Fig. 1. Structures of substrate-bound Cdc48 reveal relative motion among subunits.

A Cdc48 hexamer modeled into the 2.9 Å resolution consensus reconstruction. Subunit labels and colors are used throughout the manuscript. B 3DVA and 3D classification reveals structures with substantial variability in subunits E and F. Root mean square deviation (RMSD) measurements between Cα atoms of class 1 and 9 models shown as colorized ribbon. C Variable subunit motion observed in subunits D–F between classes 1 (gray) and 9 (color). Subunits A, B, and C positions are generally superimposable between classes 1 and 9 (subunits A and B not shown). Substrate axis shown as purple rod and its upper/lower limits denoted by dashed gray lines as a positional reference. Arrows in panels B and C indicate trajectory of motion.