Figure 2. Classification of the Needle Complex subtomogram averages from Shigella flexneri and superimposition of in vitro map on in situ map.

(a–c) Central/cross section maps of original subtomogram averaging map of the NC (a) and three classes (b), middle and bottom each corresponding cross sections at height indicated by the dashed yellow line and the dashed pink line, respectively. The number of particles in each class is indicated in the top right corner. (c) Refined map excluding class 3, which shows weak densities in cytoplasmic region. (d,e) The 3D rendering maps show pod-like densities, linker densities between membrane associated export apparatus (export apparatus) and pods, export apparatus and cytoplasmic export platform (export platform). (f,g) Superposition of in vitro NC map obtained from single particle image analysis (g, yellow) on in situ map from subtomogram averaging (f, grey). In situ and in vitro NC map show OR, Neck, IR1 and IR2. Scale bar indicates 10 nm.