Fig. 3: SHARC-exo captures spatial distances within the human ribosome.

a, b Comparing SHARC-exo captured spatial proximities to a cryo-EM structure model of the human ribosome in 25 nt × 25 nt (a) or 50nt × 50nt (b) windows (PDB:4V6X). icSHAPE-measured reactive nucleotides within 20 Å of each other in the 18S (a) and 28S (b) rRNAs are plotted on the lower-left corner of each square. SHARC-exo gapped reads with 2 arms within 20 Å of each other are plotted on the upper right corner, and the read numbers are square-root scaled. Positions of SHARC-exo reads are randomly shuffled as a control (right panels). c, d Zoom-in views of two areas in the 18S and 28S rRNAs. Blue rectangles highlight consistent distance measurements between SHARC-exo and cryo-EM. The red rectangle highlight regions missed by SHARC-exo. e An example tertiary proximity in the 28 S rRNA captured by SHARC-exo. f Secondary structure model of the two regions, showing the consensus 3′ ends of the gapped reads, expected crosslink sites, and distance. g 3D structure model of the crosslinked sites. h–m SHARC-exo captured an interaction between 5.8S and 28S rRNAs. h Gapped reads for the interactions between 5.8 S and 28 S rRNA. i The 3′ end, putative crosslinking sites and distance mapped onto the secondary structure model of rRNAs. j, k 3D model of the interaction, where the two loops involved in interactions are shown in red and purple. Interhelical stacking is shown in spheres (k). l, m icSHAPE measurement of nucleotide flexibility around the crosslinking sites (l) and all possible distances between the two interacting loops (m). m Distances between 2′OH groups at the nucleotides with high SHAPE reactivity. Tail length in the parentheses indicates the distance between the 3′ ends and the reactive nucleotides that are potentially crosslinked. Source data are provided as a Source Data file.