Extended Data Fig. 9: Stereoscopic representation of the active site electron density of pre-methylated BuMiaB in the presence of the 13-mer RNA substrate and 5’dAH+Met.
From: Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB
The structure of BuMiaB does not show any significant changes in the protein or RNA components of the complex in the pre-methylated versus non-pre-methylated states [RMSD = 0.231 Å (Cα = 371 atoms) and 0.089 Å (Cα = 439 atoms) for pre-methylated subunits A and B, respectively, versus non-pre-methylated subunit A; and 0.092 Å (Cα = 415 atoms) and 0.248 Å (Cα = 392 atoms) for pre-methylated subunits A and B, respectively, versus non-methylated subunit B]. a, The extended electron density at N3. The grey mesh corresponds to an Fo-Fc omit map for i6A contoured at 3.5σ, and the green mesh to an Fo-Fc map contoured at 3.0σ after refinement with i6A. b, The extended electron density at the sulfur atom of the [Fe3S4] cluster. The mesh corresponds to an Fo-Fc omit map for the methyl group (green colour) attached to the sulfur (grey colour) of the auxiliary cluster contoured at 3.5σ. c, In a map generated for the non-pre-methylated auxiliary cluster, no extended density is observed. The mesh corresponds to an Fo-Fc omit map for the sulfur atom of the auxiliary cluster contoured at 3.5σ. All residues have a common colour theme for the domains: tan for MTTase and grey for radical SAM.
