Fig. 5: Cryo-EM and XL-MS analyses of substrate-captured Bpa36-139. | Nature Communications

Fig. 5: Cryo-EM and XL-MS analyses of substrate-captured Bpa36-139.

From: Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa

Fig. 5

A Cryo-EM map of substrate-bound Bpa36-139 solved to a global resolution of 4.1 Å. Additional density attributed to HspRΔC9 is visible in the lower region of the Bpa ring. B Upper two panels: emerging density from Bpa residue K55 in the representative neighboring protomers (H1’ in magenta, left and H1 in purple, right) corresponding to the GA crosslink formed between Bpa and HspR. Lower two panels: substrate density localized around residue H131 of Bpa H4 helix from one protomer (purple) shown at low map threshold (left) and high map threshold (right). C XL–MS analysis of Bpa36-139 in complex with HspRΔC9. Lysine residues of HspRΔC9 crosslinked to Bpa36-139 are mapped onto the AlphaFold model of the HspRΔC9 dimer. A downsized copy of the model colored according to the per-residue confidence score is shown on the right (dark blue – high confidence; red – low confidence). D Focused 3D classification revealing considerable heterogeneity within the Bpa-HspR interaction site and demonstrating multiple conformational states of the substrate around H131 of Bpa.

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