High-resolution structures of human NHE6 and NHE9 elucidate endosomal ion and lipid interactions.

Endosomal NHE6 (SLC9A6) and NHE9 (SLC9A9) transporters are essential for maintaining pH homeostasis within endosomes and their dysfunction has been linked to neurological and neurodegenerative disorders. NHE6 and NHE9 are widely considered to function as electroneutral exchangers that couple the export of protons to the import of sodium or potassium ions across cellular membranes, thereby forming the basis of proton leak pathways for internal pH balancing and fine-tuning. Among the 13 identified SLC9 family members, only NHE6 and NHE9 are targeted to endosomes. Despite their biological importance and therapeutic potential, the structural basis for their activity and regulation remains elusive. Here, we present the cryo-EM structures of human NHE9 and two splice variants of NHE6 that differ by alternative inclusion of the β-hairpin motif-containing loop domain located between transmembrane helices 2 and 3, showcasing structural diversity within the organellar NHE subfamily. By mapping the sodium-binding site, our results provide mechanistic insights into ion transport, and for NHE6 we provide evidence for a conserved PIP2-mediated regulatory mechanism. These findings provide a framework for understanding endosomal NHE function with implications for disorders such as Alzheimer's disease and glioblastoma.