Figure 7. The internal and external motions of EF-G.

The internal and external motions of EF-G shown from (a) side, (b) top and (c) front of EF-G. The structure of EF-G in the PRE state (R₁ = 37 Å) (in white) superposed on that in the POST state (R₁ = 15 Å) is depicted as a wire model in gray. The P- and E-tRNAs in the POST state are depicted as wire models in orange. The surrounding molecules, SRL (C2646-G2674), L14 and L12-CTD (L-chain, N69-P98) in the POST and PRE states are depicted as wire models in black and brown, respectively. GDP in the POST state is depicted as a space-filling model. Dynamic domains in the ribosome-bound EF-G for structures in the POST and PRE states were analyzed by DynDom3D program [49]. Each dynamic domain is colored: dynamic domain A (a large part of domain IV) in red, dynamic domain B (a large part of domain III) in yellow, dynamic domain C (a large part of domain II, and a part of domain G and subdomain G′) in thin blue and dynamic domain D (a large part of domain V and a part of domain G and subdomain G′) in green. The regions that were not assigned to a dynamic domain are shown in blue. The axis of dynamic domain X and Y is depicted as an arrow in color for dynamic domain X with a tip in color for dynamic domain Y. Dynamic domain X rotates anticlockwise around the axis of dynamic domains X and Y with respect to dynamic domain Y from the PRE to POST state. In the input parameter for the DynDom3D, the minimum ratio of external to internal displacement of 0.65 was used (default is 1.0). The ratio of internal to external displacement determines the acceptance criterion for a given domain pair. This lower value was required due to noise often seen from MD results [30]. The axis of the external motion is shown in pink. As a reference, x-axis, y-axis (e _ratchet) and z-axis (e _tRNA) are depicted as thin black lines at the anticodon of P-tRNA. The length of these axes (1 Å) is magnified by a factor of 50. EF-G with the same orientation as (a–c) is shown as a reference on the right side in small scale, where structural domains of G, G′, II, III, IV and V of EF-G are colored in gray, black, thin blue, yellow, red and green, respectively.