Substrate coupling and inhibition in human Na+-dependent Cl−/HCO3− exchanger NCBE (SLC4A10)

This is the authors' abstract. We don't add key points for this paper.

Maintaining pH homoeostasis is essential for neuronal excitability and for regulating cerebrospinal fluid (CSF). The Na⁺-dependent Cl⁻/HCO3⁻ exchanger, NCBE (SLC4A10), abundant in the choroid plexus, contributes to CSF pH control by mediating bicarbonate flux, yet its molecular mechanism has remained unclear. Here we report cryo-EM structures of human NCBE in multiple functional states, revealing conserved binding sites for Na⁺, Cl⁻, and HCO3⁻, as well as an unexpected K⁺ site indicating relaxed cation selectivity. The inhibitor DIDS binds above the substrate cavity, locking NCBE in an outward-facing conformation and defining a subfamily-selective inhibitory mechanism. Functional assays and molecular dynamics simulations support the coordination of ions and the inhibitory effects. Comparison with an AlphaFold3-predicted inward-facing model suggests an elevator-like transport mechanism and delineates the conformational transitions in Na⁺-dependent HCO₃⁻ transporters. Together, these findings establish a structural framework for NCBE and offer insights into ion coupling and pharmacological modulation within the SLC4 family. NCBE (SLC4A10) is important for cerebrospinal fluid pH regulation. Here, authors determine cryo-EM structures of human NCBE that reveal ion binding, inhibitor recognition, and the structural basis of substrate coupling in this transporter.