Structural basis of Ca(2+)/pH dual regulation of the endolysosomal TRPML1 channel

Organellar ion channels are essential for cell physiology. Their activities are often regulated by Ca(2+) and H(+), which are concentrated in many organelles. Here we report a novel structural element critical for Ca(2+)/pH dual regulation of TRPML1, a Ca(2+) release channel crucial for endolysosomal functions. TRPML1 mutations cause mucolipidosis type IV (MLIV), a severe lysosomal storage disorder characterized by neurodegeneration, mental retardation and blindness. We obtained high-resolution crystal structures of a 213-amino acid luminal domain of human TRPML1 that harbors three missense MLIV-causing mutations. This domain forms a tetramer with a highly electronegative central pore formed by a novel luminal pore-loop. Cysteine crosslinking and cryo-EM confirm this structure in the full-length channel. Structure-function studies demonstrate that Ca(2+) and H(+) interact with the luminal pore to exert physiologically important regulation. The MLIV-causing mutations disrupt the luminal domain structure and cause TRPML1 mislocalization. Our study provides a structural underpinning for TRPML1's regulation, assembly and pathogenesis.