5ju8 | pdb_00005ju8

Cryo-EM structure of an ErmBL-stalled ribosome in complex with P-, and E-tRNA

Loading... Status: waiting for Mol* initialization Structural highlights 5ju8 is a 10 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 3.6Å Ligands: 2MA, 4SU, 5MU, 6MZ, 7MG, CM0, ERY, H2U, PSU, QUO Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RS2_ECOLI Publication Abstract from PubMed 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-A-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. 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 Nat Commun. 2016 Jul 6;7:12026. doi: 10.1038/ncomms12026. PMID:27380950 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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