Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel

• Published in: Structure (London) 2018-03, Vol.26 (3), p.437-445.e3
• Main Authors: Zhang, Yan, Hong, Samuel, Ruangprasert, Ajchareeya, Skiniotis, Georgios, Dunham, Christine M.
• Format: Article
• Language: English
• Subjects: Binding Sites; cryo-EM; Cryoelectron Microscopy; Escherichia coli - genetics; Models, Molecular; Molecular Conformation; Protein Biosynthesis; Protein Domains; protein synthesis; ribosome; Ribosomes - chemistry; RNA structure; RNA, Bacterial - chemistry; RNA, Messenger - chemistry; RNA, Messenger - metabolism; RNA, Transfer - chemistry; RNA, Transfer - metabolism; stem loop; translational control
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2018.01.013

Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3′ stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation. [Display omitted] •Cryo-EM structures of the 70S bound to an mRNA stem loop reveal interactions with uS3•E-site tRNA shows a unique conformation in the presence of the mRNA stem loop•E-site tRNA forms interactions with the 30S head domain•Structured mRNAs regulate the conformation of tRNAs to affect translation Zhang, Hong et al. solved cryo-EM structures of the 70S ribosome interacting with mRNA containing a stem loop at the mRNA entrance channel. The study provides insight into how the stem loop interacts with uS3 and into the conformation of the E-site tRNA, suggesting how structured mRNAs affect translation.