Fig. 2: Structural insights into tRNA-Met recognition, binding, and cleavage by SLFN11.

a Cryo-EM density map for SLFN11 bound to tRNA-Met (top). tRNA is colored in green and the nuclease active sites of both SLFN11 protomers are indicated. The map was postprocessed in cryoSPARC by DeepEMhancer⁴⁴. Schematic representation of type II tRNA-Met (bottom). Structural features of the tRNA are labeled and color-coded. The SLFN11 cleavage site is indicated. b Close-up views of SLFN11 nuclease active sites I and II for the tRNA-Met bound structure. The semitransparent cryo-EM map is shown together with the model. Nuclease active site residues (E209, E214, D252) and the manganese ions are labeled. c Endonuclease activity of SLFN11 on tRNA-Leu or tRNA-Met. The conditions of the nuclease assay correspond to the cryo-EM conditions. The experiment was performed in duplicates. One representative replicate is shown. d Difference in the position of tRNA-Leu and tRNA-Met relative to the nuclease ___domain of SLFN11. e MST measurements of SLFN11^wt binding to fluorescently labeled type II tRNA-Leu and type I tRNA-Met to determine equilibrium dissociation constants (K_d). The indicated SLFN11 concentrations assume a dimeric state. Data are represented as mean values +/− SD from three independent experiments. Source data for c and e are provided as a Source Data file.