Abstract . Prokaryotes have evolved intricate innate immune systems against phage infection 1-7 . Gabija is a highly abundant prokaryotic defense system consisting of two components, GajA and GajB 8 . We previously demonstrated that GajA functions as a DNA endonuclease that is inactive in the presence of ATP 9 . To reveal how the Gabija system is activated for anti-phage defense, we report its cryo-electron microscopy (cryo-EM) structures in five states, including apo GajA, GajA in...