Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

All-trans retinoic acid is a ligand for the orphan nuclear receptor RORβ

Nature Structural & Molecular Biology volume 10, pages 820–825 (2003)Cite this article

Abstract

Retinoids regulate gene expression through binding to the nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs). In contrast, no ligands for the retinoic acid receptor–related orphan receptors β and γ (RORβ and γ) have been identified, yet structural data and structure-function analyses indicate that RORβ is a ligand-regulated nuclear receptor. Using nondenaturing mass spectrometry and scintillation proximity assays we found that all-trans retinoic acid (ATRA) and several retinoids bind to the RORβ ligand-binding domain (LBD). The crystal structures of the complex with ATRA and with the synthetic analog ALRT 1550 reveal the binding modes of these ligands. ATRA and related retinoids inhibit RORβ but not RORα transcriptional activity suggesting that high-affinity, subtype-specific ligands could be designed for the identification of RORβ target genes. Our results identify RORβ as a retinoid-regulated nuclear receptor, providing a novel pathway for retinoid action.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Nondenaturing ESI-MS analysis of ligand binding to RORβ.
Figure 2: Crystal structures of the RORβ LBD in complex with ATRA and ALRT.
Figure 3: Retinoids are ligands for RORβ.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Jetten, A., Kurebayashi, S. & Ueda, E. The ROR nuclear orphan receptor subfamily: critical regulators of multiple biological processes. Prog. Nucl. Acid Res. Mol. Biol. 69, 205–247 (2001).

    Article  CAS  Google Scholar 

  2. Preitner, N. et al. The orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110, 251–260 (2002).

    Article  CAS  Google Scholar 

  3. Ueda, H.R. et al. A transcription factor response element for gene expression during circadian night. Nature 418, 534–539 (2002).

    Article  CAS  Google Scholar 

  4. Greiner, E.F. et al. Functional analysis of retinoid Z receptor β, a brain-specific nuclear orphan receptor. Proc. Natl. Acad. Sci. USA 93, 10105–10110 (1996).

    Article  CAS  Google Scholar 

  5. Greiner, E.F. et al. Differential ligand-dependent protein-protein interactions between nuclear receptors and a neuronal-specific cofactor. Proc. Natl. Acad. Sci. USA 97, 7160–7165 (2000).

    Article  CAS  Google Scholar 

  6. Moraitis, A.N., Giguère, V. & Thompson, C.C. Novel mechanism of nuclear receptor corepressor interaction dictated by activation function 2 helix determinants. Mol. Cell. Biol. 22, 6831–6841 (2002).

    Article  CAS  Google Scholar 

  7. Stehlin, C. et al. X-ray structure of the orphan nuclear receptor RORβ ligand-binding domain in the active conformation. EMBO J. 20, 5822–5831 (2001).

    Article  CAS  Google Scholar 

  8. Potier, N. et al. Using non-denaturing mass spectrometry to detect fortuitous ligands in orphan receptors. Protein Sci. 12, 725–733 (2003).

    Article  CAS  Google Scholar 

  9. Loo, J.A. Electrospray ionization mass spectrometry: a technology for studying noncovalent macromolecular complexes. Int. J. Mass Spectrom. 200, 175–186 (2000).

    Article  CAS  Google Scholar 

  10. Renaud, J.P. et al. Crystal structure of the RAR-γ ligand-binding domain bound to all-trans retinoic acid. Nature 378, 681–689 (1995).

    Article  CAS  Google Scholar 

  11. Kallen, J.A. et al. X-ray structure of the hRORα LBD at 1.63 Å. Structural and functional data that cholesterol or a cholesterol derivative is the natural ligand of RORα. Structure 10, 1697–1707 (2002).

    Article  CAS  Google Scholar 

  12. Blumberg, B. et al. Novel retinoic acid receptor ligand in Xenopus embryos. Proc. Natl. Acad. Sci. USA 93, 4873–4878 (1996).

    Article  CAS  Google Scholar 

  13. Kurlandsky, S.B. et al. Plasma delivery of retinoic acid to tissues in the rat. J. Biol. Chem. 270, 17850–17857 (1995).

    Article  CAS  Google Scholar 

  14. Forman, B.M. et al. Androstane metabolites bind to and deactivate the nuclear receptor CAR-β. Nature 395, 612–615 (1998).

