Fig. 2. Comparison of the FliD structures across bacterial species.

a Overlay of the FliD D2–D3 domains structures from C. jejuni (FliD_cj, 6SIH—this study, orange), S. marcescens (FliD_sm, 5XLJ, blue), S. enterica (FliD_se, 5H5T, purple), E. coli (FliD_ec, 5H5V, green), P. aeruginosa (FliD_pa, 5FHY, yellow), and H. pylori (FliD_hp, 6IWY, cyan). b Alignments of X-ray crystallography derived oligomeric structures of the head domains from FliD_sm, FliD_se, and FliD_ec, to that of the FliD_cj pentamer. The diameter of the lumen as well as the outer diameter of the capping protein is similar in the pentamer formed by FliD_se, but significantly smaller in the tetramer formed by FliD_sm, and larger in the hexamer formed by FliD_ec. c 2D classes obtained from negative-stain data of recombinant FliD_pa and FliD_sm (Supplementary Fig. 1b). FliD_pa shows three different sets of particles: a class with particles showing 6-fold symmetry (~120 Å in diameter), a class showing smaller particles with 5-fold symmetry (~100 Å diameter), and classes of particles with 4-fold symmetry (~80 Å and ~110 Å in classes 3 and 4, respectively). FliD_sm shows two different sets of particles: large particles with 4-fold symmetry (~150 Å in diameter), and smaller particles with 5-fold symmetry (~100 Å diameter). The size of the 5-fold symmetry particles in both orthologues is similar to that observed in 2D classification of FliD_cj. The red squares indicate classes with particles of similar shape and dimensions to the FliD_cj structure, with distinctive five-fold symmetry. FliD_cj negative stain top view is shown as a reference to the right. d Sequence alignment for FliD from different species. The secondary structure elements for FliD_cj are shown at the top. The domains are color coded as follows: Yellow: D0 terminal domains. Red: D1 domain. Blue: D2 domain. Green: D3 domain. Uncolored: D4 domain found only in FliD_cj. Stars indicate important residues in terminal interactions, for which mutagenesis experiments were performed in Fig. 3.