Structure of the proton-powered secretion motor at the heart of the bacterial flagellum

Bacterial type III secretion systems export proteins across the inner membrane using the proton-motive force (PMF), but how proton flow is coupled to opening of the export channel is unknown^XX,XX. Here we present single-particle cryo-EM structures at 2.5-4.2 Å resolution of the intact flagellar Export Apparatus from Salmonella enterica, obtained using optimized extraction conditions of the endogenous assembly that retain the complete transmembrane complex. The transmembrane domain of FlhA forms a nonameric funnel-shaped basket beneath the Export Gate, with each subunit harboring a buried pathway of conserved hydrophilic residues spanning the hydrophobic core of the membrane. FlhB is resolved for the first time within the intact gate, revealing helices that thread through the FlhA channel, completely sealing it at rest. A symmetry-free reconstruction captures one FlhA protomer hinged outward at the water-filled cavity, breaking the rotational symmetry. Together, these structures define the architecture of the proton-transducing element of the type III secretion system and suggest a rotary gating mechanism, with parallels to the F₀ motor of ATP synthase, in which PMF-driven conformational cycling of FlhA drives regulated opening of the export channel.