Conformational landscape and clustering of human type 2 IP₃ receptor in lipid nanodiscs

Inositol 1,4,5-trisphosphate (IP₃) receptors (IP₃Rs) are tetrameric ER Ca²⁺ channels that shape intracellular Ca²⁺ signaling in response to IP₃, regulating many physiological processes. The structural basis for subtype-specific regulation of three subtypes (IP₃R-1-3) remains incompletely understood, due to the lack of IP₃R-2 structures. Here, we determined cryo-electron microscopy (cryo-EM) structures of human IP₃R-2 in distinct conformations with and without IP₃, Ca²⁺, and ATP. These structures define the conformational ensembles adopted by IP₃R-2 and delineate ligand-binding interactions. Comparison with rat IP₃R-1 and human IP₃R-3 highlights shared architectural features and isoform-specific differences that underlie subtype-specific functional properties. We also resolved structures of IP₃R-2 clusters, providing insight into mechanisms of ligand-dependent clustering. Together, these findings establish a structural framework for human IP₃R-2, linking ligand recognition to conformational transitions and interchannel interfaces, and illuminate how subtype-specific features and clustering may shape cellular Ca²⁺ signaling.