ABC toxins are large (1.5–2.5 MDa), tripartite protein toxins secreted by a wide range of Gram positive and Gram negative bacteria. They are the predominant virulence factors in many insecticidal bacteria, where they function as cytotoxins that target actin polymerization pathways, triggering apoptotic cell death in selectively targeted host cells and genes encoding related toxins are found in bacterial pathogens of significance to humans. Recent breakthroughs in the structural characterisation of two prototypical bacterial ABC toxin systems have revealed two distinct structural classes of toxins. Here we present the first near-atomic resolution structure of a representative type II toxin – the 2.3MDa YenTc from the insect pathogen Yersinia entomophaga – determined using single particle cryo-electron microscopy and X-ray crystallography. Our studies reveal the structural basis for novel aspects of a mechanism by which bacteria package, translocate and deliver potent cytotoxins to targeted inter-cellular destinations. Likely functional parallels with much smaller pore-forming toxins such as anthrax and diphtheria are revealed, while the structure is suggestive of a mechanism that may be harnessed by eukaryotic cells to produce and translocate proteins involved in divergent cellular functions including neuronal cell signalling.