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Structure paper

TitleThe ribosome termination complex remodels release factor RF3 and ejects GDP.
Journal, issue, pagesNat Struct Mol Biol, Year 2024
Publish dateJul 19, 2024
AuthorsLi Li / Mariia Yu Rybak / Jinzhong Lin / Matthieu G Gagnon /
PubMed AbstractTranslation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then ...Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then exchange GDP for GTP. The 70S ribosome termination complex (70S-TC) accelerates GDP exchange in RF3, suggesting that the 70S-TC can function as the guanine nucleotide exchange factor for RF3. Here, we use cryogenic-electron microscopy to elucidate the mechanism of GDP dissociation from RF3 catalyzed by the Escherichia coli 70S-TC. The non-rotated ribosome bound to RF1 remodels RF3 and induces a peptide flip in the phosphate-binding loop, efficiently ejecting GDP. Binding of GTP allows RF3 to dock at the GTPase center, promoting the dissociation of RF1 from the ribosome. The structures recapitulate the functional cycle of RF3 on the ribosome and uncover the mechanism by which the 70S-TC allosterically dismantles the phosphate-binding groove in RF3, a previously overlooked function of the ribosome.
External linksNat Struct Mol Biol / PubMed:39030416
MethodsEM (single particle)
Resolution2.9 - 3.6 Å
Structure data

29620

8fzd

EMDB-29620, PDB-8fzd:
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (Composite state I-B)
Method: EM (single particle) / Resolution: 3.1 Å

29621

8fze

EMDB-29621, PDB-8fze:
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State I-A)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-29622: Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-29623: RF3-ppGpp bound to an E. coli rotated ribosome, from focused classification and refinement (State I-C)
Method: EM (single particle) / Resolution: 3.6 Å

29624

8fzf

EMDB-29624, PDB-8fzf:
Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C)
Method: EM (single particle) / Resolution: 3.2 Å

29627

8fzg

EMDB-29627, PDB-8fzg:
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF3-GDPCP, RF1, P- and E-site tRNAPhe (Composite state II-A)
Method: EM (single particle) / Resolution: 3.1 Å

29628

8fzh

EMDB-29628, PDB-8fzh:
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State II-D)
Method: EM (single particle) / Resolution: 2.9 Å

29631

8fzi

EMDB-29631, PDB-8fzi:
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-B)
Method: EM (single particle) / Resolution: 3.1 Å

29634

8fzj

EMDB-29634, PDB-8fzj:
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-C)
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-G4P:
GUANOSINE-5',3'-TETRAPHOSPHATE

ChemComp-GCP:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM

Source
  • escherichia coli (E. coli)
  • escherichia phage t4 (virus)
  • escherichia coli k-12 (bacteria)
KeywordsRIBOSOME / release factor 1 / release factor 3 / termination complex / cryo-EM / tRNA / RIBOSOME/RNA / RIBOSOME-RNA complex

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