a, b, Side (a) and top (b) view from the matrix for the alignment of the open class structure (in cyan) and closed class structure (in grey). To generate the closed class structure, the final structure of the open class was refined in real space in Phenix (5 macro cycles with morphing at each cycle) against 4.6 Å map of the closed class (Extended Data Fig. 1). All of the α-helices were well fit into density, but owing to low resolution of the closed class no further refinement was performed and the comparison of structures involves only the relative positions of secondary structure elements. The two structures were aligned via transmembrane core subunits and are displayed as cartoon models. In the closed class the peripheral arm undergoes a hinge-like motion around the Q site towards the tip of the membrane arm, with the direction of shift indicated by the arrow in b. As a result, subunit B13 moves ~3 Å closer to the 42-kDa subunit, allowing for direct contacts. The shift is larger at the periphery, reaching 7 Å at the tip of the peripheral arm. Additionally, subunit ND5 and its matrix bulge move about 3 Å towards peripheral arm.