Fig. 5: Conformation and interaction of tRNA^Gln(UUG) in complete vRNAP.

a, ASL structure from the cryo-EM model of complete vRNAP (strained state) depicted as a stick model, overlaid with the cryo-EM density shown as a transparent isosurface. b, ASL structure from the cryo-EM model of complete vRNAP depicted as cartoon-and-stick model. Please note that the relaxed state (free tRNA) is a manually created model because no experimental structure of this state is available (left, bound strained state; right, free relaxed state). c,d, Sketch of the ASL structure in the strained state (c) and in the relaxed state (d; free tRNA). Please note that this is a manually created model because no experimental structure of this state is available. e, Sketch of the ASL structure in the relaxed state. f, Scheme of the tRNA^Gln(UUG) base pairing in the bound strained state. g, Right, ASL region in cartoon-and-stick depiction with the adjacent NPH-I solvent-accessible surface (red) as observed in the model of complete vRNAP (strained state). Left, details of the NPH-I–tRNA interaction in the region of A37and U34. h, Codon ‘sun’ with recognition-relevant bases marked in color. i, ASL base-pairing scheme for tRNA^Gln(UUG) as observed in complete vRNAP in the strained state (bottom left). Sequences of several other tRNA species are threaded into the scheme for the other depictions. Unfavorable base pairing is indicated by two red bars; canonical base pairs are shown in gray and nonconical base pairs are shown in red. If present, pictograms in insets symbolize the relaxed (unbound) or strained (bound) states (Supplementary Video 2). Please note that there is no high-confidence tRNA^Arg(GCG) sequence available in the database.