The Type III secretion system is a widespread bacterial secreting machine that drives assembly of important motility and virulence structures, with a large human impact on agricultural and human diseases. A conserved core module common to flagella and injectisomes, the type III secretion system uses both a proton motive force (PMF) and energy of ATP hydrolysis to unfold and secrete protein substrates that refold in self-assembling structures like a molecular 3D printer. The mechanism of secretion, and the co-operating roles of the PMF and an associated ATPase are not well understood. This thesis presents three complementary structural biology approaches to advance our understanding of how T3SSs operate. In Chapter 2, the first cryo- EM structure of the major component protein of the type III secretion system is resolved to 3.5Å. The structure of an SsaVc nonameric ring resembles that of the homologous MxiAc nonamer, and a comparison of homologue structures shows a highly conserved D3 domain which forms the subunit interfaces, and variable opening of the large cleft between D2 and D4. The unique acidic C-terminus of SsaV is disordered in our map, and the linker and transmembrane regions that are involved in energising secretion are not resolved. In Chapter 3, the assembly and structure of the ATPase complex is investigated by comparing mutant complexes in situ with tomography. We find that FliH functions as a structural scaffold for the ATPase and can assemble independently to FliY on the C-ring. We find evidence for overlapping functional roles of the ATPase and the substrate chaperones, as well as heavy binding of the C-ring in the absence of FliH; the top candidate identity for the C-ring binding factor is the initial isoprenoid pathway enzyme DXP. In Chapter 4, computational predictions are made for the protein folds of the inner membrane export apparatus proteins. A recent breakthrough in the field allows assessment of some of the predicted folds against experimental structures, confirming some of our predictions of the pore structure. The picture of type III secretion that emerges is one where the ATPase complex is stably-assembled and is dispensable for secretion, as are chaperones, but together contribute assistance to an essential PMF-driven step of substrate processing that occurs at the SctV nonameric cytoplasmic ring.