Fig. 1.

Design of the HAV IRES dV crystallization construct and its overall structure in complex with Fab HAVx. a Proposed secondary structure of HAV IRES (wild-type HM175 strain)²⁸ showing major RNA domains (I–VI), polypyrimidine tracts (py) and the start codon (AUG). Dotted box highlights the dV crystallization construct. b Proposed secondary structure of the dV crystallization construct according to Brown et al²⁹. Empty and filled arrowheads indicate sites of cleavage with dsRNA and ssRNA specific RNases, respectively. Boxed regions indicate the sites of nucleotide covariations. c Global structure of the dV–Fab HAVx complex. d Secondary structure of dV derived from the crystal structure. Major structural elements and the corresponding nucleotides in b–d are colored analogously for facile comparison. Nucleotides involved in binding interactions with Fab HAVx and the nucleotides that form an A_L are colored green and red, respectively. Modeling of three nucleotides G627–G629 (colored gray in c, d) was ambiguous due to poor electron density