Integrative structural analysis of the human endosomal Na⁺/H⁺ exchanger NHE6 reveals a lipid-stabilized intracellular gate and a disordered C-terminus

Human NHE6 (HsNHE6) is an endosomal Na+/H+ exchanger essential for maintaining luminal pH and endo-lysosomal trafficking in neurons. HsNHE6 mutations are implicated in devastating neurological syndromes, but mechanistically the transporter remains poorly understood. Here, we present the single particle cryo-electron microscopy structure of HsNHE6 at 3.4 A, captured in an inward-open conformation. The structure reveals a homodimeric architecture with 13 transmembrane helices per protomer and the conserved ion-binding site. Functional assays demonstrate that HsNHE6 mediates the exchange of both Na⁺ and K⁺ for protons. A structured C-terminal helix interacts with the transmembrane core, jointly forming a hydrophobic cavity that accommodates two lipid molecules, potentially modulating cation access to the ion-binding site. The distal C-terminus of HsNHE6 is intrinsically disordered, as revealed by NMR and small-angle X-ray scattering and equips HsNHE6 with a large cytosolic span. Our integrative model of full-length HsNHE6 provides a comprehensive framework for understanding HsNHE6-mediated ion exchange and its disruption in neurological diseases such as Christianson syndrome.