Fig. 2: The structure of mtRNASer(UGA).
a Secondary structure diagram of mtRNASer(UGA). b Tertiary structure of mtRNASer(UGA) as bound to mSerRS. The portion of the anticodon arm missing in the reconstruction is indicated as a dashed yellow line. c Comparison of the tRNA core region in human mtRNASer(UGA) (right) and the canonical S. cerevisiae ctRNAPhe (left; PDB 4TRA)75 centered on the D-arm (green). Deletion of A9 (cyan spheres in tRNAPhe) results in an upward shift of the first D-arm base-pair (green sticks) in mtRNASer(UGA) by one base-plane (indicated by dashed lines), allowing canonical interactions between the shortened D-loop and T-loop. The upward-shift of the D-arm by one base-plane is compensated in mtRNASer(UGA) by the introduction of the additional anticodon stem base-pair G27A:U43A (yellow spheres). d Details of the D-loop-T-loop tertiary interactions forming the elbow region in mtRNASer(UGA). The T-loop of mature human mtRNASer(UGA) contains modifications in positions U54 (m5U), U55 (ψ), and A58 (m1A)41. Colored as in a and b. e Details of the tertiary core region in mtRNASer(UGA), centered on the V-loop. Colored as in a and b. f Close-up view of the hollow core structure of mtRNASer(UGA) (circle), lacking most tertiary interactions known from canonical tRNAs.