    Article  CAS  Google Scholar 

  15. Tremblay, G.B. et al. Diethylstilbestrol regulates trophoblast stem cell differentiation as a ligand of orphan nuclear receptor ERRβ. Genes Dev. 15, 833–838 (2001).

    Article  CAS  Google Scholar 

  16. Coward, P., Lee, D., Hull, M.V. & Lehmann, J. 4-Hydroxytamoxifen binds to and deactivates the estrogen-related receptor γ. Proc. Natl. Acad. Sci. USA 98, 8880–8884 (2001).

    Article  CAS  Google Scholar 

  17. Greschik, H. et al. Structural and functional evidence for ligand-independent transcriptional activation by the estrogen-related receptor 3. Mol. Cell 9, 303–313 (2002).

    Article  CAS  Google Scholar 

  18. Pike, A.C.W. et al. Structure of the ligand-binding domain of oestrogen receptor β in the presence of a partial agonist and a full antagonist. EMBO J. 18, 4608–4618 (1999).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  20. Watkins, R.E. et al. The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity. Science 292, 2329–2333 (2001).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  22. McNamara et al. Regulation of CLOCK and MOP4 by nuclear hormone receptors in the vasculature: a humoral mechanism to reset a peripheral clock. Cell 105, 877–889 (2001).

    Article  CAS  Google Scholar 

  23. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  24. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 (1994).

    Article  Google Scholar 

  25. Brünger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. A 47, 110–119 (1998).

    Google Scholar 

  26. Kleywegt, G.J. & Jones, T.A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D 50, 178–185 (1994).

    Article  CAS  Google Scholar 

  27. Müller, J.M. et al. The transcriptional coactivator FHL2 transmits Rho signals from the cell membrane into the nucleus. EMBO J. 21, 736–748 (2002).

    Article  Google Scholar 

  28. Geoghegan, K.F. et al. Spontaneous α-N-6-phosphogluconoylation of a 'His tag' in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal. Biochem. 267, 169–184 (1999).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Salvati from Bristol-Myers Squibb for the gift of ALRT 1550 and M. Klaus from Roche for the gift of RO 41-5253 and all-trans-4-oxo retinoic acid, P. Eberling for peptide synthesis, B. Blumberg for advice in performing scintillation proximity assays, P. Carpentier for support on ESRF beamline BM14 CRG and C. Schulze-Briese for support on the SLS X065A beamline, J. Cavarelli for help with the ALRT-complex data, and G. Tocchini-Valentini, V. Lamour and P. Hublitz for useful discussions. This work was supported by grants from the Deutsche Forschungsgemeinschaft to R.S. and by funds from the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, Université Louis Pasteur de Strasbourg and the Fond National de la Science to the Strasbourg Génopole. We acknowledge the financial support of the European Union for the international research project SPINE. S.S. acknowledges a grant from the CNRS and Eli Lilly.

Author information

Author notes

  1. Catherine Stehlin-Gaon and Dominica Willmann: These authors contributed equally to the work.

Authors and Affiliations

  1. Département de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, Illkirch, 67404, France

    Catherine Stehlin-Gaon, Denis Zeyer, Jean-Paul Renaud & Dino Moras

  2. Universitäts-Frauenklinik, Zentrum für Klinische Forschung, Klinikum der Universität Freiburg, Breisacherstrasse 66, Freiburg, 79106, Germany

    Dominica Willmann & Roland Schüle

  3. Laboratoire de Spectrométrie de Masse Bio-Organique, Ecole de Chimie, Polymères et Matériaux, 25 rue Becquerel, Strasbourg, 67087, France

    Sarah Sanglier & Alain Van Dorsselaer

Authors
  1. Catherine Stehlin-Gaon
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dominica Willmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Denis Zeyer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sarah Sanglier
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alain Van Dorsselaer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jean-Paul Renaud
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Dino Moras
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Roland Schüle
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dino Moras.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Stehlin-Gaon, C., Willmann, D., Zeyer, D. et al. All-trans retinoic acid is a ligand for the orphan nuclear receptor RORβ. Nat Struct Mol Biol 10, 820–825 (2003). https://doi.org/10.1038/nsb979

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb979

This article is cited by

Search

Advanced search

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