Supplementary Figure 6: Interactions between the Rpt ring and the CP, and structural comparison between the AAA motor protein p97 and the Rpt subunits.

(a) An overall view on the interface between the Rpt ring and the CP, centered on Rpt1 (left panel). The carboxyl-terminal sequences of Rpt1 run parallel with the surface of the α-ring, and the carboxyl-terminus is not inserted into the α-pocket between subunits α4 and α5 (right panel). (b) An overall view on the interface between the Rpt ring and the CP, centered on Rpt4 (left panel). The carboxyl-terminal sequences of Rpt4 run parallel with the surface of the α-ring, and the carboxyl-terminus is not inserted into the α-pocket between subunits α7 and α1 (right panel). (c) An overall view on the interface between the Rpt ring and the CP, centered on Rpt2 (left panel), and a close-up view on the carboxyl-terminus of Rpt2 (right panel). The carboxyl-terminal nine residues of Rpt2 exhibit no apparent EM density and are left out in the final atomic model. (d) An overall view on the interface between the Rpt ring and the CP, centered on Rpt6 (left panel), and a close-up view on the carboxyl-terminus of Rpt6 (right panel). The carboxyl-terminal 11 residues of Rpt6 exhibit no apparent EM density and are left out in the final atomic model. (e) Structural comparison between p97 and each of the six Rpt subunits with alignment of their large AAA domains. Structures of p97 bound to ADP (PDB accession code 5FTM) and ATP-γS (PDB accession code 5FTN) are colored green and magenta, respectively. This comparison reveals that the conformations of Rpt1, Rpt3, Rpt4, and Rpt5 more closely resemble that of the ATP-γS-bound p97. The conformations of Rpt2 and Rpt6 are closer to that of the ADP-bound p97. (f) Structural comparison between p97 and each of the six Rpt subunits with alignment of both large and small domains. Compared to panel a, the conclusions remain unchanged for all but one Rpt subunit. Rpt3 shows a better overall alignment to the ADP-bound p97.