Structural insights into the binding of bS1 to the ribosome

Abstract

The multidomain ribosomal protein bS1 is the biggest and the most flexible and dynamic protein in the 30S small subunit. Despite being essential for mRNA recruitment and its primary role in the accommodation of the start codon within the decoding centre, there has not yet been a high-resolution description of its structure. Here, we present a 3D atomic model of OB1 and OB2, bS1's first two N-terminal domains, bound to an elongation-competent 70S ribosome. Our structure reveals that, as previously reported, bS1 is anchored both by a π-stacking to the 30S subunit and via a salt bridge with the Zn2+ pocket of bS1. These contacts are further stabilized by other interactions with additional residues on OB1. Our model also shows a new conformation of OB2, interacting with the Shine-Dalgarno portion of the mRNA. This study confirms that OB1 plays an anchoring role, but also highlights a novel function for OB2, which is directly involved in the modulation and support of mRNA binding and accommodation on the ribosome.

Figure 1.

Structure of the EC ribosome in complex with bS1. (A) Atomic model of the translating E. coli ribosome in complex with the first two N-terminal domains of bS1, OB1 and OB2. The 50S subunit is grey, 30S is gold, P-site tRNA is aquamarine, E-site tRNA is green, the mRNA SD sequence is purple and bS1 is red. (B) Cryo-EM density map of the 70S ribosome. bS1 is in red. (C) Focus on the bS1 binding site, with uS2 orange, 16S aSD khaki, bS21 aquamarine, SD purple and bS1 red. (D) Secondary structure and atomic model of OB1 and OB2. In the secondary structure, the domains present in our model are highlighted in red.

Figure 2.

bS1 interaction with uS2. (A) Interaction between loop 2 in bS1 (red) and the Zn²⁺-binding pocket of uS2 (orange). (B) Interactions between uS2 (orange) and the OB1 N-terminal helix of bS1 (red). (C) Close-up of the novel stacking between bS1 Phe79 and uS2 His18 residues.

Figure 3.

bS1 OB1 interactions with bS21. (A) The ribosomal protein bS21 shows a novel hinge activity between the 16S rRNA (khaki) and OB1 (red), the first N-terminal domain of bS1. (B) Close-up showing the interaction between bS21 (aquamarine) and the SD portion of mRNA (purple).

Figure 4.

bS1 OB2 interactions with the mRNA exit channel. Close-up showing the interactions between the bS1 OB2 pocket (red) and the SD portion of the mRNA (purple).