXS data and modeled the complexes; N.R. and D.M. planned the project, integrated and analyzed the data and wrote the manuscript; all authors commented on the manuscript.

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Correspondence to Natacha Rochel or Dino Moras.

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Rochel, N., Ciesielski, F., Godet, J. et al. Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat Struct Mol Biol 18, 564–570 (2011). https://doi.org/10.1038/nsmb.2054

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