ABC toxin complexes are virulence factors found in a range of bacterial pathogens of insects and humans. They are large, tripartite proteins and, due to their pathogenicity, of particular interest for agriculture and medical research. Here we used single particle cryo-electron microscopy to investigate the structure of Yen-Tc, an ABC toxin complex that is the main determinant of virulence associated with the entomopathogenic bacterium Yersinia entomophaga. We determined the 3D structure of the main Yen-Tc A subunit at an average resolution of 5 Å, with a varying resolution throughout the map, as typical for macromolecular EM structures. However, the majority of the map is resolved to 4 Å or better, allowing us to build an atomic model for more than 85% of the structure using a combination of X-ray crystallography, homology models and de novo chain tracing followed by molecular dynamics-guided structure refinement. Our refined EM structure provides new insights into the mechanisms that underpin the function of this ABC protein complex including a striking conformational change to a biologically active state.