Fig. 5. Interactions between compact IF2 and the ribosome.

a Overview of compact IF2-GDP bound to the 70 S ribosome. Domain C1 (yellow) locates under the uL11-stalk (light blue) while domain C2 (red) is disposed along the aminoacyl-tRNA accommodation corridor in the vicinity of 23 S rRNA helices H89 (pale yellow), H91 (light pink), H92 (light blue), and the SRL (pale green), and the C-terminal of r-protein uL6 (light orange). Domain II (blue) interacts with helix h5 of 16 S rRNA (orange). b–e Magnified views of the insets shown in a. b Domain C1 is sandwiched between the G- and C2-domains, together surrounding the SRL of 23 S rRNA (pale green). Residue Asp⁷⁸⁴ in domain C2 (red) interacts with G2648 (E. coli G2661) in the SRL. Residues Val⁶⁷⁶ and Gly⁶⁷⁷ in domain C1 (yellow) form a flat surface that stacks with the apical nucleotide A2647 (A2660) in the SRL. EM density shown as gray mesh. c Residue Ser⁸¹⁸ in domain C2 (red) is within hydrogen bonding distance to nucleotides A2458 (A2471) and G2459 (G2472) in 23 S rRNA helix H89 (pale yellow). d The main chain of residues Gly⁵²⁸ and Arg⁵²⁹, and the side chain of Arg⁵⁵⁸ in domain II (blue) stack with base pair A55-U362 (A55-U368) in helix h5 of 16 S rRNA (orange). e The conserved Tyr⁷²³ in helix H12 of domain C1 (yellow) stacks with nucleotide A1057 (A1067) in 23 S rRNA helix H43 of the uL11-stalk.