There is little structural information about the protein complexes conferring resistance in
Mycobacterium tuberculosis (Mtb)
to anti-microbial oxygen and nitrogen radicals in the phagolysosome. Here, we expose the model Mycobacterium,
Mycobacterium smegmatis,
to simulated oxidative-stress conditions and apply a shotgun EM method for the structural detection of the resulting protein assemblies. We identified: glutamine synthetase I, essential for
Mtb
virulence; bacterioferritin A, critical for
Mtb
iron regulation; aspartyl aminopeptidase M18, a protease; and encapsulin, which produces a cage-like structure to enclose cargo proteins. After further investigation, we found that encapsulin carries dye-decolourising peroxidase, a protein antioxidant, as its primary cargo under the conditions tested.