Fig. 6.

The UPS XL-PPI networks. (A) An interaction network composed of the identified UPS components and their direct interactors. The UPS components were grouped and color coded based on complexes and functions, including 26S proteasome (19S lid, purple; 19S base, red; 20S α ring, orange; 20S β ring, yellow), E1 (cyan), E2 (light blue), E3 ubiquitin enzymes (royal blue), and DUBs (green). (B) Extended XL-PPI network of proteins found to interact with ubiquitin, DUBs, and ubiquitin ligases. Core ubiquitination machinery was color coded and shown in the center of the network. They were encircled by a ring of directly interacting proteins, shown in white. Proteins found to be cross-linked to direct interactors are shown in gray and categorized into groups based on their PPI similarities.