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Subsequent ATP binding allows subunit F to pack against subunit A, bind to the next dipeptide of ESCRT-III, and assume the subunit A configuration. ( BC ) Conservation of helical pore loop structure in AAA ATPases. This is because subunit E will disengage from substrate as it moves toward the F configuration while the F subunit is moving toward the substrate-binding A configuration. It also explains the importance of the pore loop residues and the integral role of the class I and II pockets, because once a substrate residue binds at the top of the Vps4 helix it does not substantially change conformation until released at the bottom of the helical conveyor belt. These proteins are hexameric protein translocases, whose conserved pore loops emanate from equivalent structural elements, although their N-terminal domains are variable and only Vps4 has a ? domain. Still others, such as the eukaryotic proteasome ATPases, form part of a much larger complex and comprise six different, albeit related, subunits. W206 is always W, F, or Y, all of which could perform the role of sandwiching substrate side chains. The preceding K205 residue is usually K but sometimes M, which like K could flank the class I binding pocket. The more variable third residue, M207, is usually I, L or V, but there are examples of M (Vps4), A, F, K, R, and Y, all of which could provide hydrophobic sides to the class II binding pocket. Pore loop 2 residues are less conserved and are typically disordered in other published structures, which is consistent with the lack of distinctive roles in contacting substrate. A very recently published 3. A structure of the YME1 AAA ATPase in complex with a mixed polypeptide substrate ( Puchades et al. 2017 ) also presents a very similar structure and mechanism to that described here, although coordinates are not yet available during final preparation of this manuscript. A possible resolution is that a hexamer that has only one active ATPase site may allow inactive subunits to diffuse through the entire helical cycle.

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Micrographs with poor CTF cross correlation scores were excluded from downstream analyses. A total of 1,987 dose-weighted sums were used for all subsequent image processing steps. 4,429 particles were manually selected from 30 micrographs in EMAN2 using the e2boxer. y program ( Tang et al. 2007 ) to generate preliminary 2D classes in RELION ( Scheres, 2012 ). The non-CTF-corrected class averages were used for template-based autopicking in gautomatch. A total of 599,085 particles were extracted and used as input for full CTF-corrected image processing ( Figure 1—figure supplement 1B ). After multiple rounds of 2D classification, 124,743 particles were retained based on visual inspection of classes with high-resolution Vps4 features and used for an initial round of 3D classification. After 3D classification, 109,241 particles were used for RELION auto-refinement ( Scheres, 2012 ), which generated a 4. A density map of the Hcp1-Vps4 fusion complex based on the gold-standard FSC criterion ( Figure 1—figure supplement 1D ). To improve the resolution of Vps4, we performed signal subtraction of Hcp1 densities using the same approach as described previously ( Bai et al. 2015; Monroe et al. 2017 ) ( Figure 1—figure supplement 2 ). After Hcp1 signal subtraction, we performed an additional round of 3D classification, which assigned 82,225 particles into a single class with excellent Vps4 features. These particles were used for a final round of RELION auto-refinement, producing a 3.

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