Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.

Publication Type:

Journal Article

Source:

Nat Chem (2022)

Abstract:

<p>During protein synthesis, the growing polypeptide threads through the ribosomal exit tunnel and modulates ribosomal activity by itself or by sensing various small molecules, such as metabolites or antibiotics, appearing in the tunnel. While arrested ribosome-nascent chain complexes (RNCCs) have been extensively studied structurally, the lack of a simple procedure for the large-scale preparation of peptidyl-tRNAs, intermediates in polypeptide synthesis that carry the growing chain, means that little attention has been given to RNCCs representing functionally active states of the ribosome. Here we report the facile synthesis of stably linked peptidyl-tRNAs through a chemoenzymatic approach based on native chemical ligation and use them to determine several structures of RNCCs in the functional pre-attack state of the peptidyl transferase centre. These structures reveal that C-terminal parts of the growing peptides adopt the same uniform β-strand conformation stabilized by an intricate network of hydrogen bonds with the universally conserved 23S rRNA nucleotides, and explain how the ribosome synthesizes growing peptides containing various sequences with comparable efficiencies.</p>

PDB: 
8CVJ for the T. thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAPhe, peptidyl P-site fMSEAC-NH-tRNAiMet and deacylated E-site tRNAPhe; 8CVK for the T. thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAPhe, peptidyl P-site fMRC-NH-tRNAiMet and deacylated E-site tRNAPhe; 8CVL for the T. thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAPhe, peptidyl P-site fMTHSMRC-NH-tRNAiMet and deacylated E-site tRNAPhe
Detector: 
EIGER
EIGER2
Beamline: 
24-ID-C
24-ID-E
Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution