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.

Crystal structure of the endogenous agonist-bound prostanoid receptor EP3

Abstract

Prostanoids are a series of bioactive lipid metabolites that function in an autacoid manner via activation of cognate G-protein-coupled receptors (GPCRs). Here, we report the crystal structure of human prostaglandin (PG) E receptor subtype EP3 bound to endogenous ligand PGE2 at 2.90 Å resolution. The structure reveals important insights into the activation mechanism of prostanoid receptors and provides a molecular basis for the binding modes of endogenous ligands.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Global structure of EP3 bound to the endogenous ligand PGE2.
Fig. 2: Ligand-binding pocket in EP3 for PGE2.
Fig. 3: EP3 is in an active-like conformation.

Data availability

The atomic coordinates and structure factor files have been deposited in the Protein Data Bank with accession codes 6AK3.

References

  1. 1.

    Woodward, D. F., Jones, R. L. & Narumiya, S. Pharmacol. Rev. 63, 471–538 (2011).

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Toyoda, Y. et al. Nat. Chem. Biol. https://doi.org/10.1038/s41589-018-0131-3 (2018).

  3. 3.

    Ballesteros, J. A. & Weinstein, H. in Methods in Neurosciences. Vol. 25, (ed. Sealfon, S.) 366–428 (Elsevier, Amsterdam, 1995).

  4. 4.

    Jin, J., Mao, G. F. & Ashby, B. Br. J. Pharmacol. 121, 317–323 (1997).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Zhang, H. et al. Nature 544, 327–332 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 6.

    Kedzie, K. M., Donello, J. E., Krauss, H. A., Regan, J. W. & Gil, D. W. Mol. Pharmacol. 54, 584–590 (1998).

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Neuschäfer-Rube, F., Engemaier, E., Koch, S., Böer, U. & Püschel, G. P. Biochem. J. 371, 443–449 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Stitham, J., Stojanovic, A., Merenick, B. L., O’Hara, K. A. & Hwa, J. J. Biol. Chem. 278, 4250–4257 (2003).

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Funk, C. D., Furci, L., Moran, N. & Fitzgerald, G. A. Mol. Pharmacol. 44, 934–939 (1993).

    CAS  PubMed  Google Scholar 

  10. 10.

    Scheerer, P. et al. Nature 455, 497–502 (2008).

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Koehl, A. et al. Nature 558, 547–552 (2018).

    CAS  Article  Google Scholar 

  12. 12.

    Draper-Joyce, C. J. et al. Nature 558, 559–563 (2018).

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    García-Nafría, J., Nehmé, R., Edwards, P. C. & Tate, C. G. Nature 558, 620–623 (2018).

    Article  CAS  PubMed  Google Scholar 

  14. 14.

    Katritch, V. et al. Trends. Biochem. Sci. 39, 233–244 (2014).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Hanson, M. A. et al. Science 335, 851–855 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Chrencik, J. E. et al. Cell 161, 1633–1643 (2015).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Hua, T. et al. Cell 167, 750–762.e14 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Hua, T. et al. Nature 547, 468–471 (2017).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Choe, H. W. et al. Nature 471, 651–655 (2011).

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Shiroishi, M. et al. Microb. Cell. Fact. 11, 78 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Hattori, M., Hibbs, R. E. & Gouaux, E. Structure 20, 1293–1299 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Chu, R. et al. J. Mol. Biol. 323, 253–262 (2002).

    CAS  Article  PubMed  Google Scholar 

  23. 23.

    Caffrey, M. & Cherezov, V. Nat. Protoc. 4, 706–731 (2009).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Ueno, G. et al. AIP Conf. Proc. 1741, 050021 (2016).

    Article  Google Scholar 

  25. 25.

    Hirata, K., Foadi, J., Evans, G., Hasegawa, K. & Zeldin, O. B. in Advanced Methods in Structural Biology. (eds. Senda, T. & Maenaka, K.) 241–273 (Springer Protocol Handbooks, 2016).

  26. 26.

    Yamashita, K., Hirata, K. & Yamamoto, M. Acta Crystallogr. D Struct. Biol. 74, 441–449 (2018).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Kabsch, W. Acta Crystallogr, D. Biol. Crystallogr. 66, 125–132 (2010).

    CAS  Article  Google Scholar 

  28. 28.

    Foadi, J. et al. Acta Crystallogr. D Biol. Crystallogr. 69, 1617–1632 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. 29.

    McCoy, A. J. et al. J. Appl. Crystallogr. 40, 658–674 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Murshudov, G. N. et al. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Adams, P. D. et al. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. 33.

    Inoue, A. et al. Nat. Methods 9, 1021–1029 (2012).

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by AMED under grant Numbers JP18gm0910007 (CREST; T.K.) and JP18am0101079 (S.I.), JP18am0101070 (M.Y.) (Platform Project for Supporting Drug Discovery and Life Science Research; Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) and JSPS KAKENHI grant Number 15J00102 (K.M.). The authors acknowledge support from the Toray Science Foundation (T.K.), Takeda Science Foundation (R.S. and T.K.), Naito Foundation (T.K.), and Koyanagi Foundation (T.K.). The synchrotron radiation experiments were performed at BL32XU of SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (Proposal No. 2017A2524, 2017B2524, and BINDS0483). We thank the staff members of BL32XU for help with X-ray data collection. DNA sequencing analysis was performed at the Medical Research Support Center, Graduate School of Medicine, Kyoto University. We are grateful to A. Inoue for providing instruction on the TGFα shedding assay, M. Shiroishi for providing instruction on FSEC-TS, D. Im and T. Shimamura (Kyoto University) for providing the plasmid encoding mbIIG2, S. Horita for support for structure refinement, and H. Tsujimoto and M. Sasanuma for technical assistance.

Author information

Affiliations

Authors

Contributions

K.M. initiated the project; optimized the construct; developed the purification procedure; purified the EP3 protein for crystallization; performed crystallization trials, ligand-binding assay, and TGFα shedding assay; and wrote the manuscript. Y.H. helped with construct optimization. R.S. collected X-ray diffraction data and solved the structure. K.Y. and K.H. helped with data collection. M.Y. oversaw data collection. S.N. helped with interpretation and edited the manuscript. S.I. helped with structure analysis and interpretation and edited the manuscript. T.K. supervised the research.

Corresponding authors

Correspondence to Kazushi Morimoto or So Iwata or Takuya Kobayashi.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–15, Supplementary Tables 1–2

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Morimoto, K., Suno, R., Hotta, Y. et al. Crystal structure of the endogenous agonist-bound prostanoid receptor EP3. Nat Chem Biol 15, 8–10 (2019). https://doi.org/10.1038/s41589-018-0171-8

Download citation

Further reading

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