Fig. 3: Cryo-EM characterization of TcdB1 and TcdB4 in complex with minibinder 43829. | Nature Communications

Fig. 3: Cryo-EM characterization of TcdB1 and TcdB4 in complex with minibinder 43829.

From: De novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants

Fig. 3

a A cryo-EM map of the TcdB1-43829 complex, with an overall resolution of 3.13 Å and a contour level set at 0.5. b Superimposition of the computational design model (gray) on the experimentally determined cryo-EM structure. The minibinder 43829 is depicted in pink, while TcdB1 is shown in cyan. c The cryo-EM density of the 43829 binder in the TcdB1-43829 complex. The FSC curve was generated using Mtriage by comparing the structural model of 43829 to the map of 43829 complexed with TcdB1. The map-to-model resolution for minibinder 43829 alone in the TcdB1-43829 map is 4.05 Å. d–e Zoomed views of the cryo-EM structures. Possible hydrogen bonds are highlighted by yellow dashed lines. f A 3.04 Å cryo-EM map of TcdB4-43829 complex with a contour level set at 0.5. g Superimposition of the computational design model (gray) on the experimentally determined cryo-EM structure, with the minibinder 43829 depicted in pink and TcdB4 in tan. h The cryo-EM density of the 43829 binder in the TcdB4-43829 complex. The FSC curve was generated using Mtriage by comparing the structural model of 43829 to the map of TcdB4-43829. The map-to-model resolution for minibinder 43829 alone in the TcdB4-43829 map is 4.45 Å. i, j Zoomed views of the cryo-EM structures. Possible hydrogen bonds are highlighted by yellow dashed lines. Interactions between 43829 (pink) and the RBI-1 of TcdB4 (tan).

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