An Introduction to Ribosome Structure
David Marcey
© 2021

I. Introduction
II. Subunit Structure
III. tRNA Binding and Codon Recognition
IV. References
Directions

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I. Introduction

Ribosomes are the large, ribonucleoprotein factories in which proteins are synthesized. In this process, messenger RNA (mRNA) codons are read by the anticodons of adaptor, transfer RNAs (tRNAs) that carry codon-specific amino acids. These amino acids are added to a growing protein chain by peptide bond formation in the heart of the ribosome.

The massive, macromolecular assemblage at left is the crystal structure of the 70S ribosome from Thermus thermophilus, an archaebacterium. The structure contains 42 proteins and 3 ribosomal RNAs (rRNA).

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II. Subunit Structure

The 70S ribosome comprises two subunits: a large 50S subunit, and a small 30S subunit. The 50S subunit contains a 23S and a 5S rRNA plus over 30 proteins, 22 of which are resolved in the crystal structure. The 30S subunit contains a 16S rRNA plus 20 proteins. The RNAs of each subunit serve as the core structural and functional components of the ribosome. The ribosomal proteins are involved in subunit bridges and tRNA contact, and support the key roles of the RNAs in each subunit. The positions and conformations of the rRNA components of each subunit can be visualized as follows:

  • The 16S rRNA of the small, 30S subunit folds into four domains: 5', central, 3' major, and 3' minor. The structural autonomy of these domains implies that they move relative to one another during protein synthesis. Viewed from the subunit interface, the 16S rRNA forms most of the interface surface, with proteins located mainly at the periphery.
  • The 23S rRNA of the large, 50S subunit folds into six secondary structural domains containing over 130 RNA helices: I, II, III, IV, V, VI. These six domains, unlike those of the 16S rRNA of the small subunit, are thoroughly intertwined. The 5S rRNA forms a seventh domain of rRNA tertiary structure in the large subunit. Like the RNA of the small subunit, the rRNAs of the large subunit form most of the subunit interface surface, with proteins located mainly at the periphery.

 

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III. tRNA Binding and Codon Recognition

3 tRNAs associate with the ribosome in the cavity between the 50S and 30S subunits. Each tRNA is bound in a distinctive site made from structural elements contributed by both ribosomal subunits.

The A-site tRNA, P-site tRNA, and E-site tRNA exhibit slight conformational differences. However, all adopt the classical "L shape" tertiary structure. Their 3' ends are bound by the 50S subunit and attach to amino acids and peptides through an acyl bond. Their anticodon stem-loops point into binding pockets of the 30S subunit . These features can be seen by briefly focusing on the P-site tRNA.

Note the tight juxtaposition of the 3' ends of the A-site and P-site tRNAs in the peptidyl transferase site of the 50S subunit (not shown). The A-site tRNA bears an incoming amino acid (not shown), and the P-site tRNA carries the growing peptide chain (not shown). Peptide bond formation attaches the peptide to the A-site tRNA's amino acid. The P-site tRNA then moves to the E-site (E stands for "exit"), replacing the former, uncharged E-site tRNA. The A-site tRNA, now bearing the growing peptide, is shifted into the P position. A new tRNA bearing the next amino acid is then brought into the A-site.

Turning now to codon recognition, it can be seen that the 30S subunit binds the anticodon stem loops of the tRNAs as well as the mRNA being translated (two, triplet codons are shown).

The A-site and P-site tRNAs (phe-tRNAs in the structure shown at left) bear the anticodon residues (AAG) that hydrogen bond with the two UUU codons of the mRNA:

codon-anticodon pairing

The G-U bonding in third position of each codon is an example of "wobble" base pairing. Wobble pairing allows some codons that differ in the third, 3' base to be recognized by the same tRNA anticodon. This, together with examples of isoaccepting tRNAs that carry the same amino acid but whose anticodons differ in the wobble base, allows for the high degree of degeneracy found in the genetic code.

The conformation of the mRNA and the A- and P-site tRNA anticodons helps to ensure that there is no confusion as to which codon should be bound to which tRNA. The conformation is partially achieved by a significant kinking of the mRNA backbone. This results in a significant distancing of the A- and P-site anticodons. The distance between the 5'G of the P-site anticodon and the 3'A of the A-site anticodon is ~14 Angstroms (1.4 nm), much larger than the separation needed if the mRNA were not kinked.

 

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IV. References

Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., Noller, H. F.: Crystal Structure of the Ribosome at 5.5 A Resolution. Science 292:883-896 (2001).

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