6AK3 | pdb_00006ak3

Crystal structure of the human prostaglandin E receptor EP3 bound to prostaglandin E2

• PDB DOI: https://doi.org/10.2210/pdb6AK3/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-08-29 Released: 2018-12-05 
• Deposition Author(s): Morimoto, K., Suno, R., Iwata, S., Kobayashi, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.295 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Literature

Crystal structure of the endogenous agonist-bound prostanoid receptor EP3.

Morimoto, K., Suno, R., Hotta, Y., Yamashita, K., Hirata, K., Yamamoto, M., Narumiya, S., Iwata, S., Kobayashi, T.

(2019) Nat Chem Biol 15: 8-10

• PubMed: 30510192 
• DOI: https://doi.org/10.1038/s41589-018-0171-8
• Primary Citation Related Structures: 
  6AK3


• PubMed 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 PGE ₂ 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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Organizational Affiliation: 
• Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, 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].
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.
Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan.
RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan.
Medical Innovation Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. [e-mail].
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, 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].
Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.31 kDa 
• Atom Count: 4,251 
• Modeled Residue Count: 544 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin E2 receptor EP3 subtype,Soluble cytochrome b562	A [auth B], B [auth A]	418	Homo sapiens, Escherichia coli	Mutation(s): 9  Gene Names: PTGER3, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P43115 (Homo sapiens) Explore P43115  Go to UniProtKB:  P43115
PHAROS:  P43115 GTEx:  ENSG00000050628
UniProt Groups	P0ABE7P43115

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV	D [auth B], F [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C42 H82 N O8 P WTJKGGKOPKCXLL-PFDVCBLKSA-N
P2E	C [auth B], E [auth A]	(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid C20 H32 O5 XEYBRNLFEZDVAW-ARSRFYASSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.295 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1482880

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.09	α = 90
b = 42.28	β = 96.09
c = 161.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP18gm0910007
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101079

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: 2019-01-30
  Changes: Data collection, Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references
• Version 1.5: 2024-11-06
  Changes: Structure summary