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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.295 (Depositor), 0.300 (DCC)
R-Value Work:
0.251 (Depositor), 0.250 (DCC)
R-Value Observed:
0.253 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 30510192 Search on PubMed
DOI: https://doi.org/10.1038/s41589-018-0171-8
Primary Citation of 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.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P43115
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth A] MOL2 format, chain D [auth B] MOL2 format, chain F [auth A] mmCIF format, chain D [auth B] mmCIF format, chain F [auth A]	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		Interactions Focus chain D [auth B] Focus chain F [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth A]
P2E Query on P2E Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
P2E	BindingDB: 6AK3	Ki: min: 0.33, max: 5 (nM) from 3 assay(s)
		IC50: min: 0.94, max: 3 (nM) from 2 assay(s)
		EC50: 2.5 (nM) from 1 assay(s)