High-resolution RNA tertiary structures in Zika virus stem–loop A for the development of inhibitory small molecules

Structure of ZIKV bottom stem. (A) Overall structure of bottom stem of ZIKV SLA. The asymmetric unit contains two ssRNA chains (A and B) that contain two bottom stem sites. Sites 1 and 2 are shown in tan and brown, respectively, and the GGGCCC linker is shown in pink. The 5′ and 3′ termini of chains A and B are labeled. (B) Superposition of bottom stem ssRNA chains. Chains A and B are shown in yellow and dark brown, respectively. (C) Comparison of bottom stem sites with the full-length SLA. The bottom stem sites 1 and 2 (tan and brown, respectively), are superposed onto that of the full-length SLA (gray). (D) The U15•G8′-C11′ base triple interaction. The U15 bulge at site 1 (tan) interacts with the G8-C11 base pair along the minor groove of the ⁷GGGCCC¹² linker of the adjacent symmetry-related RNA molecule (light green). The 2F_o − F_c map surrounding the base triple is contoured at 1.0 σ. Hydrogen bond distances are listed in angstroms (Å). (E) The U15•A3′-U17′ base triple interaction. The U15 bulge at site 2 (brown) interacts along the minor groove of the symmetry-related A3′-U17′ base pair (light green). Hydrogen bond distances are listed in angstroms (Å). The 2F_o − F_c map surrounding the base triples is contoured at 1.0 σ.