Abstact

P2Y purinergic receptors are GPCRs that recognize extracellular nucleotides to mediate diverse physiological processes. Among 12-like subfamily members, P2Y(13)R has well-documented roles in neuroprotection and cholesterol metabolism. Notably, P2Y(13)R displays robust activity toward the G(q) pathway in addition to its canonical G(i) 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 P2Y(13)R-G(q) complex bound to ADP at a resolution of 2.83 A. The structure reveals the distinctive ligand recognition mechanism of P2Y(13)R, in which an N-terminal arginine caps the orthosteric binding pocket. Furthermore, we also elucidated the structure of P2Y(14)R, which shows the lowest G(i) activation ability among the 12-like P2Y receptors, in complex with UDP and G(i) at a resolution of 2.93 A. Structural comparison with the 12-like P2Y receptors implicates ICL2-mediated contacts with the Galpha hydrophobic cavity as a key structural determinant of G(q) 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.