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Structure paper

TitleMechanism of ribosome rescue by alternative ribosome-rescue factor B.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 4106, Year 2020
Publish dateAug 14, 2020
AuthorsKai-Hsin Chan / Valentyn Petrychenko / Claudia Mueller / Cristina Maracci / Wolf Holtkamp / Daniel N Wilson / Niels Fischer / Marina V Rodnina /
PubMed AbstractAlternative 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 ...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.
External linksNat Commun / PubMed:32796827 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.7 Å
Structure data

10905

6ysr

EMDB-10905, PDB-6ysr:
Structure of the P+9 stalled ribosome complex
Method: EM (single particle) / Resolution: 3.1 Å

10906

6yss

EMDB-10906, PDB-6yss:
Structure of the P+9 ArfB-ribosome complex in the post-hydrolysis state
Method: EM (single particle) / Resolution: 2.6 Å

10907

6yst

EMDB-10907, PDB-6yst:
Structure of the P+9 ArfB-ribosome complex with P/E hybrid tRNA in the post-hydrolysis state
Method: EM (single particle) / Resolution: 3.2 Å

10908

6ysu

EMDB-10908, PDB-6ysu:
Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis state
Method: EM (single particle) / Resolution: 3.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • escherichia coli (E. coli)
  • apis mellifera (honey bee)
KeywordsRIBOSOME / translation / rescue / release

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