Transistors, regardless of their size, rely on electrical gates to control the conductance between source and drain contacts. In atomic-scale transistors, this conductance is sensitive to single electrons hopping via individual orbitals. Single-electron transport in molecular transistors has been previously studied using top-down approaches to gating, such as lithography and break junctions. But atomically precise control of the gate--which is crucial to transistor action at the smallest size scales--is not possible with these approaches. Here, we used individual charged atoms, manipulated by a scanning tunnelling microscope, to create the electrical gates for a single-molecule transistor. This degree of control allowed us to tune the molecule into the regime of sequential single-electron tunnelling, albeit with a conductance gap more than one order of magnitude larger than observed previously. This unexpected behaviour arises from the existence of two different orientational conformations of the molecule, depending on its charge state. Our results show that strong coupling between these charge and conformational degrees of freedom leads to new behaviour beyond the established picture of single-electron transport in atomic-scale transistors.