Cryo-EM structures and transport mechanism of human multifunctional transporter BTR1

Human Bicarbonate Transporter Related protein-1 (BTR1/SLC4A11), a member of the SLC4 family, is a multifunctional transporter implicated in corneal dystrophies and ammonia metabolism. Here, we present cryo-EM structures of BTR1 in 13 distinct conformational states under various conditions, revealing its unique dimeric architecture and an inward-open conformation in the apo state. We demonstrate that BTR1 transports Na⁺, H⁺/OH⁻, and NH₃, but not boric acid. Its activity and conformational transitions are pH- and substrate-dependent: acidic conditions promote Na⁺/H⁺ transport, while alkaline pH and NH₃ induce an outward-open state, with Na⁺ enhancing NH₃ transport efficiency. Molecular dynamics simulations reveal substrate-specific transport dynamics, showing a transport efficiency hierarchy of H⁺ > Na⁺ > NH₃, and identify key residues (e.g., T434, T435, H719) essential for substrate binding and transport. Our findings establish BTR1's dual functional modes and a unique transport mechanism within the SLC4 family.