Fig. 3: Model for the NSP13 5′ to 3′ translocation mechanism.

a Proposed translocation mechanism for NSP13 based on the transition from the closed (pre hydrolysis) to open (Product and APO) forms. The transitions are initiated by the binding, hydrolysis and release of ATP which triggers the conformational changes and remodels the RNA interface. b Close up view of the active site with ATP in the closed conformation (left) and ADP and Pi in the open conformation (right). Hydrolysis as subsequent charge repulsion could trigger the opening of the cleft between the two domains with conserved motifs on the 2A domain primarily contacting the product phosphate whilst the ADP product interacts with the 1A domain. Several of the phosphate interacting motifs are proximal to regions of the RNA binding interface indicating the possibility of modulation based on hydrolysis status. c Remodeling of the RNA interface based on the position adopted by the 1B domain. The closed conformation shows on the left and the open on the right. The contact areas for the 5′ and 3′ RNA regions (depicted in gray and black) is shown.