Organellar two-pore channels (TPCs) contain two copies of a Shakerlike six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in plants and animals. Interestingly, plant and animal TPCs share high sequence similarity in the filter region, yet exhibit drastically different ion selectivity. Plant TPC1 functions as a nonselective cation channel on the vacuole membrane, whereas mammalian TPC channels have been shown to be endo/lysosomal Na + -selective or Ca 2+ -release channels. In this study, we performed systematic characterization of the ion selectivity of TPC1 from Arabidopsis thaliana (AtTPC1) and compared its selectivity with the selectivity of human TPC2 (HsTPC2). We demonstrate that AtTPC1 is selective for Ca 2+ over Na Our results also confirm that HsTPC2 is a Na + -selective channel activated by phosphatidylinositol 3,5-bisphosphate. Guided by our recent structure of AtTPC1, we converted AtTPC1 to a Na + -selective channel by mimicking the selectivity filter of HsTPC2 and identified key residues in the TPC filters that differentiate the selectivity between AtTPC1 and HsTPC2. Furthermore, the structure of the Na + -selective AtTPC1 mutant elucidates the structural basis for Na + selectivity in mammalian TPCs.two-pore channel | ion selectivity | crystal structure T wo-pore channels (TPCs) are organellar cation channels ubiquitously expressed in animals and plants (1, 2) and belong to the voltage-gated ion channel superfamily (3). TPC channels contain two homologous Shaker-like six-transmembrane (6-TM) domains in each subunit and function as homodimers. They are believed to be evolutionary intermediates between homotetrameric voltage-gated potassium channels and the four-domain, single-subunit, voltage-gated sodium/calcium channels (4).In human and animals, TPC channels (TPC1 and TPC2) are localized to the endo/lysosomal membranes and regulate the ionic homeostasis within these acidic organelles. Their functions have been shown to be involved in various physiological processes, such as endocytosis and endosomal trafficking (5, 6), lysosomal morphology and pigmentation (7,8), autophagy (9, 10), and nutrient metabolism via the mammalian target of rapamycin (mTOR) complex (11). Not surprisingly, given their central physiological role, defects in TPC channels are associated with a variety of disabling human disorders (9,(12)(13)(14)(15)(16)(17).Despite their physiological importance, some biophysical properties of mammalian TPC channels are still under debate (18). Mammalian TPC channels were initially identified as receptors of nicotinic acid adenine dinucleotide phosphate (NAADP), a Ca 2+ -mobilizing second messenger, and responsible for Ca 2+ release from the acidic organelles (19)(20)(21). Although the NAADP-dependent endo/lysosomal Ca 2+ release is attributed directly to the Ca 2+ conduction of TPC channels activated by NAADP in some studies (16,(22)(23)(24)(25)(26), several recent studies demonstrate that TPCs are Na + -selective channels that are activated by phosphatidylinositol 3...