The RelE and RelB proteins constitute the RNA interferase (toxin) and its cognate inhibitor (antitoxin) components of the Escherichia coli relBE toxin-antitoxin system. Despite the well-described functionality and physiological activity of this system in E. coli, no structural study was performed on the folding and stability of the protein pair in solution. Here we structurally and thermodynamically characterize the RelBE system components from E. coli in solution, both separately and in their complexed state. The RelB antitoxin, an alpha-helical protein according to circular dichroism and infrared spectroscopy, forms oligomers in solution, exhibits high thermostability with a TM of 58.5 degrees C, has a considerable heat resistance, and has high unfolding reversibility. In contrast, the RelE toxin includes a large portion of antiparallel beta-sheets, displays lower thermostability with a TM of 52.5 degrees C, and exhibits exceptional sensitivity to heat. Complex formation, accompanied by a structural transition, leads to a 12 degrees C increase in the TM and substantial heat resistance. Moreover, in vivo interaction and protein footprint experiments indicate that the C-terminal part of RelB is responsible for RelB-RelE interaction, being protease sensitive in its free state, while it becomes protected from proteolysis when complexed with RelE. Overall, our findings support the notion that RelB lacks a well-organized hydrophobic core in solution whereas RelE is a well-folded protein. Furthermore, our results support that RelB protein from E. coli is similar to ParD and CcdA antitoxins in both fold and thermodynamic properties. The differential folding state of the proteins is discussed in the context of their physiological activities.