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Crystal structure of the endogenous agonist-bound prostanoid receptor EP3

Nature Chemical Biology volume 15, pages8–10(2019)Cite this article

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.

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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.

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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

  1. Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan

    Kazushi Morimoto, Ryoji Suno, Yunhong Hotta, So Iwata & Takuya Kobayashi

  2. Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan

    Kazushi Morimoto, Ryoji Suno & Takuya Kobayashi

  3. RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan

    Keitaro Yamashita, Kunio Hirata & Masaki Yamamoto

  4. Medical Innovation Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan

    Shuh Narumiya

  5. Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka, Japan

    Takuya Kobayashi

Authors
  1. Kazushi Morimoto
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  2. Ryoji Suno
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  3. Yunhong Hotta
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  4. Keitaro Yamashita
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  5. Kunio Hirata
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  6. Masaki Yamamoto
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  7. Shuh Narumiya
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  8. So Iwata
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  9. Takuya Kobayashi
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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.

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The authors declare no competing interests.

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Supplementary Figures 1–15, Supplementary Tables 1–2

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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

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