› 5yhl

X-ray diffraction
4.2Å resolution

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

Released:
DOI: 10.2210/pdb5yhl/pdb
PDB entry 5yhl coloured by chain, front view.
PDB entry 5yhl coloured by chain, side view.
PDB entry 5yhl coloured by chain, top view.
Source organisms:
Primary publication:
Ligand binding to human prostaglandin E receptor EP4 at 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
Nat Chem Biol 15 18-26 (2019)
PMID: 30510193

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211103 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Prostaglandin E2 receptor EP4 subtype Chain: A
Molecule details ›
Chain: A
Length: 332 amino acids
Theoretical weight: 37.06 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P35408 (Residues: 4-366; Coverage: 66%)
Gene names: PTGER2, PTGER4
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Heavy chain of Fab fragment Chain: H
Molecule details ›
Chain: H
Length: 253 amino acids
Theoretical weight: 27.57 KDa
Source organism: Mus musculus
Expression system: hybrid
Light chain of Fab fragment Chain: L
Molecule details ›
Chain: L
Length: 236 amino acids
Theoretical weight: 26.61 KDa
Source organism: Mus musculus
Expression system: hybrid

Ligands and Environments

1 bound ligand:
Ligand 8VL 1 x 8VL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2221
Unit cell:
a: 101.97Å b: 392.23Å c: 81.08Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.334 0.333 0.359
Expression systems:
  • Spodoptera frugiperda
  • hybrid

Quick links

Citations

8 review citations

Harnessing Ion-Binding Sites for GPCR Pharmacology.
Zarzycka et al. (2019)
7 more

7 mentions without citation

G protein-coupled receptors: structure- and function-based drug discovery.
Yang et al. (2021)
6 more