Fig. 4: Molecular modeling of CtTrl1-LIG in complex with tRNA-derived substrates.

a, Surface representation of the CtTrl1-LIG (blue) model with bound ASL exon halves (pink and purple). The model was derived from the MD simulation trajectory based on frames demonstrating the most stable RNA-protein interaction energies. b, Modeled structure of the ASL RNA in the active site with the 5′-end activated AppRNA 3′ exon half (pink) and the 5′ exon harboring a 2′P/3′OH end (purple). The structure is illustrated as a schematic (top) and as sticks (bottom, colored by element). The dashed line (gray) indicates the opened A-U base pair toward the loop. c, Cartoon representation of superposition with CtTrl1-LIG–RNA crystal structure (gray) and CtTrl1-LIG–ASL model (blue) without RNA depiction. The structures were superimposed along the core β-sheets of the adenylyltransferase domain. Superposition reveals CTD clamping, indicated by arrows towards the NTD active site. d, Cartoon representation of SimRNA models of CtTrl1-LIG with full-length tRNA. The starting model tRNA (pink) and medoids of the five largest clusters of best-energy conformations of the tRNA (dark green, light green, yellow, orange and red) are shown as ribbons.