Crystal structure of the ss-HP92/DbpA complex in the closed state. (A) Interaction of the ssRNA with the active site of the helicase core. For clarity, only the ssRNA (chain L) and one DbpA molecule (chain I) are shown (left). Schematic diagram of the 2:2 complex observed in the crystal (right). (B) SEC chromatograms of free ss-HP92 (black), the ss-HP92/DbpA complex (orange), and the ss-HP92/DbpA/ADP/BeF3 complex (blue). (C) Close-up of the interaction between the ssRNA region (chain L, orange) in conformation 1 and the active site of the helicase core (chain I, RecA_N blue, RecA_C cyan). For comparison, the complex between a 6 nt RNA (pink) and the DEAD-box helicase VASA (gray; PDB ID 2db3) is shown. The nucleotides that interact with the active site are numbered 1–6. The ssRNA sequence is shown on top with identical numbering. (D) Close-up of the interaction between the ssRNA region (chain C, orange) in conformation 2 and the active site of the helicase core (chain A, RecA_N blue, RecA_C cyan). (E) Comparison of the interactions between nucleotides in positions 5 and 6 for DbpA and VASA. The top row and the bottom-left panel show complexes between DbpA and ds-HP92 and ss-HP92 in conformation 1 and 2. The lower-right panel shows the VASA/ssRNA complex (PDB ID 2db3). Hydrogen bonds formed by R132 (DbpA) or the corresponding R378 (VASA) are indicated by dashed-red lines.
