Figure 4.

(A) Rendering of a low-energy tertiary structure snapshot of the truncated construct BVDVsegment_180_425 overlaid with coarse-grained 3D elements. Green cylinders highlight helical regions, with the rightmost representing H-type pseudoknot, and the middle and leftmost green cylinders portraying stem-loops IIIf and IIIg, respectively. The bulge between SL IIIf and IIIg is depicted in yellow, and the multiloop enclosed by the formation of the pseudoknot is plotted as a long red connection. The short red connection between the pseudoknot helix and SL IIIf represents a single unpaired C between these helices. Other structural elements are greyed out. The quasi-colinear arrangement of the pseudoknot and SL IIIf is noticeable, while the bulge induces a marked twist between SL IIIf and IIIg. (B) Schematic representation of the three helices encompassing the pseudoknot, SL IIIf, and IIIg, sketching their approximate spatial arrangement. Angles between adjacent helical segments are defined by stem vectors, i.e. angle α between SL IIIf and SL IIIg (orange and red vectors), and β between SL IIIf and the pseudoknot helix (blue vectors). The directionality of the backbone is indicated by black arrows. Regions of BVDVsegment_180_425, which are not directly involved in the spatial arrangement of these helices, are depicted as a dashed segment along the backbone.