8EMM

Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates

This is a non-PDB format compatible entry.

Summary for 8EMM

• Entry DOI: 10.2210/pdb8emm/pdb
• EMDB information: 28254 28255 28256 28257
• Descriptor: 23S rRNA, 50S ribosomal protein L14, 50S ribosomal protein L15, ... (62 entities in total)
• Functional Keywords: ribosome, trna, e. coli
• Biological source: Escherichia coli; More
• Total number of polymer chains: 55
• Total formula weight: 2210520.53

Authors

Watson, Z.L.,Cate, J.H.D. (deposition date: 2022-09-28, release date: 2023-05-31, Last modification date: 2025-02-12)

Primary citation

Watson, Z.L.,Knudson, I.J.,Ward, F.R.,Miller, S.J.,Cate, J.H.D.,Schepartz, A.,Abramyan, A.M.
Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates.
Nat.Chem., 15:913-921, 2023

PubMed Abstract: As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi-Dunitz angle of 76-115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

PubMed: 37308707
DOI: 10.1038/s41557-023-01226-w

Experimental method

ELECTRON MICROSCOPY (2.1 Å)