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TitleStructural insights into the mechanism of activation and inhibition of the prostaglandin D2 receptor 1.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 8944, Year 2025
Publish dateOct 8, 2025
AuthorsBehnaz Davoudinasab / Aleksey Raskovalov / Woojin Lee / Donggyun Kim / Heesoo Kim / Jordy Homing Lam / Gye Won Han / Vsevolod Katritch / Vadim Cherezov /
PubMed AbstractThe prostaglandin D2 receptor 1 (DP1), a member of the prostanoid G protein-coupled receptor (GPCR) family, plays critical roles in allergic responses, sleep regulation, immune modulation, and ...The prostaglandin D2 receptor 1 (DP1), a member of the prostanoid G protein-coupled receptor (GPCR) family, plays critical roles in allergic responses, sleep regulation, immune modulation, and vasodilation. Here, we present five high-resolution cryo-electron microscopy (cryo-EM) structures of the human DP1 receptor, including an apo structure, two inactive state structures bound to two different inverse agonists developed by ONO Pharmaceutical, and two active state structures in complex with the G protein and bound to the endogenous agonist PGD2 and its selective derivative BW245C. Structural analysis, complemented by molecular dynamics simulations and site-directed mutagenesis, reveals key residues involved in ligand recognition and suggests a distinct activation mechanism for DP1, which lacks most of the conserved class A GPCR motifs. Notably, the unique residue K76 within the conserved sodium pocket acts as a major activation switch, while amphiphilic helix 8 adopts an unconventional orientation essential for receptor function. These findings offer valuable insights into the structure and function of prostanoid receptors and may facilitate the development of therapeutics targeting DP1.
External linksNat Commun / PubMed:41062467 / PubMed Central
MethodsEM (single particle)
Resolution2.67 - 3.2 Å
Structure data

47950

9ee5

EMDB-47950, PDB-9ee5:
Cryo-EM structure of the ONO2550289-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex
Method: EM (single particle) / Resolution: 2.89 Å

48077

9ei5

EMDB-48077, PDB-9ei5:
Cryo-EM structure of Apo form of prostaglandin D2 receptor (DP1)-bRIL-Fab complex
Method: EM (single particle) / Resolution: 2.84 Å

48122

9ekh

EMDB-48122, PDB-9ekh:
Cryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-71379: Cryo-EM structure of the ONO2550289-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex (Receptor-focused)
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-71392: Cryo-EM structure of the ONO2550289-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex (Concensus map)
Method: EM (single particle) / Resolution: 2.91 Å

EMDB-71393: Cryo-EM structure of the ONO2550289-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex (Fab-foucsed map)
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-71651: Cryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex (Concensus map)
Method: EM (single particle) / Resolution: 2.87 Å

EMDB-71656: Cryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex (Receptor-focused map)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-71657: Cryo-EM structure ONO3030297-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex (Fab-focused map)
Method: EM (single particle) / Resolution: 2.67 Å

Chemicals

PDB-1bil:
CRYSTALLOGRAPHIC STUDIES ON THE BINDING MODES OF P2-P3 BUTANEDIAMIDE RENIN INHIBITORS

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

PDB-1bi8:
MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN/Immune System / GPCR / cryo-EM / DP1 / inverse agonist / ONO2550289 / prostaglandin D2 receptor / prostanoid DP receptor / PGD receptor / PTGDR / DP1-bRIL chimera / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Immune System complex / Apo form / ONO3030297

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