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:

Structure of the retinoid X receptor α–liver X receptor β (RXRα–LXRβ) heterodimer on DNA

Nature Structural & Molecular Biology volume 21, pages 277–281 (2014)Cite this article

Subjects

Abstract

Nuclear receptors (NRs) are conditional transcription factors with common multidomain organization that bind diverse DNA elements. How DNA sequences influence NR conformation is poorly understood. Here we report the crystal structure of the human retinoid X receptor α–liver X receptor β (RXRα–LXRβ) heterodimer on its cognate element, an AGGTCA direct repeat spaced by 4 nt. The complex has an extended X-shaped arrangement, with DNA- and ligand-binding domains crossed, in contrast to the parallel domain arrangement of other NRs that bind an AGGTCA direct repeat spaced by 1 nt. The LXRβ core binds DNA via canonical contacts and auxiliary DNA contacts that enhance affinity for the response element. Comparisons of RXRα–LXRβs in the crystal asymmetric unit and with previous NR structures reveal flexibility in NR organization and suggest a role for RXRα in adaptation of heterodimeric complexes to DNA.

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: Organization of the RXRα–LXRβ heterodimer.
Figure 2: Flexibility in the LXRβ–RXRα complex.
Figure 3: Differences between RXRα–LXRβ DBD positions in the two heterodimers.
Figure 4: RXRα–LXRβ DNA contacts.
Figure 5: Reorganization of RXRα in LXRβ and PPARγ heterodimers.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Evans, R.M. The nuclear receptor superfamily: a Rosetta Stone for physiology. Mol. Endocrinol. 19, 1429–1438 (2005).

    Article  CAS  Google Scholar 

  2. Chawla, A., Repa, J.J., Evans, R.M. & Mangelsdorf, D.J. Nuclear receptors and lipid physiology: opening the X-files. Science 294, 1866–1870 (2001).

    Article  CAS  Google Scholar 

  3. Kliewer, S.A., Lehmann, J.M. & Willson, T.M. Orphan nuclear receptors: shifting endocrinology into reverse. Science 284, 757–760 (1999).

    Article  CAS  Google Scholar 

  4. Huang, P., Chandra, V. & Rastinejad, F. Structural overview of the nuclear receptor superfamily: insights into physiology and therapeutics. Annu. Rev. Physiol. 72, 247–272 (2010).

    Article  CAS  Google Scholar 

  5. 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 

  6. Chandra, V. et al. Multidomain integration in the structure of the HNF-4α nuclear receptor complex. Nature 495, 394–398 (2013).

    Article  CAS  Google Scholar 

  7. Repa, J.J. et al. Regulation of mouse sterol regulatory element-binding protein-1c gene (SREBP-1c) by oxysterol receptors, LXRα and LXRβ. Genes Dev. 14, 2819–2830 (2000).

    Article  CAS  Google Scholar 

  8. Gerin, I. et al. LXRβ is required for adipocyte growth, glucose homeostasis, and β cell function. J. Biol. Chem. 280, 23024–23031 (2005).

    Article  CAS  Google Scholar 

  9. Kalaany, N.Y. et al. LXRs regulate the balance between fat storage and oxidation. Cell Metab. 1, 231–244 (2005).

    Article  CAS  Google Scholar 

  10. Korach-André, M. et al. Separate and overlapping metabolic functions of LXRα and LXRβ in C57Bl/6 female mice. Am. J. Physiol. Endocrinol. Metab. 298, E167–E178 (2010).

    Article  Google Scholar 

  11. Korach-André, M., Archer, A., Barros, R.P., Parini, P. & Gustafsson, J.-Å. Both liver-X receptor (LXR) isoforms control energy expenditure by regulating brown adipose tissue activity. Proc. Natl. Acad. Sci. USA 108, 403–408 (2011).

    Article  Google Scholar 

  12. Steffensen, K.R. et al. Genome-wide expression profiling; a panel of mouse tissues discloses novel biological functions of liver X receptors in adrenals. J. Mol. Endocrinol. 33, 609–622 (2004).

    Article  CAS  Google Scholar 

  13. Venteclef, N. et al. GPS2-dependent corepressor/SUMO pathways govern anti-inflammatory actions of LRH-1 and LXRβ in the hepatic acute phase response. Genes Dev. 24, 381–395 (2010).

    Article  CAS  Google Scholar 

  14. Blaschke, F. et al. A nuclear receptor corepressor–dependent pathway mediates suppression of cytokine-induced C-reactive protein gene expression by liver X receptor. Circ. Res. 99, e88–e99 (2006).

