EMD-8175
Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA
EMD-8175
Single-particle3.6 Å
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Map released: 20/07/2016
Last modified: 16/10/2024
Sample Organism:
Escherichia coli
Sample: ErmBL-stalled E.coli 70S ribosome
Fitted models: 5jte (Avg. Q-score: 0.315)
Deposition Authors: Arenz S, Bock LV
Sample: ErmBL-stalled E.coli 70S ribosome
Fitted models: 5jte (Avg. Q-score: 0.315)
Deposition Authors: Arenz S, Bock LV
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A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.
Arenz S,
Bock LV
,
Graf M
,
Innis CA
,
Beckmann R,
Grubmuller H,
Vaiana AC
,
Wilson DN
(2016) Nat Commun , 7 , 12026 - 12026
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(2016) Nat Commun , 7 , 12026 - 12026
Abstract:
Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.
Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.