Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

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


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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.


  1. 1

    Lonard, D.M., Lanz, R.B. & O'Malley, B.W. Nuclear receptor coregulators and human disease. Endocr. Rev. 28, 575–587 (2007).

    CAS  Article  Google Scholar 

  2. 2

    Aoyagi, S. & Archer, T.K. Dynamics of coactivator recruitment and chromatin modifications during nuclear receptor mediated transcription. Mol. Cell. Endocrinol. 280, 1–5 (2008).

    CAS  Article  Google Scholar 

  3. 3

    O'Malley, B. The Year in Basic Science: nuclear receptors and coregulators. Mol. Endocrinol. 22, 2751–2758 (2008).

    CAS  Article  Google Scholar 

  4. 4

    Chandra, V. et al. Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA. Nature 456, 350–356 (2008).

    Article  Google Scholar 

  5. 5

    Darimont, B.D. et al. Structure and specificity of nuclear receptor-coactivator interactions. Genes Dev. 12, 3343–3356 (1998).

    CAS  Article  Google Scholar 

  6. 6

    Shiau, A.K. et al. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95, 927–937 (1998).

    CAS  Article  Google Scholar 

  7. 7

    Nolte, R.T. et al. Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Nature 395, 137–143 (1998).

    CAS  Article  Google Scholar 

  8. 8

    Meijsing, S.H. et al. DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324, 407–410 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Svergun, D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76, 2879–2886 (1999).

    CAS  Article  Google Scholar 

  10. 10

    Rastinejad, F., Wagner, T., Zhao, Q. & Khorasanizadeh, S. Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1. EMBO J. 19, 1045–1054 (2000).

    CAS  Article  Google Scholar 

  11. 11

    Bourguet, W. et al. Crystal structure of a heterodimeric complex of RAR and RXR ligand-binding domains. Mol. Cell 5, 289–298 (2000).

    CAS  Article  Google Scholar 

  12. 12

    Egea, P.F. et al. Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid. EMBO J. 19, 2592–2601 (2000).

    CAS  Article  Google Scholar 

  13. 13

    Rochel, N., Wurtz, J.M., Mitschler, A., Klaholz, B. & Moras, D. The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand. Mol. Cell 5, 173–179 (2000).

    CAS  Article  Google Scholar 

  14. 14

    Shaffer, P.L. & Gewirth, D.T. Structural basis of VDR-DNA interactions on direct repeat response elements. EMBO J. 21, 2242–2252 (2002).

    CAS  Article  Google Scholar 

  15. 15

    Shaffer, P.L. & Gewirth, D.T. Structural analysis of RXR-VDR interactions on DR3 DNA. J. Steroid Biochem. Mol. Biol. 89–90 215–219 (2004).

  16. 16

    Petoukhov, M.V. & Svergun, D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys. J. 89, 1237–1250 (2005).

    CAS  Article  Google Scholar 

  17. 17

    Kurokawa, R. et al. Regulation of retinoid signalling by receptor polarity and allosteric control of ligand binding. Nature 371, 528–531 (1994).

    CAS  Article  Google Scholar 

  18. 18

    Kurokawa, R. et al. Polarity-specific activities of retinoic acid receptors determined by a co-repressor. Nature 377, 451–454 (1995).

    CAS  Article  Google Scholar 

  19. 19

    Mader, S. et al. The patterns of binding of RAR, RXR and TR homo- and heterodimers to direct repeats are dictated by the binding specificites of the DNA binding domains. EMBO J. 12, 5029–5041 (1993).

    CAS  Article  Google Scholar 

  20. 20

    Towers, T.L., Luisi, B.F., Asianov, A. & Freedman, L.P. DNA target selectivity by the vitamin D3 receptor: mechanism of dimmer binding to an asymmetric repeat element. Proc. Natl. Acad. Sci. USA 90, 6310–6314 (1993).

    CAS  Article  Google Scholar 

  21. 21

    IJpenberg, A., Jeannin, E., Wahli, W. & Desvergne, B. Polarity and specific sequence requirements of peroxisome proliferator-activated receptor (PPAR)/retinoid X receptor heterodimer binding to DNA. A functional analysis of the malic enzyme gene PPAR response element. J. Biol. Chem. 272, 20108–20117 (1997).

    CAS  Article  Google Scholar 

  22. 22

    Rachez, C. et al. The DRIP complex and SRC-1/p160 coactivators share similar nuclear receptor binding determinants but constitute functionally distinct complexes. Mol. Cell. Biol. 20, 2718–2726 (2000).

    CAS  Article  Google Scholar 

  23. 23

    Wright, E., Vincent, J. & Fernandez, E.J. Thermodynamic characterization of the interaction between CAR-RXR and SRC-1 peptide by isothermal titration calorimetry. Biochemistry 46, 862–870 (2007).

    CAS  Article  Google Scholar 

  24. 24

    Pogenberg, V. et al. Characterization of the interaction between retinoic acid receptor/retinoid X receptor (RAR/RXR) heterodimers and transcriptional coactivators through structural and fluorescence anisotropy studies. J. Biol. Chem. 280, 1625–1633 (2005).

    CAS  Article  Google Scholar 

  25. 25

    Rastinejad, F., Perlmann, T., Evans, R.M. & Sigler, P.B. Structural determinants of nuclear receptor assembly on DNA direct repeats. Nature 375, 203–211 (1995).