    Article  CAS  Google Scholar 

  15. Koldamova, R., Fitz, N.F. & Lefterov, I. The role of ATP-binding cassette transporter A1 in Alzheimer's disease and neurodegeneration. Biochim. Biophys. Acta 1801, 824–830 (2010).

    Article  CAS  Google Scholar 

  16. Saijo, K., Crotti, A. & Glass, C.K. in Advances in Immunology, Vol. 106 (ed. Frederick W. Alt) 21–59 (Academic Press, 2010).

  17. Hindinger, C. et al. Liver X receptor activation decreases the severity of experimental autoimmune encephalomyelitis. J. Neurosci. Res. 84, 1225–1234 (2006).

    Article  CAS  Google Scholar 

  18. Xu, J., Wagoner, G., Douglas, J.C. & Drew, P.D. Liver X receptor agonist regulation of Th17 lymphocyte function in autoimmunity. J. Leukoc. Biol. 86, 401–409 (2009).

    Article  CAS  Google Scholar 

  19. Cui, G. et al. Liver X receptor (LXR) mediates negative regulation of mouse and human Th17 differentiation. J. Clin. Invest. 121, 658–670 (2011).

    Article  CAS  Google Scholar 

  20. Wang, L. et al. Liver X receptors in the central nervous system: from lipid homeostasis to neuronal degeneration. Proc. Natl. Acad. Sci. USA 99, 13878–13883 (2002).

    Article  CAS  Google Scholar 

  21. Cermenati, G. et al. Activation of the liver X receptor increases neuroactive steroid levels and protects from diabetes-induced peripheral neuropathy. J. Neurosci. 30, 11896–11901 (2010).

    Article  CAS  Google Scholar 

  22. Nguyen-Vu, T. et al. Liver X receptor ligands disrupt breast cancer cell proliferation through an E2F-mediated mechanism. Breast Cancer Res. 15, R51 (2013).

    Article  Google Scholar 

  23. Lo Sasso, G. et al. Liver X receptors inhibit proliferation of human colorectal cancer cells and growth of intestinal tumors in mice. Gastroenterology 144, 1497–1507 (2013).

    Article  CAS  Google Scholar 

  24. Gabbi, C. et al. Central diabetes insipidus associated with impaired renal aquaporin-1 expression in mice lacking liver X receptor β. Proc. Natl. Acad. Sci. USA 109, 3030–3034 (2012).

    Article  CAS  Google Scholar 

  25. Gabbi, C. et al. Pancreatic exocrine insufficiency in LXRβ−/− mice is associated with a reduction in aquaporin-1 expression. Proc. Natl. Acad. Sci. USA 105, 15052–15057 (2008).

    Article  CAS  Google Scholar 

  26. Fan, X., Kim, H.-J., Bouton, D., Warner, M. & Gustafsson, J.-A. Expression of liver X receptor β is essential for formation of superficial cortical layers and migration of later-born neurons. Proc. Natl. Acad. Sci. USA 105, 13445–13450 (2008).

    Article  CAS  Google Scholar 

  27. Kim, H.-J. et al. Liver X receptor β (LXRβ): a link between β-sitosterol and amyotrophic lateral sclerosis-Parkinson's dementia. Proc. Natl. Acad. Sci. USA 105, 2094–2099 (2008).

    Article  CAS  Google Scholar 

  28. Sacchetti, P. et al. Liver X receptors and oxysterols promote ventral midbrain neurogenesis in vivo and in human embryonic stem cells. Cell Stem Cell 5, 409–419 (2009).

    Article  CAS  Google Scholar 

  29. Dai, Y.B., Tan, X.J., Wu, W.F., Warner, M. & Gustafsson, J.-A. Liver X receptor β protects dopaminergic neurons in a mouse model of Parkinson disease. Proc. Natl. Acad. Sci. USA 109, 13112–13117 (2012).

    Article  CAS  Google Scholar 

  30. Jakobsson, T., Treuter, E., Gustafsson, J.-Å. & Steffensen, K.R. Liver X receptor biology and pharmacology: new pathways, challenges and opportunities. Trends Pharmacol. Sci. 33, 394–404 (2012).

    Article  CAS  Google Scholar 

  31. Umesono, K., Murakami, K.K., Thompson, C.C. & Evans, R.M. Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors. Cell 65, 1255–1266 (1991).

    Article  CAS  Google Scholar 

  32. Yoshinari, K., Ohno, H., Benoki, S. & Yamazoe, Y. Constitutive androstane receptor transactivates the hepatic expression of mouse Dhcr24 and human DHCR24 encoding a cholesterogenic enzyme 24-dehydrocholesterol reductase. Toxicol. Lett. 208, 185–191 (2012).

