Extended Data Fig. 8: Cryo-EM processing of NSUN2C271A-Intron-SAH structure.
From: Substrate selectivity of the human RNA m5C methyltransferase NSUN2
a, Cryo-EM data processing workflow with a representative micrograph and 2D classes provided. Final map density for Intron Conformation 1 is colored by domain (NTD: blue, MTD: purple, CTD1: light green, CTD2: dark green, RNA: orange, SAH: pink). b-d, Comparison of the “Intron Conformation 1” (left) and “Intron Conformation 2” (right) reconstructions. Unsharpened cryo-EM maps of protein-RNA complexes (top) or protein and RNA map segments (bottom) colored by local resolution (b), gold standard FSC curves with 0.5 and 0.143 thresholds (top) and conical FSC curves with relative distribution frequencies (bottom) (c), and relative signal amounts by viewing direction in a 2D heatmap (top) and 3D projections (bottom) (d). e, Superimposition of NSUN2C271A-tRNALysCTT “D-arm Conformation” and NSUN2C271A-Intron structures by MTD, and the RNA conformational shift is depicted with orange (tRNALysCTT) and gray (Intron) ribbons. Cyt34 of Intron is colored cyan. f, Close-up view of the purines of CNNRR binding R133 and R137 in NSUN2C271A-tRNALysCTT (left) and NSUN2C271A-Intron (right) structures. Protein side chains (blue) and RNA nucleotides (orange) are shown as sticks with sharpened cryo-EM maps as transparent surfaces at σ = 6. g,h, Q-scores calculated for protein (g) and RNA (h) residues for the NSUN2C271A-Intron structure. Sigma (σ) denotes the threshold level in standard deviations from the mean.
