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. Here the authors define the conformational landscape of human IP3R-2 and identify a ligand-dependent inter-channel interface that mediates receptor clustering during calcium signalling.