We considered all possible combinations of 6, 5 and 4 transmembrane helices, within either TM1-TM6 or TM7-TM12, and compared the structure of each set of helices in the L vs T states (closed circles), T vs O (open circles) and O vs L (closed squares), through pairwise root-mean-square difference (RMSD) calculations. When these RMSD values are used as a rank, it becomes clear that combinations that exclude TM2 or TM8 (red) feature systematically smaller differences across the LTO cycle than those that include TM2 or TM8 (black). All other exclusions show no clear correlation. For example, comparing TM1-TM6 (left panel) in L vs T, this increasing ranking is ΔTM2, ΔTM4, ΔTM1, ΔTM5, ΔTM3, and ΔTM6; in T vs O: ΔTM2, ΔTM5, ΔTM4, ΔTM3, ΔTM1, and ΔTM6; and in O vs L: ΔTM2, ΔTM5, ΔTM1, ΔTM4, ΔTM3, and ΔTM6. Furthermore, the data shows that combinations of five helices excluding TM2 and TM8 are not significantly more divergent across the LTO conformers than combinations of four helices. Thus, the asymmetric crystal structure of AcrB captures collective displacements of two 5-helix bundles within each protomer, formed by TM1/TM3-TM6 and TM7/TM9-TM12 (referred to as repeats R1 and R2), relative to flanking helices TM2 and TM8, respectively. Note that comparisons of combinations of seven or more helices result in larger RMSD values than those shown here, and are therefore omitted.