Structural insights into the mechanism of phosphate recognition and transport by human XPR1

XPR1 is the only known protein responsible for transporting inorganic phosphate (Pi) out of cells, a function conserved from yeast to mammals. Human XPR1 variants lead to cerebral calcium-phosphate deposition, which are associated with a hereditary neurodegenerative disorder known as primary familial brain calcification (PFBC). Here, we present the cryo-EM structure of human XPR1 in both its Pi-unbound form and various Pi-bound states. XPR1 features 10 transmembrane α-helices that form an ion channel-like architecture. Multiple Pi recognition sites are arranged along the channel, facilitating Pi ion transport. Two arginine residues, subject to pathogenic mutation in PFBC families, line the translocation channel and serve to bind Pi ion. Clinically linked mutations in these arginines impair XPR1’s Pi transport activity. To gain dynamic insights into the channel-like transport mechanism, we conducted molecular dynamics simulations. The simulations reveal that Pi ion undergoes a stepwise transition through the sequential recognition sites during the transport process. Together with functional analyses, our results suggest that the sequential arrangement of Pi recognition sites likely enable XPR1 to use a “relay” process to facilitate Pi ion passage through the channel, and they establish a framework for the interpretation of disease-related mutations and for the development of future therapeutics. One Sentence Summary Combined cryo-EM, molecular dynamics simulations and functional studies demonstrate that human XPR1 employs a channel-like transport mechanism to export inorganic phosphate out of cells