An extracellular allosteric gate modulates the ligand efficacy of GPR119.

GPR119 is a promising therapeutic target for metabolic diseases, yet the structural basis for its ligand-dependent efficacy remains unclear. Here, we report the cryo-EM structure of GPR119 bound to the partial agonist AS1269574 and Gs protein, revealing a non-canonical ligand-binding mode. Unlike full agonists, AS1269574 occupies a restricted pocket within the activation cavity and stabilizes a closed conformation of an extracellular allosteric "stacking gate" formed by F157ECL2 and W2657.39. Together with MD simulations, our structure shows that this confined binding mode attenuates the progression of activation switches, including the swing of W2386.48 and outward movement of TM6, thereby shifting the receptor equilibrium toward a low-efficacy state. Gate-disrupting mutations enhance AS1269574-stimulated cAMP production and shift intracellular switch conformations to a full-agonist-like state. Our work elucidates a structural mechanism for partial agonism in G protein-coupled receptors (GPCRs), in which ligand-specific engagement of an extracellular gate allosterically tunes the transmembrane conformational landscape and signaling efficacy.