Prostaglandin E receptor EP4, a G-protein-coupled receptor, is involved in disorders such as cancer and autoimmune disease. Here, we report the crystal structure of human EP4 in complex with its antagonist ONO-AE3-208 and an inhibitory antibody at 3.2 Å resolution. The structure reveals that the extracellular surface is occluded by the extracellular loops and that the antagonist lies at the interface with the lipid bilayer, proximal to the highly conserved Arg316 residue in the seventh transmembrane domain. Functional and docking studies demonstrate that the natural agonist PGE2 binds in a similar manner. This structural information also provides insight into the ligand entry pathway from the membrane bilayer to the EP4 binding pocket. Furthermore, the structure reveals that the antibody allosterically affects the ligand binding of EP4. These results should facilitate the design of new therapeutic drugs targeting both orthosteric and allosteric sites in this receptor family.
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The atomic coordinates and structure factor files for the EP4–Fab001, EP4–Fab001_Br, and Fab001 have been deposited in the Protein Data Bank with accession codes 5YWY, 5YHL, and 5YFI, respectively. The raw diffraction images have been deposited in Zenodo data repository (https://doi.org/10.5281/zenodo.1173791).
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We are grateful to Ono Pharmaceutical Company for supplying EP4 antagonists; to the beamline scientists at BL32XU and BL41XU of SPring-8 (Hyogo, Japan) for their technical assistance during data collection; to A. Inoue at Tohoku University for the TGF-α shedding assay; to B.K. Kobilka (Tsinghua University and Stanford University), W. Shihoya and R. Taniguchi (The University of Tokyo) for their useful comments; and to H. Tsujimoto, M. Sasanuma and members of the Iwata lab at Kyoto University for technical assistance. DNA sequencing analysis was performed at the Medical Research Support Center, Graduate School of Medicine, Kyoto University. This work was supported by the Strategic Basic Research Program, JST (S.I.); the Toray Science Foundation (T.K.); the Takeda Science Foundation (T.K. and R.S.); the Naito Foundation (T.K.); Koyanagi Foundation (T.K.); the Platform for Drug Discovery, Informatics, and Structural Life Science (PDIS) funded by the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Agency for Medical Research and Development (AMED) (T.K., T.M., M. Shiroishi, T.H. and M.Y.); Core Research for Evolutional Science and Technology (CREST) funded by AMED (Y. Su., S.N. and T.K.); the ImPACT Program of the Council for Science, Technology and Innovation (Cabinet Office, Government of Japan; T.M. and M.K.); MEXT as a “Priority Issue on Post-K computer” (Building Innovative Drug Discovery Infrastructure Through Functional Control of Biomolecular Systems) (hp160213) (T. Hi.); and the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grant Nos. 15K08268 to R.S., 15J00102 to K.M., 15J04343 to S.H., 15H06862 to K.Y., and 15H05905 to Y. Su.). K.M. and S.H. are recipients of JSPS postdoctoral fellowships. X-ray crystallographic data were collected at SPring-8 (Proposal Nos. 2013A1379, 2013B1184, 2013B1092, 2014A1301, 2014B1355, 2014B1273, 2015A1080, 2015A1044, 2015B1092, 2015B2044, and 2015B2080).
The authors declare no competing interests.
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Toyoda, Y., Morimoto, K., Suno, R. et al. Ligand binding to human prostaglandin E receptor EP4 at the lipid-bilayer interface. Nat Chem Biol 15, 18–26 (2019). https://doi.org/10.1038/s41589-018-0131-3
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