6GXM

Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State II)

This is a non-PDB format compatible entry.

Summary for 6GXM

• Entry DOI: 10.2210/pdb6gxm/pdb
• Related: 6GWT
• EMDB information: 0080
• Descriptor: 23S ribosomal RNA, 50S ribosomal protein L13, 50S ribosomal protein L14, ... (59 entities in total)
• Functional Keywords: single particle cryo-em, gtpase, ribosome, release factor rf1, rf2, rf3, subunit rotation, translation termination
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2249820.23

Authors

Graf, M.,Huter, P.,Maracci, C.,Peterek, M.,Rodnina, M.V.,Wilson, D.N. (deposition date: 2018-06-27, release date: 2018-08-22, Last modification date: 2024-05-15)

Primary citation

Graf, M.,Huter, P.,Maracci, C.,Peterek, M.,Rodnina, M.V.,Wilson, D.N.
Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1.
Nat Commun, 9:3053-3053, 2018

PubMed Abstract: During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 mediates dissociation of the decoding RFs has been lacking. Here we have used the Apidaecin 137 peptide to trap RF1 together with RF3 on the ribosome and visualize an ensemble of termination intermediates using cryo-electron microscopy. Binding of RF3 to the ribosome induces small subunit (SSU) rotation and swivelling of the head, yielding intermediate states with shifted P-site tRNAs and RF1 conformations. RF3 does not directly eject RF1 from the ribosome, but rather induces full rotation of the SSU that indirectly dislodges RF1 from its binding site. SSU rotation is coupled to the accommodation of the GTPase domain of RF3 on the large subunit (LSU), thereby promoting GTP hydrolysis and dissociation of RF3 from the ribosome.

PubMed: 30076302
DOI: 10.1038/s41467-018-05465-1

Experimental method

ELECTRON MICROSCOPY (3.8 Å)