Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases
- University of Utah School of Medicine, United States
- New York Structural Biology Center, United States
Abstract
Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the S. cerevisiae AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains.
Data availability
The refined model comprising the Vps4 ATPase domains of subunits A-E and the cyclic peptide is accessible via the PDB (RRID: SCR_012820; PDB ID: 6NDY) together with the 3.6 Å map from the combined dataset (RRID: SCR_003207, EMDB Accession Number EMD-0443). The complete model, including regions not subjected to atomic refinement such as the 12 Vta1VSL domains and subunit F, is also available via the PDB (PDB ID: 6OO2), together with the map containing Vta1VSL densities at all six Vps4 interfaces (RRID: SCR_003207, EMDB Accession Number EMD-20142). The two maps derived from the cF30 and cFF30 complex datasets individually, and the three maps for subunit F, have been deposited to the EMDB (RRID: SCR_ 003207, EMDB Accession Numbers EMD-20144, EMD-20147, EMD-20139, EMD-20140, EMD-20141).
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Vps4 with Cyclic Peptide Bound in the Central PoreProtein Data Bank, 6NDY.
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Vps4 with Cyclic Peptide Bound in the Central PoreProtein Data Bank, 6OO2.
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Vps4 with Cyclic Peptide Bound in the Central PoreEMDataBank, EMD-20142.
Article and author information
Author details
Wesley I Sundquist
Christopher P Hill
Funding
National Institutes of Health (P50 GM082545)
- Han Han
- James M Fulcher
- Janet H Iwasa
- Michael S Kay
- Peter S Shen
- Christopher P Hill
National Institutes of Health (R01 GM112080)
- Wesley I Sundquist
National Institutes of Health (P41 GM103310)
- Venkata P Dandey
New York State Foundation for Science, Technology and Innovation
- Venkata P Dandey
Simons Foundation (SF349247)
- Venkata P Dandey
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2019, Han et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases
eLife 8:e44071.
https://doi.org/10.7554/eLife.44071
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