Electron cryomicroscopy allows the visualization of complex structures, such as the rotor, filament, and cap-filament complex, which are either difficult or impossible to study by X-ray crystallography. By developing new methods of image analysis, the density map of the flagellar filament is now beyond 5 Å resolution, and the structure of the FliF rig complex and the cap-filament complex have begun to show the details that have significant implications to their functions.

The flagellar filament grows by self-assembly of flagellin transported from the cytoplasm through the long narrow central channel of the flagellum to its distal end, where HAP2 forms a cap to prevent flagellin from diffusing away without polymerization. Electron cryomicroscopy and image analysis visualized the pentagonal cap structure with a plate and five legs, and interactions of the cap and the filament end against symmetry mismatch, which implicates a rotary cap mechanism that promotes the efficient self-assembly of flagellin by always preparing a single flagellin binding site at any time.