Insertion of the PafE GQYL motifs into the 20S CP moves helix 0 (H0) of the α-subunit ring. A, electron density map of the α-ring of the 3.4-Å 3D map of PafE(Δ155–166)-bound 20S CP with D7 symmetry. The PafE C terminus density is colored in salmon. Middle and lower panels are zoomed-in density and a schematic view of interactions between a PafE C terminus (salmon) and 20S CP α-subunits (magenta). The side chains of PafE Tyr-173 and the carbonyl oxygen of PafE Leu-174 interact with side chains of PrcA Arg-26 and PrcA Lys-52, respectively. B, sequence alignment of the proteasomal α-subunits from different organisms: Mtb and Mja, Methanococcus jannaschii; Afu, Archaeoglobus fulgidus; Sce, S. cerevisiae; and Hsa, Homo sapiens. In the cases of eukaryotes (Sce and Hsa), the sequences of α2-subunits were chosen for alignment, because these subunits interact with the activating C termini of the hexameric ATPases Rpt1–6 in the cryo-EM structures of the yeast and human 26S proteasomes (PBD codes 5WVK and 5GJQ). C, SDS-PAGE of in vitro degradation assays using HspR as a substrate. Aliquots were removed at the indicated time points (min) and analyzed by 15% SDS-PAGE. The degradation assays were repeated at least three times with essentially same results. PafE mediates HspR degradation by WT 20S CPs, but not 20S(R26A) or 20S(K52A) CPs. D, an quantification of the proteolysis reactions in C by estimating the relative intensity of each band, showing the amounts of remaining HspR substrate over a 150-min reaction time. E, a zoomed in view of superimposed 20S CP α-rings with (magenta) or without (cyan) a capping PafE ring. PafE residues are labeled in orange, and PrcA residues in black. The black arrows show the movements of the side chains in the two structures.