    Article  CAS  Google Scholar 

  33. Echchgadda, I. et al. The xenobiotic-sensing nuclear receptors pregnane X receptor, constitutive androstane receptor, and orphan nuclear receptor hepatocyte nuclear factor 4α in the regulation of human steroid-/bile acid-sulfotransferase. Mol. Endocrinol. 21, 2099–2111 (2007).

    Article  CAS  Google Scholar 

  34. Laffitte, B.A. et al. Identification of the DNA binding specificity and potential target genes for the farnesoid X-activated receptor. J. Biol. Chem. 275, 10638–10647 (2000).

    Article  CAS  Google Scholar 

  35. Stroup, D., Crestani, M. & Chiang, J.Y.L. Orphan receptors chicken ovalbumin upstream promoter transcription factor II (COUP-TFII) and retinoid X receptor (RXR) activate and bind the rat cholesterol 7α-hydroxylase gene (CYP7A). J. Biol. Chem. 272, 9833–9839 (1997).

    Article  CAS  Google Scholar 

  36. Khorasanizadeh, S. & Rastinejad, F. Nuclear-receptor interactions on DNA-response elements. Trends Biochem. Sci. 26, 384–390 (2001).

    Article  CAS  Google Scholar 

  37. Orlov, I., Rochel, N., Moras, D. & Klaholz, B.P. Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA. EMBO J. 31, 291–300 (2012).

    Article  CAS  Google Scholar 

  38. Rochel, N. et al. Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat. Struct. Mol. Biol. 18, 564–570 (2011).

    Article  CAS  Google Scholar 

  39. Bernardes, A. et al. Low-resolution molecular models reveal the oligomeric state of the PPAR and the conformational organization of its domains in solution. PLoS ONE 7, e31852 (2012).

    Article  CAS  Google Scholar 

  40. Fischer, H. et al. Low resolution structures of the retinoid X receptor DNA-binding and ligand-binding domains revealed by synchrotron X-ray solution scattering. J. Biol. Chem. 278, 16030–16038 (2003).

    Article  CAS  Google Scholar 

  41. Figueira, A.C.M. et al. Low-resolution structures of thyroid hormone receptor dimers and tetramers in solution. Biochemistry 46, 1273–1283 (2007).

    Article  Google Scholar 

  42. Shulman, A.I., Larson, C., Mangelsdorf, D.J. & Ranganathan, R. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116, 417–429 (2004).

    Article  CAS  Google Scholar 

  43. Nettles, K.W. & Greene, G.L. Ligand control of coregulator recruitment to nuclear receptors. Annu. Rev. Physiol. 67, 309–333 (2005).

    Article  CAS  Google Scholar 

  44. 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).

    Article  CAS  Google Scholar 

  45. Kurokawa, R. et al. Differential orientations of the DNA-binding domain and carboxy-terminal dimerization interface regulate binding site selection by nuclear receptor heterodimers. Genes Dev. 7, 1423–1435 (1993).

    Article  CAS  Google Scholar 

  46. Wrange, O. & Gustafsson, J.A. Separation of the hormone- and DNA-binding sites of the hepatic glucocorticoid receptor by means of proteolysis. J. Biol. Chem. 253, 856–865 (1978).

    CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  48. Chao, E.Y. et al. Structure-guided design of n-phenyl tertiary amines as transrepression-selective liver X receptor modulators with anti-inflammatory activity. J. Med. Chem. 51, 5758–5765 (2008).

    Article  CAS  Google Scholar 

  49. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Welch Foundation chair E-0004 (J.-A.G.), Emerging Technology Fund of Texas 300-9-1958 (J.-A.G.), Swedish Science Council (J.-A.G.), US National Institutes of Health DK41482 (P.W.) and an European Molecular Biology Organization long-term fellowship (X.L.). We thank J.D. Baxter for the inspiration to pursue this project.

Author information

Authors and Affiliations

  1. Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA

    Xiaohua Lou, Cindy Benod, Paul Webb & Jan-Ake Gustafsson

  2. Genomic Medicine Program, Houston Methodist Research Institute, Houston, Texas, USA

    Xiaohua Lou, Cindy Benod, Ji Ho Suh, Kevin J Philips, Paul Webb & Jan-Ake Gustafsson

  3. Department of Biosciences, Karolinska Institutet, Novum, Huddinge, Sweden

    Gudrun Toresson & Jan-Ake Gustafsson

Authors
  1. Xiaohua Lou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gudrun Toresson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cindy Benod
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ji Ho Suh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kevin J Philips
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Paul Webb
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jan-Ake Gustafsson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

X.L. expressed, purified and crystallized the complex, collected diffraction data and solved the structure. G.T. took part in expression and purification of the proteins. C.B. and J.H.S. took part in functional analysis. K.J.P. assisted in supervising the project. P.W. and J.-A.G. wrote the manuscript and supervised the project.

