PDBsum entry: 1t1o

Ribosome

PDB id: 1t1o

Contents

DNA/RNA

PDB id:

1t1o

Name:

Ribosome

Title:

Components of the control 70s ribosome to provide reference for the rrf binding site

Structure:

Dodecamer fragment of double helix from 23s rrna. Chain: a. Fragment: apical loop of helix 43. Other_details: fitted into the cryo-em map of the 70s ribosome. 19-mer fragment of the 23s rrna. Chain: b. Fragment: helix 69. Other_details: fitted into the cryo-em map of the 70s

Source:

Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600

Authors:

R.K.Agrawal,M.R.Sharma,M.C.Kiel,G.Hirokawa,T.M.Booth, C.M.Spahn,R.A.Grassucci,A.Kaji,J.Frank

Key ref:

R.K.Agrawal et al. (2004). Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications. Proc Natl Acad Sci U S A, 101, 8900-8905. PubMed id: 15178758 DOI: 10.1073/pnas.0401904101

Date:

16-Apr-04 Release date: 15-Jun-04

DOI no: 10.1073/pnas.0401904101

Proc Natl Acad Sci U S A 101:8900-8905 (2004)

PubMed id: 15178758

Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.

R.K.Agrawal, M.R.Sharma, M.C.Kiel, G.Hirokawa, T.M.Booth, C.M.Spahn, R.A.Grassucci, A.Kaji, J.Frank.

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.

Selected figure(s)

Figure 4.
Fig. 4. Sites of interaction between RRF and ribosome. X-ray crystallographic structures of both ribosomal subunits (28, 41) were fitted into the cryo-EM map of the RRF-ribosome complex. (a) The 23S rRNA helices (light blue) of the 50S ribosome that directly interact with (or lie within 3 Å of) RRF are shown. Domains I (magenta) and II (purple) of the RRF atomic structure are assigned the same colors as in Fig. 3 a and b, with conserved (red) and semiconserved (orange) residues highlighted. The RRF residues making direct contact with rRNA are shown with side chains (red). Ribosomal RNA residues making direct contacts with RRF are highlighted as beads in corresponding color. (b) Regions of ribosome that lie within 5-10 Å distant [except for helix 43 (H43) of the 23S rRNA, see below], and the position of a segment of mRNA (green, ref. 40). Relevant segments of 16S rRNA helices 18 and 44 (brown) and protein S12 (yellow) are shown. Note that residue A1067 of H43 is well within the reach ( 17 Å) of the HR probe site, S56, of RRF (ref. 14; also see supporting information). The orientation of the 70S ribosome is shown as a thumbnail on the lower right. Only some of the relevant amino acid residues of RRF and nucleotide residues of rRNA are identified. All other landmarks are the same as introduced in Figs. 1,2,3.

Figure 5.
Fig. 5. Stereo representation of relative binding position of RRF with respect to tRNAs and EF-G on the ribosome. (a) With respect to the A-(orange) and P-(green) site tRNAs. (b) With respect to EF-G (gray) in the GDP state. CCA, CCA-end side of the tRNAs; AC, anticodon side of the tRNAs; domains I and II of RRF and domains I-V of EF-G are denoted in respective matching colors. Orientations of the 70S ribosome in the two panels are represented by thumbnails at the lower right. In a, the 30S subunit is situated below the 50S subunit such that head of the 30S subunit and the CP of the 50S subunit face the viewer, whereas in b, the solvent side of the 30S subunit faces the viewer.

Figures were selected by the author.