Cryo-EM structure of the lysosomal Ca(2+)-permeable channel TRPML3

The modulation of ion channel activity by lipids is increasingly recognized as a fundamental component of cellular signaling. The mucolipin transient receptor potential (TRPML) channel family belongs to the TRP superfamily(1,2) and is composed of three members, TRPML1-3. TRPMLs are the major Ca(2+)-permeable channels on late endosomes and lysosomes (LEL). They regulate organelle Ca(2+) releases important for various physiological processes, including organelle trafficking and fusion(3). Loss-of-function mutations in the TRPML1 gene cause the neurodegenerative lysosomal storage disorder mucolipidosis IV (ML-IV), and a gain-of-function mutation in TRPML3 (Ala419Pro) gives rise to the Varitint-Waddler (Va) mouse phenotype(4–6). Notably, TRPMLs are activated by the low-abundance and LEL-enriched signaling lipid PI(3,5)P(2), while other phosphoinositides such as PI(4,5)P(2), enriched in plasma membranes, inhibit TRPMLs(7,8). Conserved basic residues at the N-terminus of the channels are important for PI(3,5)P(2) activation and PI(4,5)P(2) inhibition(8). However, due to a lack of structural information, the mechanism by which TRPML channels recognize PI(3,5)P(2) and increase its Ca(2+) conductance remains elusive. Here we present the cryo-electron microscopy (cryo-EM) structure of a full-length TRPML3, at an average resolution of 2.9 Å. Our structure reveals not only the molecular basis of ion conduction but also the unique architecture of TRPMLs, wherein the voltage sensor-like domain is linked to the pore via a cytosolic domain we term the “mucolipin domain” (MLD). Combined with functional studies, we suggest that the MLD is responsible for PI(3,5)P(2) binding and subsequent channel activation, and that it acts as a ‘gating pulley’ for lipid-dependent TRPML gating.