6AK3

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

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

  • DOI: 10.1038/s41589-018-0171-8

  • 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 ...

    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.

    Organizational Affiliation: 

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. k.morimoto@mfour.med.kyoto-u.ac.jp.,RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo, Japan.,Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan.,Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan. k.morimoto@mfour.med.kyoto-u.ac.jp.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 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. kobayashi.takuya.4r@kyoto-u.ac.jp.,Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiyoda-ku, Tokyo, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. s.iwata@mfour.med.kyoto-u.ac.jp.,Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin E2 receptor EP3 subtype,Soluble cytochrome b562
B, A
418Escherichia coli, Homo sapiens
This entity is chimeric		Mutation(s): 9 
Gene Names: cybC, PTGER3
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs)		Protein: 
prostanoid receptor EP3 with bound PGE2
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P43115 (Homo sapiens)
Go to Gene View: PTGER3
Go to UniProtKB:  P43115
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P2E
Query on P2E
Download SDF File 
Download CCD File 
A, B
(Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid
Prostaglandin E2
C20 H32 O5
XEYBRNLFEZDVAW-ARSRFYASSA-N
 Ligand Interaction
POV
Query on POV
Download SDF File 
Download CCD File 
A, B
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
POPC
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.090α = 90.00
b = 42.280β = 96.09
c = 161.300γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18gm0910007
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101079

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Structure summary
  • Version 1.2: 2018-12-19
    Type: Data collection, Database references
  • Version 1.3: 2019-01-30
    Type: Data collection, Database references