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. 2022 Feb 11;13:838. doi: 10.1038/s41467-022-28186-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Model of the Ubp6-UbVS-proteasome complex based on cryo-EM analysis. Ubp6, Rpt1, and ubiquitin are highlighted as spheres, other proteins as ribbons. Rpn1, teal; Rpn11, green; Rpn10 and other base subunits, tan; lid components, light brown; ATPases other than Rpt1, purple; core particle, gray. Boxed region is rotated and enlarged in b. (PDB: 7QO3, 7QO4). b Detail of Ubp6-Rpt1 interface with key features of Ubp6 highlighted. c Enlarged underside view of the Ubp6-Rpt1 interface with mutagenized residues rendered as spheres. Interface A is in blue for Ubp6 and pink for Rpt1; Interface B, orange for Ubp6, violet for Rpt1. d Interface A is protected from hydrogen exchange by the addition of excess Ubp6-UbVME. Ubp6-dependent deuteration differences within peptides of Rpt1-Rpt6 of purified regulatory particle are shown. See Supplementary Fig. 5 for additional HDX-MS data. All deuterium uptake values used to generate these difference maps can be found in Supplementary Data 1. e Critical loops of free Ubp6 (PDB: 1VJV).