Fig. 2: Structure of CtTrl1-LIG with an activated RNA substrate.
From: Structure of fungal tRNA ligase Trl1 with RNA reveals conserved substrate-binding principles
a, Cartoon representation of the overall structure of CtTrl1-LIG in complex with an activated RNA substrate. The N-terminal domain is colored blue, and the C-terminal domain is light blue. The AMP cofactor (lime) is depicted as sticks and the RNA strands (pink and sand) are shown in cartoon style. The RNA sequence overview contains the corresponding colors. b, A zoomed-in view of the active site with the activated AppRNA 5′ end, with the coordinating amino acid residues depicted as sticks. The 2Fo–Fc electron density OMIT map at 1σ is shown as a gray mesh. c, The nearest symmetry mates (relative to the blue molecule) of the LIG–RNA complex in the P212121 crystal. The individual molecules are shown in surface depiction. Two symmetry mates of the assembly (colored in orange and green) are enlarged for simplification (black rectangles). d, Scheme of the arrangement in c, illustrating the end-to-end bridging of LIG molecules and their active sites by the bound RNA substrate molecules (same color code as in c). e, Surface representation of CtTrl1-LIG (blue) with bound RNA duplexes (bronze and purple, pink and sand) as well as a neighboring symmetry mate in cartoon depiction (green) visualizing the binding of one RNA substrate between two LIG molecules in the crystal.
