An R-type pyocin shares structural and functional similarity with type six secretion systems. Both use a loaded, contractile, sheath-tube assembly to puncture a hole through the membrane of their target cells. A single pyocin kills a bacterium by dissipating its proton motive force. Currently, the absence of atomic structural information of this type of molecular machines has seriously hindered the understanding their mechanisms of action, particularly storage and release of energy that drives contraction. Here, by cryo electron microscopy, we report the three-dimensional reconstruction of an R-type pyocin trunk at 3.5 Å resolution and derive its atomic model at its loaded, pre-contraction state. The trunk structure consists of two coaxial cylinders, tube and sheath, with the same helical and six-fold rotational symmetries and an open, 35 Å diameter central channel. The tube is made of stacked discs, each containing a 24-strand β-barrel, spanning six subunits of the tube protein (TP), with its central channel optimized for proton conduction. The sheath layer builds upon the tube by attaching one α-helix from each sheath protein (SP) onto one tube subunit through electrostatic interactions. Comparison with our structure of post-contraction state reveals that contraction draws energy from electrostatic and shape complementarities that work as a biological battery. This understanding will inform engineering efforts to harness pyocin for antibacterial applications and to block type six secretion from hostile bacteria.