6yst

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Structure of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state

Structural highlights

6yst is a 10 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 3.2Å
Ligands:1MG, 2MA, 2MG, 3TD, 4OC, 4SU, 5MC, 5MU, 6MZ, G7M, MA6, MG, MIA, NA, OMC, OMG, OMU, PSU, UR3, ZN
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL32_ECOLI

Publication Abstract from PubMed

Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria.

Mechanism of ribosome rescue by alternative ribosome-rescue factor B.,Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV Nat Commun. 2020 Aug 14;11(1):4106. doi: 10.1038/s41467-020-17853-7. PMID:32796827[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
4 reviews cite this structure
Ribosome Rescue Pathways in Bacteria.
Müller et al. (2021)
3 more
14 other articles
No citations found

See Also

References

  1. ↑ Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV. Mechanism of ribosome rescue by alternative ribosome-rescue factor B. Nat Commun. 2020 Aug 14;11(1):4106. PMID:32796827 doi:10.1038/s41467-020-17853-7

Contents


PDB ID 6yst

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OCA

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