Molecule of the Month: Ribosome Diversity

By comparing the structures of ribosomes from different organisms, we can explore the evolution of life.

Small ribosomal subunits from diverse organisms. Ribosomal RNA is in light blue and proteins are in darker blue. The illustrations show the side that interacts with the large ribosomal subunit.
Small ribosomal subunits from diverse organisms. Ribosomal RNA is in light blue and proteins are in darker blue. The illustrations show the side that interacts with the large ribosomal subunit.
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The first atomic structures of ribosomes, determined in 2000, revealed the details of biological protein synthesis. The small ribosomal subunit manages messenger RNA, pairing it with the appropriate transfer RNA molecules and matching codons with anticodons. The large ribosomal subunit connects the amino acids carried by transfer RNA into a new protein chain. In the 25 years since then, thousands of additional structures of ribosomes have been determined, elucidating many of the steps of protein synthesis. These structures also allow us to compare structures of ribosomes from different organisms.

Evolving Complexity

Since all living organisms need to have functional ribosomes, ribosome structures are powerful tools for studying molecular evolution, allowing us to compare and contrast them across all the kingdoms of life. The image included here shows the small ribosomal subunit from several different organisms. Bacteria have relatively simple structures. The bacterial small subunit (PDB ID 1fjg) includes one RNA strand with 1522 nucleotides and 20 proteins. Similarly, the archaeal small subunit (PDB ID 6tmf) has a small RNA strand of 1485 nucleotides and 29 proteins. However, the human and plant small subunits (PDB ID 5a2q and 8auv) have evolved a more complex structure, with RNA strands of over 1800 nucleotides and more than 30 proteins.

Working Together

Mitochondria and chloroplasts make their own ribosomes, which are different from the ribosomes in the cytoplasm of plants, animals, and fungi. Both organelles are believed to have evolved from bacteria that became symbiotic residents in the cytoplasms of the progenitors of modern eukaryotic cells. The structure of chloroplast ribosomes is one piece of evidence supporting this endosymbiotic hypothesis. The chloroplast small ribosomal subunit (PDB ID 5mmj) is similar to bacteria, with a short RNA chain of 1491 nucleotides. The structure of the mitochondrial small subunit (PDB ID 6rw4) shows that mitochondrial ribosomes have diverged significantly from their putative bacterial antecedent, with an even shorter RNA chain of only 955 nucleotides and more proteins than a typical bacterial ribosome.

Translation initiation complexes, with small ribosomal subunits in blue, initiator transfer RNA in yellow, and initiation factors in red.
Translation initiation complexes, with small ribosomal subunits in blue, initiator transfer RNA in yellow, and initiation factors in red.
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Initiation Complexity

The increased complexity of eukaryotes is also seen in the many proteins that assist ribosomes in the process of protein synthesis. For example, the two structures shown here (PDB ID 5lmv and 8oz0) show the proteins that orchestrate the initiation of protein synthesis. Together, they help capture a messenger RNA and align an initiator transfer RNA at the start codon of translation. Bacterial cells only require three initiation factor proteins to accomplish this task, but eukaryotes require about 20.

Exploring the Structure

Ribosomal RNA

This interactive view compares ribosomal RNA from bacterial and human small subunits (PDB ID 1fjg and 5a2q). Notice that there is a similar core for both of them, which performs the basic tasks of bringing together the messenger and transfer RNAs. The human RNA includes many extensions around this core, producing a larger and more complex ribosomal subunit. To explore these structures in more detail, click on the JSmol tab.

Topics for Further Discussion

  1. Similar trends are seen for the large subunits of ribosomes. For example, you can compare the full ribosome structure of Escherichia coli bacteria (PDB ID 4v4a) and humans (PDB ID 4v6x).
  2. The RNA alignment shown in the JSmol was done using the free online server RNA-align.

References

  1. 8oz0: Brito Querido, J., Sokabe, M., Diaz-Lopez, I., Gordiyenko, Y., Fraser, C.S., Ramakrishnan, V. (2024) The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat Struct Mol Biol 31: 455-464
  2. 8auv: Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023) Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat Plants 9: 987-1000
  3. 6rw4: Khawaja, A., Itoh, Y., Remes, C., Spahr, H., Yukhnovets, O., Hofig, H., Amunts, A., Rorbach, J. (2020) Distinct pre-initiation steps in human mitochondrial translation. Nat Commun 11: 2932-2932
  4. 6tmf: Nurenberg-Goloub, E., Kratzat, H., Heinemann, H., Heuer, A., Kotter, P., Berninghausen, O., Becker, T., Tampe, R., Beckmann, R. (2020) Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex. EMBO J 39: e103788-e103788
  5. 5mmj: Bieri, P., Leibundgut, M., Saurer, M., Boehringer, D., Ban, N. (2017) The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. EMBO J 36: 475-486
  6. 5lmv:Hussain, T., Llacer, J.L., Wimberly, B.T., Kieft, J.S., Ramakrishnan, V.(2016) Large-scale movements of IF3 and tRNA during bacterial translation initiation. Cell 167: 133-144.e13
  7. 5a2q: Quade, N., Boehringer, D., Leibundgut, M., Van Den Heuvel, J., Ban, N. (2015) Cryo-EM structure of hepatitis C virus Ires bound to the human ribosome at 3.9 Angstrom Resolution. Nat Commun 6: 7646
  8. 1fjg: Carter, A.P., Clemons Jr., W.M., Brodersen, D.E., Morgan-Warren, R.J., Wimberly, B.T., Ramakrishnan, V. (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340-348

July 2024, David Goodsell

http://doi.org/10.2210/rcsb_pdb/mom_2024_7
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More
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