Fig. 6: Conformational changes of HTNV-L between pre-initiation and elongation.
a Cut-away view cartoon representation of HTNV-L regions that are changing in conformations between pre-initiation and elongation. On the left and middle panels, the RNA are shown as cartoon and labeled. The bridge loop, the thumb-ring β-hairpin, the residues 1399–1402 and 1341–1344 are respectively colored in green, dark blue, gray, and purple. The other elements are colored as in Fig. 1. The bridge loop position is surrounded with a dotted line. On the right panel, superimposition with the pre-initiation colored in gray and the elongation colored as in the middle panel. For clarity, the RNA is not shown. Movements are indicated with arrows. Distances between the pre-initiation model and the elongation model are indicated. b Surface representation of HTNV-L in the pre-initiation and the elongation conformations. The RNA is shown as cartoon. The template exit tunnel and the 3′secondary binding site entrance are indicated with white and black dotted lines respectively. c Zoom on the 3′ secondary binding site at pre-initiation and elongation. 3′vRNA1–25 is shown as yellow stick when present, domains are colored as in Fig. 1. The lower jaw reorganization and change of orientation at elongation is visible. Movements of the lower and upper jaws are depicted. On the right panel, superimposition with the pre-initiation colored in gray and the elongation colored as in the middle panel. For clarity the RNA is not shown. Movements are indicated with arrows. Distances between the pre-initiation and the elongation models are indicated. d Surface view of the 3′vRNA secondary site. Nucleotides and interacting domains are labeled. e Cartoon representation of the 3′vRNA secondary site. Two sub-panels are used to show residues that interact with the 3′vRNA1–25 end. Nucleotides are numbered, and interacting residues are labeled. Hydrogen bonds are indicated as dotted lines.
