Extended Data Fig. 6: Further cryo-EM data processing of resting-state (RS) proteasomes in continuation from Extended Data Fig. 2.

Classification leads to the emergence of 4 classes. Two of these classes, called ‘Slight left’ and ‘Slight right’ based on the position of the regulatory particle, show an ensemble of PITH domain densities and were further processed as described in Extended Data Fig. 7. Further classification of class 2 with variability in the Rpn1 subunit revealed 10 additional classes at moderate resolution. Three of them, class 4, class 3, and class 6 are shown in more detail below. Class 4 has TXNL1’s PITH domain in the forward conformation, whereas class 3 shows the PITH domain oriented backwards. Class 6 represents a unique class with extra density on Rpn11 that may originate from ubiquitin or a ubiquitin-like domain, for instance of FAT10. A human proteasome structure (PDB: 6MSE) with ubiquitin-bound Rpn11 was used for comparison, to color the class 6 map, and show similarities.