The MIA complex is localized to a unique position in each 96-nm repeat. (A) Nucleoflagellar apparatuses from oda1 and mia1R × oda1 were stained with the anti-HA antibody. The HA antibody detects FAP100-HA in both flagella in the mia1R × oda1 strain (fluorescence image on the bottom). Very weak or no signal was detected in oda1 flagella that do not express the FAP100-HA protein. Both basal bodies and nuclei have some nonspecific staining. (top) Differential interference contrast images show that all cells possess flagella. Arrowheads indicate cis- and trans-flagella, showing that both flagella are staining. (B) Longitudinal tomographic slices of the averaged 96-nm axonemal repeats from DMTs 1–9 of pWT, mia2, mia1, and pf9-3/ida1 reveal structural defects in the mutant axonemes. The density of the I1 dynein (red outlines) is completely missing in pf9-3/ida1 (white outlines) and appears reduced in the mia mutants. These defects are more prominent in mia1 than in mia2. The densities of other major axonemal structures, such as the ODAs, single-headed inner dynein arms (IDAs 2–6 and X), and the N-DRC are not significantly changed in the mia mutants. (C) 3D isosurface renderings of the averaged 96-nm axonemal repeats from pWT, mia2, mia1, and pf9-3/ida1 reveal the structural defects in more detail. Regions that are reduced in the mia averages are colored green; the most obvious defects are the distal density of the IC/LC of I1 dynein (orange) and the density between the I1 dynein and the N-DRC (yellow), which is reduced in mia2, missing in mia1, but fully assembled in pWT and pf9-3/ida1. The pWT and pf9-3/ida1 data were refined from data originally reported by Heuser et al. (2012b). Proximal is on the left in B and C. Bars: (A) 10 µm; (B) 25 nm.