Eukaryotic Ribosome

Movie of the eukaryotic 40S and 60S ribosomal subunits in complex with initiation factors eIF1 and eIF6, respectively. The movie visualizes the increased complexity of the eukaryotic ribosome, compared to bacterial and archaeal ribosomes.
The ribosomal rRNA conserved across all kingdoms is depicted in grey and universally conserved proteins are depicted in light blue. Protein and rRNA segments shared between eukaryotes and archaea, but not bacteria are depicted in orange, and segments exclusive to eukaryotes are depicted in red.

Downloads:

80S movie 1080p, mov format (.zip 118 MB)
80S movie for mobile, m4v format (.zip 9 MB)

Structural and Functional Studies of Eukaryotic Ribosomes

Photograph: Katharina Bohm and Felix Voigts-Hoffmann

Ribosomes are molecular machines, which catalyze the translation of genetic information into proteins. They consist of two unequal subunits (small subunit and large subunit), both of which are large assemblies consisting of ribosomal RNA (rRNA) and ribosomal proteins. While the structure and function of bacterial ribosomes is well understood, thanks largely to experiments guided by atomic structures, little is known about the more complex structure and function of eukaryotic ribosomes. Ribosomes of eukaryotic cells are significantly larger than bacterial ribosomes. While bacterial ribosomes have a molecular mass of 2.6MDa, eukaryotic ribosomes consist of a small 40S and a large 60S subunit and are almost twice as large with a molecular mass of 4.3MDa. Eukaryotic ribosomes are also more complex as they contain 45 additional ribosomal proteins, some of them involved in signaling, and additional ribosomal RNA.
The initiation of protein synthesis in eukaryotes requires at least twelve factors, compared to only three factors required for initiation in bacteria. Furthermore, translation initiation is the target of regulation in a number of cellular processes including development, differentiation, stress response, and neuronal function and consequently many diseases, including cancer and metabolic disorders, are connected with improper functioning or regulation of the initiation of protein synthesis.

Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1

To gain insight into the functioning of the eukaryotic ribosome and the process of translation initiation in eukaryotes, we have determined the crystal structure of the small (40S) subunit of the eukaryotic ribosome in complex with initiation factor 1. The structure reveals the fold of the entire 18S ribosomal RNA and of all ribosomal proteins of the 40S subunit providing unique insights into the evolution of the ribosome. Furthermore, it provides information on proteins responsible for eukaryotic-specific ribosomal functions in signaling and regulation, such as rpS6e and RACK1; rpS6e is phosphorylated in yeast and humans and is a target of the mTOR (mammalian target of rapamycin) pathway. Finally, the interactions with eIF1 provide a basis for understanding its functions during translation initiation and the role of mutations that affect start codon recognition.

Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N. (2010)
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
Science 331(6018):730-6 Pubmed

Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6

The large ribosomal subunit (60S) catalyzes peptide bond formation and contains the nascent polypeptide exit tunnel. We have determined the crystal structure of the 60S ribosomal subunit from Tetrahymena thermophila at 3.5 Å resolution, in complex with eukaryotic initiation factor 6 (eIF6) and co-crystallized with the antibiotic cycloheximide, a eukaryotic-specific inhibitor of protein synthesis. The structure shows the complex functional architecture of the eukaryotic 60S subunit, which features an intricate network of interactions between eukaryotic-specific ribosomal protein features and RNA expansion segments. Furthermore, the structure reveals the roles of eukaryotic ribosomal protein elements in the stabilization of the active site and the extent of eukaryotic-specific differences in other functional regions of the subunit and elucidates the molecular basis of the interaction with eIF6. In combination with the structure of the small ribosomal subunit from T. thermophila, a structural framework has been established for functional characterization of the eukaryotic-specific aspects of translation, including regulation and disease.

Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N. (2011)
Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6.
Science 334(6058):941-948, Published Online November 3 2011 Pubmed

Visualizing the Eukaryotic Ribosome with PYMOL

Visualizing large structures can be difficult and time-consuming. In addition, different nomenclatures are currently used in the field. We are therefore providing a ready-made PYMOL session visualizing the eukaryotic ribosomal subunits:

Instructions:
1. DOWNLOAD PYMOL SESSION (.zip 15MB)
2. unzip
3. Double-click or open from File menu in Pymol
4. (Pymol can be downloaded from http://www.pymol.org/ )

Description:
PYMOL session visualizing the structure of the 40S (PDB 2XZM) and the 60S (PDB 4A17, 4A19) ribosomal subunits of T. thermophila in complex with initiation factors eIF1 and eIF6, respectively. The subunits are positioned according to the T. thermophilus ribosome (PDB 2WRO,2WRN).
Proteins names are based on the nomenclature adopted by RPG, which applies to the human homologs, as well as T. thermophila. The names of yeast and bacterial homologs are also indicated.

Proteins are colored according to conservation: Universially conserved parts are blue, parts shared with archaea are orange, and eukaryotic-specific alements are red. RNA expansion segments are shown in wheat, 5S rRNA in pale green and 5.8S rRNA in light pink. Initiation factors and Zinc atoms are shown in green, Magnesium atoms in violet.

PYMOL Scripts

The following PYMOL scripts will automatically download the files from PDB and setup names, colors etc. as described above. Instructions are included in the scripts.

60S Pymol Script (.txt 12kb)

40S Pymol Script (.txt 12kb)

Links to the Protein Data Bank

Large subunit

PDB file of the 60S, part I (link to www.rcsb.org)

PDB file of the 60S, part II (link to www.rcsb.org)

PDBs will be released on November 30, 2011

Small subunit

PDB file of the 40S (link to www.rcsb.org)

Research Articles

• Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N. (2011)
  Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6.
  Science 334(6058):941-948, Published Online November 3 2011 Pubmed
• Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N. (2010)
  Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science 331(6018):730-6 Pubmed

Reviews and Comments

• Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N.
  Atomic structures of the eukaryotic ribosome.
  Trends Biochem Sci. 2012 May;37(5):189-98. Epub 2012 Mar 20. Pubmed
• Ramakrishnan V. (2011)
  Molecular biology. The eukaryotic ribosome.
  Science 331(6018):681-2 Pubmed