Bacterial flagella are rotary nano-machines that contribute to bacterial fitness in many settings, including host colonization. The flagellar motor relies on the multiprotein flagellar motor-switch complex to govern flagellum formation and rotational direction. Different bacteria exhibit great diversity in their flagellar motors. One such variation is exemplified by the motor-switch apparatus of the gastric pathogen Helicobacter pylori, which carries an extra switch protein, FliY, along with the more typical FliG, FliM, and FliN proteins. All switch proteins are needed for normal flagellation and motility in H. pylori, but the molecular mechanism of their assembly is unknown. To fill this gap, we examined the interactions among these proteins. We found that the C-terminal SpoA domain of FliY (FliY C ) is critical to flagellation and forms heterodimeric complexes with the FliN and FliM SpoA domains, which are β-sheet domains of type III secretion system proteins. Surprisingly, unlike in other flagellar switch systems, neither FliY nor FliN self-associated. The crystal structure of the FliY C -FliN C complex revealed a saddle-shape structure homologous to the FliN-FliN dimer of Thermotoga maritima, consistent with a FliY-FliN heterodimer forming the functional unit. Analysis of the FliY C -FliN C interface indicated that oppositely charged residues specific to each protein drive heterodimer formation. Moreover, both FliY C -FliM C and FliY C -FliN C associated with the flagellar regulatory protein FliH, explaining their important roles in flagellation. We conclude that H. pylori uses a FliY-FliN heterodimer instead of a homodimer and creates a switch complex with SpoA domains derived from three distinct proteins.Bacterial flagella are rotary nano-machines that contribute to bacterial fitness in a variety of settings, including mammalian and plant colonization (1,2). Although the basic function of flagella as a motor organelle is conserved, substantial variation exists among microbes in the components used to build and operate key aspects of the flagella. For example, we now know that there are diverse motor structures from cryo-electron tomography studies (3,4), and that bacterial motors consist of FliG, FliM and either FliN or FliY or the combination of both FliN and FliY (5) The flagellar motor switch complex, also called the C-ring, is found at the base of each flagellum and resides within the cytoplasm (6). It plays an important role in flagellar assembly, torque generation, and rotational switching. Numerous studies have dissected the composition, arrangement, and structure of the switch proteins, with a focus on those from Escherichia coli and Salmonella typhimurium that possess FliG, FliM and FliN. The motor C-rings of these bacteria contain 26 copies of FliG, 34 copies of FliM and >110 copies of . Most of these structures were determined using proteins from other organisms, and their assembly models have been recently proposed (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22). Electron microscop...