Structure of ZIKV top stem. (A) Overall structure of the top stem of ZIKV SLA. The asymmetric unit contains four ssRNA molecules (A–D). The four top stem sites, 1, 2, 3, and 4 are shown in teal, light blue, indigo, and purple, respectively. The GGGCCC linker is shown in pink. The G7 base of sites 2 and 4 did not contain a well-defined electron density and were thus omitted from the model. (B) Superposition of top stem ssRNA chains. Chains A (blue), B (gray), C (black), and D (lavender) are colored. (C) Comparison of top stem sites with that of the full-length ZIKV SLA. The four top stem sites, colored as in A, are superposed onto that of the full-length SLA (gray). (D) The G7•C8-G19 base triple interaction. The G7 bulge at site 1 is positioned inside the dsRNA helix and interacts with the C8-G19 base pair within the same plane (teal). Additionally, the G7 nucleotide is stabilized by interactions with water and a sulfate molecule. The 2Fo − Fc map surrounding the base triple is contoured at 1.5 σ. Hydrogen bond distances are listed in angstroms (Å). (E) The G7•U6′-A20′ base triple interaction. The G7 bulge at site 3 (indigo) interacts with both sugar edges of the U6′-A20′ base pair (light green). The Watson–Crick face of G7 is additionally stabilized by a glycerol, a water, and ribose sugar of the preceding U6 nucleotide. The 2Fo − Fc map surrounding the base triple is contoured at 1.5 σ. (F) Wobble G-U base-pair interactions. The four G-U bases at sites 1, 2, 3, and 4 are stabilized by hydrogen bonding with water molecules (red spheres) along the Watson–Crick, Hoogsteen, and sugar edges of the nucleotides. A glycerol molecule replaces a water molecule in the G-U wobble pair at site 4 (purple). Hydrogen bonds <3.1 Å are designated by solid lines.
