Cryo-EM structure of human Na+/H+ exchanger NHA1 in an inward-open conformation

The human Na+/H+ exchanger NHA1 (SLC9B1) plays a critical role in sperm motility and male fertility by regulating intracellular pH through its sodium-proton antiport activity. Despite its physiological importance, the structural and mechanistic basis of NHA1 function has remained elusive. Here, we present the cryo-EM structure of human NHA1 at 3.6 Å resolution, captured in an inward-open conformation. Structural comparisons with modeled outward-open states reveal substantial conformational changes in the core domain, supporting an elevator-like transport mechanism. Additionally, several key residues are identified that modify their interaction patterns, likely aiding in the conformational switches necessary for substrate transport. Their contribution to substrate transport is further supported by mutagenesis and sodium transport assays, providing insights into the molecular mechanism of NHA1. Here the authors report the cryo-EM structure of human NHA1, a sodium-proton exchanger essential for sperm motility, revealing an inward-open conformation and an elevator-like transport mechanism. Mutagenesis and functional assays further identify key residues governing ion transport.