Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading

• Published in: Nature (London) Vol. 584; no. 7822; pp. 640 - 645
• Main Authors: Loveland, Anna B., Demo, Gabriel, Korostelev, Andrei A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27-08-2020; Nature Publishing Group
• Subjects: 101/28; 631/337/574/1789; 631/45/500; 631/535/1258/1259; Amino acids; Cryoelectron Microscopy; Dissociation; Editing; Electron microscopy; Elongation; Escherichia coli; GTP Phosphohydrolases - metabolism; Guanosine Diphosphate - chemistry; Guanosine Diphosphate - metabolism; Guanosine triphosphate; Guanosine Triphosphate - chemistry; Guanosine Triphosphate - metabolism; Humanities and Social Sciences; Hydrolysis; Locking; Locks; Microscopy; Models, Molecular; mRNA; multidisciplinary; Peptide Elongation Factor Tu - chemistry; Peptide Elongation Factor Tu - metabolism; Peptide Elongation Factor Tu - ultrastructure; Peptides; Proofreading; Ribosomes; Ribosomes - chemistry; Ribosomes - metabolism; Ribosomes - ultrastructure; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Transfer - chemistry; RNA, Transfer - genetics; RNA, Transfer - metabolism; RNA, Transfer - ultrastructure; Rotation; Science; Science (multidisciplinary); tRNA
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-020-2447-x

Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu
1
. To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge
2
–
4
. Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon–anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states
5
,
6
and in proofreading states, which together govern the efficient rejection of incorrect tRNA.
Time-resolved cryogenic electron microscopy structures of a ribosome during the delivery of aminoacyl-tRNA by EF-Tu•GTP capture 33 ribosomal states, enabling visualization of the initial selection, proofreading and peptidyl transfer stages.