Conformational landscape and ligand-dependent clustering of the human type 2 IP₃ receptor

Inositol 1,4,5-trisphosphate (IP₃) receptors (IP₃Rs) are tetrameric ER Ca²⁺ channels that shape intracellular Ca²⁺ signaling in response to IP₃, regulating diverse physiological processes. The structural basis for subtype-specific regulation among the three subtypes (IP₃R-1-3) remains incompletely understood due to the lack of IP₃R-2 structures. Here, we report cryo-electron microscopy (cryo-EM) structures of human IP₃R-2 in distinct conformations in the presence and absence of IP₃, Ca²⁺, and ATP. These structures define the conformational landscape of IP₃R-2, delineate ligand-binding interactions, and reveal shared architectural features alongside isoform-specific differences. We also resolve ligand-dependent IP₃R-2 assemblies, identifying a conformation-dependent inter-channel interface. Live-cell imaging demonstrates that IP₃R-2 undergoes clustering following ligand-induced Ca²⁺ release, and disruption of this interface selectively abolishes clustering without impairing channel activity. Together, these findings provide a structural framework for human IP₃R-2 and establish a mechanism linking ligand-dependent conformational changes to inter-channel interactions and post-activation cellular clustering.