The opening of a non-specific channel, known as the permeability transition pore (PTP), in the inner membranes of mitochondria, can be triggered by calcium ions, leading to swelling of the organelle, disruption of the inner membrane and ATP synthesis, and cell death. Pore opening can be inhibited by cyclosporin A mediated via cyclophilin D. It has been proposed that the pore is associated with the dimeric ATP synthase, and that the OSCP (oligomycin sensitivity conferral protein), a component of the enzyme’s peripheral stalk, provides the site where cyclophilin D interacts. Subunit b contributes a central α-helical structure to the peripheral stalk, extending from near the top of the enzyme’s catalytic domain and crossing the membrane domain of the enzyme via two α-helices. We investigated the possible involvement of the subunit b and the OSCP in the PTP by generating clonal cells, HAP1-Δb and HAP1-ΔOSCP, lacking the membrane domain of subunit b or the OSCP, respectively, in which the correponding genes ATP5F1 and ATP5O had been disrupted. Both cell lines preserve the characteristic properties of the PTP. Therefore, the membrane domain of subunit b does not contribute to the PTP, and the OSCP does not provide the site of interaction with cyclophilin D. The membrane subunits ATP6, ATP8 and subunit c have been eliminated previously from possible participation in the PTP. Therefore, the only subunits of ATP synthase that could participate in pore formation are e, f, g, DAPIT (diabetes associated protein in insulin sensitive tissues) and the 6.8 kDa proteolipid.