Figure 3: Carbene footprinting of USP5 reveals di-ubiquitin-binding sites. | Nature Communications

Figure 3: Carbene footprinting of USP5 reveals di-ubiquitin-binding sites.

From: Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions

Figure 3

(a) Fractional modification (by 2) of USP5 peptides in the presence (black bars) and absence (white bars) of di-ubiquitin. Error bars are±s.d. (n=3) and significant differences (Student’s t-test, P<0.05) are highlighted with a red dot. (b) Model of USP5 (based on PDB 3IHP) with di-ubiquitin (orange, PDB 2W9N) bound. The ubiquitin-binding domains are shown in blue, and the catalytic domain in green. The motion required for the ZnF-UBP-bound substrate to approach the catalytic site is indicated by an arrow. (c) Model of USP5 (based on PDB 3IHP) showing the locations of the five peptides (red) masked from labelling by di-ubiquitin binding, and their correspondence to the ZnF-UBP and catalytic domains.

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