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NFκB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses

Nature Chemical Biology volume 4, pages 241–247 (2008)Cite this article

A Corrigendum to this article was published on 01 June 2008

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Abstract

Our understanding of how steroid hormones regulate physiological functions has been significantly advanced by structural biology approaches. However, progress has been hampered by misfolding of the ligand binding domains in heterologous expression systems and by conformational flexibility that interferes with crystallization. Here, we show that protein folding problems that are common to steroid hormone receptors are circumvented by mutations that stabilize well-characterized conformations of the receptor. We use this approach to present the structure of an apo steroid receptor that reveals a ligand-accessible channel allowing soaking of preformed crystals. Furthermore, crystallization of different pharmacological classes of compounds allowed us to define the structural basis of NFκB-selective signaling through the estrogen receptor, thus revealing a unique conformation of the receptor that allows selective suppression of inflammatory gene expression. The ability to crystallize many receptor-ligand complexes with distinct pharmacophores allows one to define structural features of signaling specificity that would not be apparent in a single structure.

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Figure 1: Overall structure of the Y537S ERα–Grip1 complex.
Figure 2: Identification of a mutation that stabilizes the antagonist conformation of ERα.
Figure 3: A solvent-accessible channel in the Y537S ERα LBD.
Figure 4: Comparison of ERα wild type and Y537S crystal structures.
Figure 5: Transcriptional activity of NFκB-selective ER ligands.
Figure 6: Crystal structures of ER bound to NFκB-selective compounds.
Figure 7: Structural and biological characterization of an intermediate agonist.

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  • 01 May 2008

    In the version of this article initially published, the 13th author's last name is misspelled. The author's name should read 'Andrzej Joachimiak'. Additionally, Figure 5 of this article inadvertently contains pink traces in each panel that are not attributed to any specific molecule. These errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We are very grateful to S. Rajan for her work on refinement and model building of the structures. We thank T. Tellinghiusen and J. Cleveland for comments on the manuscript. The authors also thank J. Chrzas, G. Sahle and J. Habel for data collection at APS SER-CAT, and C. Smith, G. Card and J. Habel for data collection at SSRL beamlines. Portions of data were collected at Southeast Regional Collaborative Access Team (SER-CAT) 22-ID (or 22-BM) beamline at the Advanced Photon Source, Argonne National Laboratory. Portions of this research were carried out at the Stanford Synchrotron Radiation Laboratory, a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. This work was supported by the US National Institutes of Health (1R21 NS056998-01 (K.W.N.); 5R01 CA89489 (G.L.G.); 5R37 DK15556 (J.A.K.); 5R01 CA18119 (B.S.K.); R01 HL61432 and R01 CA37799 (R.B.H.)), the Ludwig Fund for Cancer Research (G.L.G.) and US Department of Defense grant W81XWH-04-1-0791 (G.L.G.).

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Author notes

  1. Kendall W Nettles and John B Bruning: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cancer Biology, The Scripps Research Institute, 5353 Parkside Drive, Jupiter, 33458, Florida, USA

    Kendall W Nettles, John B Bruning, German Gil & Jason Nowak

  2. Ben May Department for Cancer Research, University of Chicago, 929 East 57th Street, Chicago, 60637, Illinois, USA

    Sanjay K Sharma, Johnnie B Hahm & Geoffrey L Greene

  3. Biosciences and Biotechnology Division, Chemistry Materials and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue L-452, Livermore, 94550, California, USA

    Kristen Kulp

  4. Department of Obstetrics/Gynecology and Reproductive Sciences, and the Comprehensive Cancer Center, Yale University School of Medicine, 310 Cedar Street, New Haven, 06520, Connecticut, USA

    Richard B Hochberg

  5. Department of Chemistry, 600 South Mathews Avenue, Urbana, 61801, Illinois, USA

    Haibing Zhou & John A Katzenellenbogen

  6. Departments of Molecular and Integrative Physiology, Cell and Developmental Biology, University of Illinois, 600 South Mathews Avenue, Urbana, 61801, Illinois, USA

    Benita S Katzenellenbogen

  7. Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, 60439, Illinois, USA

    Younchang Kim & Andrzej Joachimiak

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  1. Kendall W Nettles
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Contributions

K.W.N., J.B.B., J.N., S.K.S. and J.B.H. worked on crystallization. K.W.N., J.B.B. and Y.K. worked on X-ray data collection and data analysis. K.K., R.B.H., H.Z., J.A.K. and B.S.K. worked on generating reagents and chemical synthesis. G.G. performed the mammalian cell–based experiments. K.W.N., J.B.B., J.A.K., A.J. and G.L.G. designed and supervised experiments and wrote the paper.

Corresponding authors

Correspondence to Kendall W Nettles or Geoffrey L Greene.

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Nettles, K., Bruning, J., Gil, G. et al. NFκB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses. Nat Chem Biol 4, 241–247 (2008). https://doi.org/10.1038/nchembio.76

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