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Among coupled exchangers, CLCs uniquely catalyze the exchange of oppositely charged ions (Cl –  for H + ). Transport-cycle models to describe and explain this unusual mechanism have been proposed based on known CLC structures. While the proposed models harmonize with many experimental findings, gaps and inconsistencies in our understanding have remained. One limitation has been that global conformational change – which occurs in all conventional transporter mechanisms – has not been observed in any high-resolution structure. Here, we describe the 2.6 Å structure of a CLC mutant designed to mimic the fully H + -loaded transporter. This structure reveals a global conformational change to improve accessibility for the Cl –  substrate from the extracellular side and new conformations for two key glutamate residues. Together with DEER measurements, MD simulations, and functional studies, this new structure provides evidence for a unified model of H + /Cl –  transport that reconciles existing data on all CLC-type proteins.

A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl – /H + transport cycle