Fig. 5.

SDASO and DSSO XL-maps of the yeast 26S Proteasome.A, circular 2-D XL-maps of the 26S Proteasome derived from all three SDASO linkers (top) and DSSO (bottom). Intrasubunit linkages are shown red and intersubunit linkages are colored black for SDASO and blue for DSSO. Outer circle represents the subunits within the two subcomplexes of the 26S proteasome, i.e., the 19S RP (Lid [blue] and base [dark orange]) and 20S CP (α ring [yellow] and β ring [green]). B, 3D XL-maps of the 19S RP using SDASO (top) and DSSO (bottom) cross-links, in which 19S lid subunits are colored light blue and base subunits colored light red. Cross-links are also color coded: 19S lid-lid (blue lines), 19S base-base (red lines), 19S lid-base (purple). C, 3D XL-maps of the 20S CP based on SDASO (top) and DSSO (bottom) cross-links, in which 20S α subunits are colored as light yellow, 20S β subunits as aqua green, and 20S linkages as lime green. Note: high-resolution structure of the yeast 26S proteasome (PDB: 4CR2 (s1) was used for the maps in (B) and (C). Subunits are color coordinated as shown in supplemental Table S3C. CP, core particle; DSSO, disuccinimidyl sulfoxide; RP, regulatory particle; SDASO, succinimidyl diazirine sulfoxide.