Fig. 3

Ribbon representation of the overall 3D structure of the nigritoxin molecule. The polypeptide chain is color-coded following the domain architecture (blue: N-terminal; yellow: central; magenta: C-terminal; domains) schematically represented in the upper panel of a. The central panel highlights the 3D domain organization observed in the crystal structure, revealing the Mg²⁺ bound to a surface loop of the N-terminal domain and the linker regions (orange) (see also Fig. 4). The lower panel displays the 3D structure turned by 90° around the horizontal axis, showing a disordered loop in the N-terminal domain for which no electron density is visible in the crystal structure. The overall fold as well as those of the three individual domains do not superimpose to any known structure when submitting a “blast against PDB”. b Close-up view of a particular structural feature present in the C-terminal domain, which is formed by two loops projecting into the solvent region. The arginine (R512) and tryptophan (W540) residues that stack against each other, as well as some selected residues pointing toward the exterior of the protein are highlighted in stick representation. c Surface representation of the C-terminal domain (gray), highlighting a local groove, in which a series of histidine and arginine residues (surface color corresponds to the color of the residue in the sequence extract) form a large patch that could represent a region important for the biological function. The patch is localized in front of a cavity (Supplementary Fig. 12)