Extended Data Fig. 2: Detailed views of the PTEX protein-conducting channel and symmetry mismatch in the engaged state.

a–c, Cryo-EM densities and atomic models of cargo and pore loops from the near-atomic resolution structures of Clp/HSP100 ATPases YME1⁵⁹ (a), PTEX HSP101 (b) and HSP104³¹ (c). Tyrosine sidechain densities are clearly visibly intercalating with the cargo densities. The modelled engaged state PTEX cargo has a calculated r.m.s.d. of 1.09 Å and 1.25 Å to the published YME1 and HSP104 cargo models, respectively. Pore loops are labelled by NBD and protomer (for example, D2PL,P1 is NBD2 pore loop, protomer 1). d, Side view of the bisected engaged state PTEX cryo-EM map. The protein-conducting channel, calculated using HOLE⁴⁰, is shown superimposed over the bisected map in translucent white with a navy outline. The HSP101 NBD2 pore loop densities are coloured by HSP101 protomer, and the cargo density is coloured pink. e–j, The transition from the asymmetric HSP101 spiral to the C7-pseudosymmetric PTEX150(668–823)–EXP2 heptamer is depicted using a series of cross-sections taken perpendicular to the central axis of the translocon, spanning the area of symmetry mismatch. The section of the translocon corresponding to each cross-sectional image is indicated with a bracket in d.