Ribosome Structure and Shape

Abstract

The ribosome is a macromolecular machine, composed of RNAs and proteins, that synthesizes proteins by stringing together amino acids according to genetic instructions.

Keywords: protein synthesis; transfer RNA; messenger RNA; amino acids; elongation factors; cryoelectron microscopy; three‐dimensional reconstruction

Figure 3.

Cryoelectron microscopy maps of prokaryotic (Escherichia coli, left) and eukaryotic (yeast, right) ribosome, with small subunit coloured in yellow, large subunit in blue. The maps are positioned in such a way that the large subunits are in corresponding orientations. The leader lines point to the intersubunit space. E. coli ribosome map from Malhotra A, Penczek P, Agrawal RK et al. (1998) Escherichia coli 70S ribosome at 15Åresolution by cryo‐electron microscopy: localization of fMet‐tRNAfMet and fitting of L1 protein. Journal of Molecular Biology280: 103–116. Copyright © 1998 Academic Press Ltd.; yeast ribosome map from A Verschoor, D Bubeck, R Grassucci, JPG Ballesta and J Frank, unpublished.

Figure 1.

Topography of the intersubunit space of the Escherichia coli ribosome. The ribosome map was computationally separated into the two subunits by severing several connecting bridges. Landmarks: small subunit: h, head; pl, platform; cl, cleft. Large subunit: L1, L1 protein; St, L7/L12 stalk; IC, interface canyon; CP, central protuberance.

Figure 2.

Cryoelectron microscopy map of the Escherichia coli ribosome (yellow, small subunit; blue, large subunit) depicted in the pretranslocational state. The path of the mRNA, the positions of tRNA in A (pink) and P (green) sites, and the exit path of the polypeptide chain are indicated as inferred by other cryo‐EM experiments. This positioning of A‐ and P‐site tRNAs, with their anticodons bound to adjacent codons of the mRNA, ensures the placement of their amino acids in the correct order as they are strung together to form the polypeptide chain. From Frank J (1998) How the ribosome works. American Scientist86: 428–439.

Figure 4.

Three‐dimensional binding positions of tRNA (a), elongation factor G (b) and Sec61 protein channel (c) as visualized using cryoelectron microscopy. (a) 70S ribosome of Escherichia coli with initiation‐tRNA bound at the P site (green). Adapted from Malhotra A, Penczek P, Agrawal RK et al. (1998) Escherichia coli 70S ribosome at 15Åresolution by cryo‐electron microscopy: localization of fMet‐tRNAfMet and fitting of L1 protein. Journal of Molecular Biology280: 103–116. Copyright © 1998 Academic Press. (b) 70S ribosome of E. coli bound with EF‐G GDP (purple). Adapted from Agrawal RK, Penczek P, Grassucci RA et al. (1998) Visualization of elongation factor G on Escherichia coli 70S ribosome: the mechanism of translocation. Proceedings of the National Academy of Sciences of the USA95: 6134–6138. Copyright © 1998 National Academy of Sciences, USA. (c) 80S ribosome of yeast with Sec61 channel complex (red) attached near the polypeptide tunnel exit. Reprinted with permission from Beckmann R, Bubeck D, Grassucci R et al. (1997) Alignment of conduits for the nascent polypeptide chain in the ribosome‐Sec61 complex. Science278: 2123–2126. Copyright © 1997 American Association for the Advancement of Science. Note: The ribosomes are shown in different orientations to best reveal the binding positions of ligands.

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Further Reading

Bielka H (ed.) (1982) The Eukaryotic Ribosome. Berlin: Springer Verlag.

Brimacombe R (1995) The structure of ribosomal RNA: a three‐dimensional jigsaw puzzle. European Journal of Biochemistry 230: 365–383.

Dube P, Wieske M, Stark H et al. (1998) The 80S rat liver ribosome at 25 Å resolution by electron cryomicroscopy and angular reconstitution. Structure 6: 389–399.

Frank J (1998) How the ribosome works. American Scientist 86: 428–439.

Green R and Noller HF (1997) Ribosomes and translation. Annual Review of Biochemistry 66: 679–716.

Hill WE, Moore P, Dahlberg A, Schlessinger R, Garrett R and Warner J (1990) The Ribosome: Structure, Function, and Evolution. Washington DC: American Society for Microbiology.

Matheson AT, Davies JE, Dennis PP and Hill WE (eds) (1995) Frontiers in Translation. Canada: National Research Council.

Verschoor A, Warner J, Srivastava S, Grassucci RA and Frank J (1998) Three‐dimensional structure of the yeast ribosome. Nucleic Acids Research 26: 655–661.

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Frank, Joachim, Agrawal, Rajendra K, and Verschoor, Adriana(Dec 2001) Ribosome Structure and Shape. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000534]