Ultraweak interactions drive cap-mediated positioning and elongation of the bacterial flagellar filament

The bacterial flagellum, essential for motility and pathogenesis, requires the filament cap (FliD) to polymerize flagellin (FliC). However, the mechanisms governing the transition from the hook junction to the filament elongation remain elusive, obscured by stoichiometric mismatches and barely detectable interactions. To resolve this, we deploy solution NMR to characterize ultra-weak interactions, quantify affinities (K_D ≈ 0.1 mM for junction protein FlgL; 1.65 mM for FliC). These data enable rational complex stabilization for cryo-EM structure determination of Salmonella FliD pentamers complexed with FlgL or FliC, revealing that both substrates engage an identical conserved surface in a 5:5 stoichiometry. Integrating these structures into native flagellar tip densities reveal a 5:11 FliD:FlgL/FliC architecture, where six additional subunits barely detected by NMR dock at secondary sites. Mutations that disrupt or enhance these interfaces impair motility and filament integrity, while disulfide-locked FliD pentamers confirm that cap rigidity is crucial for elongation. These findings support a rotary cap mechanism where ultra-weak binding and structural fidelity of the cap ensure efficient flagellin polymerization. Our study resolves the long-standing paradox of stoichiometric mismatch in flagellar filament biogenesis, providing a blueprint for the assembly of dynamic macromolecular machines.