Structure of the melatonin-related orphan receptor, GPR50

GPR50 is an orphan G-protein-coupled receptors that belongs to the member of melatonin-related receptor family. GPR50 plays roles in various physiological processes, including cancer progression, Notch signaling, and insulin, leptin, and glucocorticoid signaling. GPR50 forms a complex with melatonin-receptor type 1A or 1B, and regulates signaling activity of melatonin-receptor type 1A. Although endogenous agonists have not been characterized, GPR50 may have its own signaling activity, which is undefined at present. In this study, in an attempt to characterize the orphan activity of GPR50, we determined the 3.4 Å structure of ligand-free GPR50 using cryo-electron microscopy. We showed that GPR50 exhibits moderate constitutive activity through interaction with Gα₁₂. The structure reveals a putative ligand-binding pocket and ligand access channels of GPR50 that differ from those of melatonin receptors. Based on the comparison with the AlphaFold3-predicted active state, we propose an activation mechanism of GPR50. Our findings could serve as a platform for identifying the synthetic or endogenous ligands of GPR50, providing insights into the elusive G-protein-dependent signaling of GPR50.