Localization of the regulatory particle subunit Sem1 in the 26S proteasome

• 26S proteasome subunit Sem1 was mapped using cryo-EM and cross-linking data.
• C-terminal helix of Sem1 located near winged helix motif of Rpn7.
• N-terminal part of Sem1 tethers Rpn7, Rpn3 and lid helical bundle.
• Sem1 binds differently to PCI-domains of proteasome subunit Rpn7 and TREX-2 subunit Thp1.

The ubiquitin–proteasome system is responsible for regulated protein degradation in the cell with the 26S proteasome acting as its executive arm. The molecular architecture of this 2.5 MDa complex has been established recently, with the notable exception of the small acidic subunit Sem1. Here, we localize the C-terminal helix of Sem1 binding to the PCI domain of the subunit Rpn7 using cryo-electron microscopy single particle reconstruction of proteasomes purified from yeast cells with sem1 deletion. The approximate position of the N-terminal region of Sem1 bridging the cleft between Rpn7 and Rpn3 was inferred based on site-specific cross-linking data of the 26S proteasome. Our structural studies indicate that Sem1 can assume different conformations in different contexts, which supports the idea that Sem1 functions as a molecular glue stabilizing the Rpn3/Rpn7 heterodimer.