    CAS  Article  Google Scholar 

  26. 26

    Shaffer, P.L., McDonnell, D.P. & Gewirth, D.T. Characterization of transcriptional activation and DNA-binding functions in the hinge region of the vitamin D receptor. Biochemistry 44, 2678–2685 (2005).

    CAS  Article  Google Scholar 

  27. 27

    Hsieh, J.C. et al. Characterization of unique DNA-binding and transcriptional-activation functions in the carboxyl-terminal extension of the zinc finger region in the human vitamin D receptor. Biochemistry 38, 16347–16358 (1999).

    CAS  Article  Google Scholar 

  28. 28

    Vestergaard, B. et al. The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Mol. Cell 20, 929–938 (2005).

    CAS  Article  Google Scholar 

  29. 29

    Darst, S.A. et al. Conformational flexibility of bacterial RNA polymerase. Proc. Natl. Acad. Sci. USA 99, 4296–4301 (2002).

    CAS  Article  Google Scholar 

  30. 30

    Lee, K.K. & Johnson, J.E. Complementary approaches to structure determination of icosahedral viruses. Curr. Opin. Struct. Biol. 13, 558–569 (2003).

    CAS  Article  Google Scholar 

  31. 31

    Suino, K. et al. The nuclear xenobiotic receptor CAR: structural determinants of constitutive activation and heterodimerization. Mol. Cell 16, 893–905 (2004).

    CAS  PubMed  Google Scholar 

  32. 32

    Ren, Y. et al. Specific structural motifs determine TRAP220 interactions with nuclear hormone receptors. Mol. Cell. Biol. 20, 5433–5446 (2000).

    CAS  Article  Google Scholar 

  33. 33

    Malik, S. et al. Structural and functional organization of TRAP220, the TRAP/mediator subunit that is targeted by nuclear receptors. Mol. Cell. Biol. 24, 8244–8254 (2004).

    CAS  Article  Google Scholar 

  34. 34

    Yang, W., Rachez, C. & Freedman, L.P. Discrete roles for peroxisome proliferator-activated receptor gamma and retinoid X receptor in recruiting nuclear receptor coactivators. Mol. Cell. Biol. 20, 8008–8017 (2000).

    CAS  Article  Google Scholar 

  35. 35

    Belakavadi, M. & Fondell, J.D. Role of the mediator complex in nuclear hormone receptor signaling. Rev. Physiol. Biochem. Pharmacol. 156, 23–43 (2006).

    CAS  Article  Google Scholar 

  36. 36

    Taatjes, D.J., Schneider-Poetsch, T. & Tjian, R. Distinct conformational states of nuclear receptor-bound CRSP-Med complexes. Nat. Struct. Mol. Biol. 11, 664–671 (2004).

    CAS  Article  Google Scholar 

  37. 37

    Lefebvre, P., Mouchon, A., Lefebvre, B. & Formstecher, P. Binding of retinoic acid receptor heterodimers to DNA. A role for histones NH2 termini. J. Biol. Chem. 273, 12288–12295 (1998).

    CAS  Article  Google Scholar 

  38. 38

    Ong, M.S., Richmond, T.J. & Davey, C.A. DNA stretching and extreme kinking in the nucleosome core. J. Mol. Biol. 368, 1067–1074 (2007).

    CAS  Article  Google Scholar 

  39. 39

    Wong, J., Li, Q., Levi, B.Z., Shi, Y.B. & Wolffe, A.P. Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J. 16, 7130–7145 (1997).

    CAS  Article  Google Scholar 

  40. 40

    Truss, M., Bartsch, J., Schelbert, A., Haché, R.J. & Beato, M. Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J. 14, 1737–1751 (1995).

    CAS  Article  Google Scholar 

  41. 41

    Juntunen, K., Rochel, N., Moras, D. & Vihko, P. Large-scale expression and purification of the human vitamin D receptor and its ligand-binding domain for structural studies. Biochem. J. 344, 297–303 (1999).

    CAS  Article  Google Scholar 

  42. 42

    Roessle, M.W. et al. Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J. Appl. Crystallogr. 40, S190–S194 (2007).

    CAS  Article  Google Scholar 

  43. 43

    Konarev, P.V., Volkov, V.V., Sokolova, A.V., Koch, M.H.J. & Svergun, D.I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36, 1277–1282 (2003).

    CAS  Article  Google Scholar 

  44. 44

    Kozin, M.B. & Svergun, D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 34, 33–41 (2001).

    CAS  Article  Google Scholar 

  45. 45

    Volkov, V.V. & Svergun, D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36, 860–864 (2003).

    CAS  Article  Google Scholar 

  46. 46

    Tocchini-Valentini, G., Rochel, N., Wurtz, J.M., Mitschler, A. & Moras, D. Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands. Proc. Natl. Acad. Sci. USA 98, 5491–5496 (2001).

    CAS  Article  Google Scholar 

  47. 47

    Bernacchi, S. et al. HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence. J. Mol. Biol. 317, 385–399 (2002).

    CAS  Article  Google Scholar 

  48. 48

    Mellet, P. et al. Comparative trajectories of active and S195A inactive trypsin upon binding to serpins. J. Biol. Chem. 277, 38901–38914 (2002).

    CAS  Article  Google Scholar 

Download references


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.

Author information




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.

Corresponding authors

Correspondence to Natacha Rochel or Dino Moras.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–4 and Supplementary Methods (PDF 762 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing