1T1M

Binding position of ribosome recycling factor (RRF) on the E. coli 70S ribosome

Summary for 1T1M

• Entry DOI: 10.2210/pdb1t1m/pdb
• Related: 1DD5 1EK8 1FJF 1KC9 1T1O
• EMDB information: 1077
• Descriptor: dodecamer fragment of double helix from 23S rRNA, 42-mer fragment of double helix from 16S rRNA, ribosome recycling factor (3 entities in total)
• Functional Keywords: rrf binding position on the ribosome, ribosome
• Biological source: Escherichia coli; More
• Cellular location: Cytoplasm (By similarity): P84154
• Total number of polymer chains: 3
• Total formula weight: 38981.49

Authors

Agrawal, R.K.,Sharma, M.R.,Kiel, M.C.,Hirokawa, G.,Booth, T.M.,Spahn, C.M.,Grassucci, R.A.,Kaji, A.,Frank, J. (deposition date: 2004-04-16, release date: 2004-06-15, Last modification date: 2024-02-14)

Primary citation

Agrawal, R.K.,Sharma, M.R.,Kiel, M.C.,Hirokawa, G.,Booth, T.M.,Spahn, C.M.,Grassucci, R.A.,Kaji, A.,Frank, J.
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications
Proc.Natl.Acad.Sci.USA, 101:8900-8905, 2004

PubMed Abstract: After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), disassembles this posttermination complex into mRNA, tRNA, and the ribosome. We have obtained a three-dimensional cryo-electron microscopic map of a complex of the Escherichia coli 70S ribosome and RRF. We find that RRF interacts mainly with the segments of the large ribosomal subunit's (50S) rRNA helices that are involved in the formation of two central intersubunit bridges, B2a and B3. The binding of RRF induces considerable conformational changes in some of the functional domains of the ribosome. As compared to its binding position derived previously by hydroxyl radical probing study, we find that RRF binds further inside the intersubunit space of the ribosome such that the tip of its domain I is shifted (by approximately 13 A) toward protein L5 within the central protuberance of the 50S subunit, and domain II is oriented more toward the small ribosomal subunit (30S). Overlapping binding sites of RRF, EF-G, and the P-site tRNA suggest that the binding of EF-G would trigger the removal of deacylated tRNA from the P site by moving RRF toward the ribosomal E site, and subsequent removal of mRNA may be induced by a shift in the position of 16S rRNA helix 44, which harbors part of the mRNA.

PubMed: 15178758
DOI: 10.1073/pnas.0401904101

Experimental method

ELECTRON MICROSCOPY (12 Å)