Fig. 4: Water molecules that interact with ZYA and the intersubunit pocket residues appear to be important for gating regulation. | Communications Biology

Fig. 4: Water molecules that interact with ZYA and the intersubunit pocket residues appear to be important for gating regulation.

From: High resolution structures define divergent and convergent mechanisms of archaeal proteasome activation

Fig. 4

a Overlay of ZYA-T20S electron density map (transparent surface) and model (pink sticks), showing waters (red spheres) modeled into the map and interactions (blue dotted lines) with the model. b Model of ZYA (red) docked in α intersubunit pocket, aligned by β subunits, showing interactions with waters (spheres) and residues (sticks) in the ZYA-T20S model (blue). ZYA-T20S model is overlapped with doused WT T20S model (yellow) for comparison. c 7 nM T20S (WT or E25A) incubated with 44 nM PA26 or 15 nM PAN (supplemented with ATP and MgCl2). LFP degradation rate (rfu/min) normalized to control and the amount of proteasome from different preparations is normalized to their rate of LLVY-AMC hydrolysis, which is insensitive to gating affects (see methods for details). *Data (means) are representative of three or more independent experiments each performed in triplicate. Error bars represent ± standard deviation.

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