Fig. 6
Topological remodeling of the pore loops along the substrate–translocation channel. a Close-up view of the pore-1 loops from six Rpt subunits constricting the AAA channel in the SA state. The solvent accessible surface of the AAA channel was estimated using the program HOLE and is shown in gray dots. The AAA channel is aligned top-down vertically, whereby the substrates are supposed to enter from the top end of the pathway. b–d Close-up views of the pore-1 loops from six Rpt subunits constricting the AAA channel in the SD1, SD2, and SD3 states. The lower right inset in each panel shows an illustrative graph summarizing the pore-1 loop organization topology. The arrows show the clockwise direction of oligomeric ATPase organization from Rpt3, through Rpt4, Rpt5, Rpt1, and Rpt2, to Rpt6. The pore-1 loops in SD2 and SD3 show saddle-like topologies versus the spiral topology in SD1 and SA. The AAA channels are aligned to that shown in a based on their positions relative to the common reference of the CP. e Close-up view of the pore-2 loops from six Rpt subunits decorating the AAA channel in the SA state. f-h, g Close-up view of the pore-2 loops from six Rpt subunits constricting the AAA channel in the SD1, SD2, and SD3 states. i The relative positional changes of each pore loop in the SA, SD1, SD2, and SD3 states. The arrows show the direction of the movements in the pore loops during state transitions from SA to SD1(f), SD2(g), and SD3(h), respectively. The vertical axis indicates the relative height of the pore loops along the axis of the ATPase channel and the CP gate. The horizontal axis indicates the lateral distance orthogonal to the channel axis
