Supplementary Figure 7: Image processing of the Cdc48–UN complex in the presence of ATP-γS.
From: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1–Npl4
a, An area of a cryo-EM image of a vitrified sample is shown with some particles circled. Scale bar: 50 nm. b, Selected 2D class averages obtained with ISAC. Side length of individual averages: 33 nm. c, Initial 3D map obtained with cryoSPARC. d, Image-processing workflow for 3D classification and refinement in RELION-2 that yielded a density map at 4.3 Å. Asterisks (*) indicate 3D classes that consist of particles with their N domains in the up-conformation. Daggers (†) indicate 3D classes that consist of particles with an extra density near an N domain (only seen with a lower contouring threshold) that likely represents the UBX-like domain of Npl4. See Methods section for details.
