Extended Data Fig. 4: Structural analysis of the CapRel^SJ46-Gp54^Bas11 complex.

(a) Cartoon representation of the crystal structure of CapRel^SJ46-Gp54^Bas11 complex bound to ATP. ATP coordination residues of CapRel^SJ46 toxin domain (R79 and R116) are labeled. (b) Cartoon representation and the corresponding m2Fo-DFc electron density map of Gp54^Bas11 in the CapRel^SJ46-bound state. (c) The unbiased mFo-DFc electron density map of ATP and Mg²⁺ observed in the crystal structure of CapRel^SJ46-Gp54^Bas11 complex. (d) Left, crystal structure of the complex of Gp54^Bas11 (purple) bound to CapRel^SJ46 (colored by domains). Right, predicted structural model of the complex of CapRel^SJ46 and MCP^SECΦ27 (pink) by AlphaFold. A different view of Fig. 3c. (e) Detailed interface of CapRel^SJ46-Gp54^Bas11 complex structure indicating interaction with Gp54^Bas11 via K269 (top) tethers Y355 of the YXXY neutralization motif away from the toxin active site of CapRel^SJ46 (bottom). (f) Top, experimental SAXS analysis of CapRel^SJ46 (open black circles). The theoretical scattering of CapRel^SJ46 in the closed state predicted by AlphaFold is shown in red. Bottom, comparison of the model of CapRel^SJ46 in the unbound closed state with an ab-initio envelope calculated from the experimental SAXS data using DAMMIF⁴⁸. (g) Top, experimental SAXS analysis of CapRel^SJ46-Gp54^Bas11 complex (open black circles). The theoretical scattering of the CapRel^SJ46-Gp54^Bas11 crystal structure is shown in red. Bottom, comparison of the crystal structure of CapRel^SJ46-Gp54^Bas11 with an ab-initio envelope calculated from the experimental SAXS data using DAMMIF⁴⁸.