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TitleStructural insights into the ligand and G protein recognition by P2YR.
Journal, issue, pagesBiochem Biophys Res Commun, Vol. 827, Page 153976, Year 2026
Publish dateMay 21, 2026
AuthorsHidetaka S Oshima / Hiroaki Akasaka / Fumiya K Sano / Osamu Nureki /
PubMed AbstractP2Y purinergic receptors are GPCRs that recognize extracellular nucleotides to mediate diverse physiological processes. Among 12-like subfamily members, P2YR has well-documented roles in ...P2Y purinergic receptors are GPCRs that recognize extracellular nucleotides to mediate diverse physiological processes. Among 12-like subfamily members, P2YR has well-documented roles in neuroprotection and cholesterol metabolism. Notably, P2YR displays robust activity toward the G pathway in addition to its canonical G coupling, yet the structural basis for its ligand recognition and G protein selectivity has remained unclear. Here, we present the cryo-EM structure of the P2YR-G complex bound to ADP at a resolution of 2.83 Å. The structure reveals the distinctive ligand recognition mechanism of P2YR, in which an N-terminal arginine caps the orthosteric binding pocket. Furthermore, we also elucidated the structure of P2YR, which shows the lowest G activation ability among the 12-like P2Y receptors, in complex with UDP and G at a resolution of 2.93 Å. Structural comparison with the 12-like P2Y receptors implicates ICL2-mediated contacts with the Gα hydrophobic cavity as a key structural determinant of G selectivity. Together, these findings provide mechanistic insights into nucleotide signaling and a structural foundation for advancing structure-based approaches to targeting the 12-like P2Y receptors.
External linksBiochem Biophys Res Commun / PubMed:42208230
MethodsEM (single particle)
Resolution2.72 - 3.3 Å
Structure data

EMDB-69760: P2Y13R-Gq complex bound to ADP (consensus)
Method: EM (single particle) / Resolution: 2.83 Å

EMDB-69761: P2Y13R-Gq complex bound to ADP (receptor-focused)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-69762: P2Y13R-Gq complex bound to ADP (G protein-focused)
Method: EM (single particle) / Resolution: 2.72 Å

EMDB-69813: P2Y14R-Gi complex bound to UDP (consensus)
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-69814: P2Y14R-Gi complex bound to UDP (receptor-focused)
Method: EM (single particle) / Resolution: 3.24 Å

EMDB-69816: P2Y14R-Gi complex bound to UDP (G protein-focused)
Method: EM (single particle) / Resolution: 2.84 Å

69904

24xy

EMDB-69904, PDB-24xy:
P2Y13R-Gq complex bound to ADP
Method: EM (single particle) / Resolution: 3.0 Å

69905

24xz

EMDB-69905, PDB-24xz:
P2Y14R-Gi complex bound to UDP
Method: EM (single particle) / Resolution: 2.93 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

Source
  • homo sapiens (human)
  • human respiratory syncytial virus
  • rattus norvegicus (Norway rat)
  • bos taurus (domestic cattle)
  • lama glama (llama)
  • mus musculus (house mouse)
  • rattus rattus (black rat)
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsSIGNALING PROTEIN / GPCR / Nucleotide / G protein

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