Corresponding author

Correspondence to Jan-Ake Gustafsson.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Schematic diagram of expression constructs.

Domain organization and amino acid coordinates of full length LXRβ and RXRα with truncated versions of the proteins used to generate crystals. At the side is an image of an SDS-PAGE gel used to verify integrity and purity of RXRα/LXRβ proteins in the complex.

Supplementary Figure 2 Electron density maps for part structures.

(a) Close up of H1 interactions that bridge the two heterodimers in the asymmetric unit of the crystal. The two heterodimer pairs interact through nearly symmetric interactions between LXRβ LBD H1. Stereo view of 2Fo-Fc map for LXRβ H1 from the two heterodimers with key contact residues marked. (b-c) Localization of ligands in RXRα and LXRβ LBDs. Fo-Fc electron density maps (in orange) for ligands reveal (b), 9-cis Retinoic Acid in RXRα and (c), GW3965 in LXRβ.

Supplementary Figure 3 Spacing between RXRα and LXRβ domains.

Ribbon diagram representations of the RXRα-LXRβ complex with a, the overall shape of LXRβ highlighted in blue and structural elements marked and b, RXRα shape highlighted in red. Note that there is clear separation between LBDs and DBDs in both receptors.

Supplementary Figure 4 Influences of the LXRβ CTE helix upon DNA-element selection.

(a) Overlapping CTE positions in LXRβ and TR DBDs on DR-4 elements. Comparison of RXRα-LXRβ and RXRα-TRβ heterodimers created by superposing two helices of the helix-turn-helix motifs of LXRβ (blue) and TRβ (cyan) DBDs. The RXRα DBD (red) occupies a similar position and the CTE helices from the two proteins partly overlap at the N-terminus and diverge over the length of the extended TRβ CTE helix. (b-d), Steric Clashes in RXRα-LXRβ DBD heterodimer on DR elements with shortened spacing. Representation of models of the RXRα-LXRβ DBD heterodimer on DR elements with shortened spacers. RXRα DBD is in red; LXRβ DBD is in marine. RXRα/LXRβ DBDs on (b), DR-3, with the clashing regions are shown by blue arrows. (c), DR-2. (d), DR-1.

Supplementary Figure 5 RXRα-LXRβ interactions in paired heterodimers.

(a) Close contact between RXRα LBD and LXRβ DBD in the heterodimer represented in Figure 1 of the main text. The figure shows stereo view with RXRα in red and the LXRβ in blue with key contact residues marked. Residues from the loop preceding RXRα LBD H1 and the N-terminus of H1 contact the LXR DBD; side chains of Asn227 and Glu228 point to a small dimple upon the LXRβ DBD formed by residues 115-122, 143 and 146-147 and 156. Additionally, RXRα His288 and Glu291 side chains, located in H3 and the H3-H4 loop, contact LXRβ DBD Gln143 and side chains of Glu233 and Arg234 in RXRα H1 also lie close to LXR DBD surface. (b) Contacts appear different and weaker in the second heterodimer. Stereo view of contacts from the other heterodimer reveal interactions are different from those seen in (a) with few close contacts. (c) Canonical LXRβ DBD/DNA contacts. The figure is a stereo view of the bases on AGGTCA half-site recognized by side chains of the LXRβ helix that merges in the major groove. Contacts resemble those of other receptors with DNA.

Supplementary Figure 6 LXRβ LBD–DNA crystal-packing contacts.

(a, b) Two views of a stick model of one of the RXRα-LXRβ heterodimer on its cognate DNA element and positions of nearby DNA elements in the crystal packing arrangement reveals close contacts between the LBD and DNA. The ligands are represented by sticks, LXRβ H12 helix is represented in cyan and cofactor peptide in red. The two LXRβ LBD DNA contact surfaces are marked “1” and “2”. (c) Stereo close up view of the contact surface of LXRβ LBD with DNA “1”. (d) Stereo close up view of the contact surface of LXRβ LBD with DNA “2”. (e) Gel shift assay to check LXRβ LBD binding on DNA. Note that the LXRβ LBD exhibits binding to the DR-4 element that is unaffected by heterodimer formation and the RXRα LBD shows no evidence for DNA binding.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 3168 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lou, X., Toresson, G., Benod, C. et al. Structure of the retinoid X receptor α–liver X receptor β (RXRα–LXRβ) heterodimer on DNA. Nat Struct Mol Biol 21, 277–281 (2014). https://doi.org/10.1038/nsmb.2778

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2778

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