title: tmRNA.SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes.
abstract: Bacterial ribosomes stalled on faulty, often truncated, mRNAs lacking stop codons are rescued by trans-translation. It relies on an RNA molecule (tmRNA) capable of replacing the faulty mRNA with its own open reading frame (ORF). Translation of tmRNA ORF results in the tagging of faulty protein for degradation and its release from the ribosome. We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu). Three-dimensional reconstruction and heterogeneity analysis resulted in a 15A resolution structure of the tmRNA.SmpB complex accommodated in the A site of the ribosome, which shows that SmpB mimics the anticodon- and D-stem of native tRNAs missing in the tRNA-like domain of tmRNA. We conclude that the tmRNA.SmpB complex accommodates in the ribosomal A site very much like an aminoacyl-tRNA during protein elongation.
authors.affiliation: Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, Novum, S-141 57 Huddinge, Sweden. kimberley.cheng@ki.se
authors.forename: Kimberley
authors.initials: K
authors.lastname: Cheng
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Sjors H W
authors.initials: SH
authors.lastname: Scheres
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Pavlov
authors.forename: José María
authors.initials: JM
authors.lastname: Carazo
authors.forename: Hans
authors.initials: H
authors.lastname: Hebert
authors.forename: Måns
authors.initials: M
authors.lastname: Ehrenberg
authors.forename: Martin
authors.initials: M
authors.lastname: Lindahl
mesh_terms: D020285:Cryoelectron Microscopy; D004926:Escherichia coli / Q000378:metabolism / Q000648:ultrastructure; D010444:Peptide Elongation Factor Tu / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000378:metabolism* / Q000648:ultrastructure; D012346:RNA, Transfer, Amino Acyl / Q000378:metabolism* / Q000648:ultrastructure; D016601:RNA-Binding Proteins / Q000378:metabolism* / Q000648:ultrastructure; D012270:Ribosomes / Q000378:metabolism* / Q000648:ultrastructure
chemical_list: D012329:RNA, Bacterial; D012346:RNA, Transfer, Amino Acyl; D016601:RNA-Binding Proteins; C430328:small protein B; C096222:tmRNA; D010444:Peptide Elongation Factor Tu