5YHL | pdb_00005yhl

Crystal structure of the human prostaglandin E receptor EP4 in complex with Fab and an antagonist Br-derivative

• PDB DOI: https://doi.org/10.2210/pdb5YHL/pdb

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda, hybrid
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2017-09-28 Released: 2018-12-05 
• Deposition Author(s): Toyoda, Y., Morimoto, K., Suno, R., Horita, S., Iwata, S., Kobayashi, T.
• Funding Organization(s): Japan Science and Technology Agency, Japan Agency for Medical Research and Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.359 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.333 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.334 (Depositor) 

Starting Model: experimental

Literature

Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.

Toyoda, Y., Morimoto, K., Suno, R., Horita, S., Yamashita, K., Hirata, K., Sekiguchi, Y., Yasuda, S., Shiroishi, M., Shimizu, T., Urushibata, Y., Kajiwara, Y., Inazumi, T., Hotta, Y., Asada, H., Nakane, T., Shiimura, Y., Nakagita, T., Tsuge, K., Yoshida, S., Kuribara, T., Hosoya, T., Sugimoto, Y., Nomura, N., Sato, M., Hirokawa, T., Kinoshita, M., Murata, T., Takayama, K., Yamamoto, M., Narumiya, S., Iwata, S., Kobayashi, T.

(2019) Nat Chem Biol 15: 18-26

• PubMed: 30510193 
• DOI: https://doi.org/10.1038/s41589-018-0131-3
• Primary Citation of Related Structures:  
  5YFI, 5YHL, 5YWY


• PubMed Abstract: 
  

  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 PGE ₂ 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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Organizational Affiliation: 
• Department of Medical Chemistry and Cell Biology, Kyoto University Graduate School of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.
School of Medicine, Tsinghua University, Beijing, China.
RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan.
Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan.
Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan.
Japan Science and Technology Agency (JST), Platform for Drug Discovery, Informatics, and Structural Life Science, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.
NB Health Laboratory Co. Ltd., Kita Ward Sapporo City, Hokkaido, Japan.
Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.
Molecular Profiling Research Center for Drug Discovery (MOLPROF), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
Department of Pharmaceutical Biochemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, Oe-Honmachi, Kumamoto, Japan.
JST, the Strategic Basic Research Program, Membrane Protein Crystallography Project, Kyoto, Japan.
Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan.
Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan.
Biomedical Department, Mitsui Knowledge Industry Co., Minato-ku, Tokyo, Japan.
Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan. [e-mail].
Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan. [e-mail].
Department of Medical Chemistry and Cell Biology, Kyoto University Graduate School of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. [e-mail].
RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan. [e-mail].
JST, the Strategic Basic Research Program, Membrane Protein Crystallography Project, Kyoto, Japan. [e-mail].
Department of Medical Chemistry and Cell Biology, Kyoto University Graduate School of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. [e-mail].
Japan Science and Technology Agency (JST), Platform for Drug Discovery, Informatics, and Structural Life Science, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. [e-mail].
JST, the Strategic Basic Research Program, Membrane Protein Crystallography Project, Kyoto, Japan. [e-mail].
Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.72 kDa 
• Atom Count: 5,613 
• Modeled Residue Count: 717 
• Deposited Residue Count: 821 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin E2 receptor EP4 subtype	A	332	Homo sapiens	Mutation(s): 4  Gene Names: PTGER4, PTGER2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P35408 (Homo sapiens) Explore P35408  Go to UniProtKB:  P35408
PHAROS:  P35408 GTEx:  ENSG00000171522

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab fragment	B [auth H]	253	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab fragment	C [auth L]	236	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8VL	D [auth A]	4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid C24 H21 Br N2 O3 MCJIJRUBPRBSIT-OAHLLOKOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.359 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.333 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.334 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.1173791

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.97	α = 90
b = 392.23	β = 90
c = 81.08	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Toyoda, Y., Morimoto, K., Suno, R., Horita, S., Iwata, S., Kobayashi, T.

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Funding Organization	Location	Grant Number
Japan Science and Technology Agency	Japan	--
Japan Agency for Medical Research and Development	Japan	--

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Structure summary
• Version 1.2: 2018-12-19
  Changes: Data collection, Database references
• Version 1.3: 2019-01-16
  Changes: Data collection, Structure summary
• Version 1.4: 2019-01-30
  Changes: Data collection, Structure summary
• Version 1.5: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2024-11-06
  Changes: Structure summary