Fig. 2: A structure of RdRP translocation intermediate contains two alternative conformations of the product RNA.
a Electron density maps (orange: 2Fo-Fc contoured at 1.3 σ; green: Fo-Fc contoured at 3.5 σ) with a pre-translocation state model overlaid suggest alternative conformations for the product strand. Green triangles indicate an array of phosphate density inconsistent with the model. b Stereo-pair images of the intermediate structure S6A/S6B with a composite SA omit electron density map (contoured at 0.7 σ) overlaid. Coloring scheme: template in cyan (+1 nucleotide in orange), S6A product in green, S6B product in brown, palm in gray (YGDD sequence in magenta), ring finger subdomain in yellow, and PPi in orange. Capital letters with gray background indicate corresponding RdRP motifs. The side chains of several conserved residues, I176 of motif F, D238 of motif A, and D329 of motif C, are shown as sticks. c RNA-only comparison of the translocation intermediate (color) and the pre-translocation state (dark gray, PDB entry 3OL9, chain A complex). d Schematic illustration of the RNA movement suggested by the intermediate structure. Vertical lines indicate reference nucleotide positions. Zigzagged red symbol indicates the unusual backbone conformation of the template −2 position. The dashed lines indicate baseparing interactions. Capital letter G indicates motif G hurdle residues. The “+” symbols indicate the basic residues K127/R188 that can interact with the -1/-2 template phosphates, respectively. The red arrows indicate the distance and direction of backbone movement of the product nucleotides. Forty and 60% denote the crystallographic occupancy of S6A and S6B, respectively.
