Eukaryotic large ribosomal subunit (60S)

Overall structure

Characteristic features of the large subunit, shown below in the "Crown View", include the central protuberance (CP) and the two stalks, which are named according to their bacterial protein components (L1 stalk on the left as seen from the subunit interface and L7/L12 on the right). There are three binding sites for tRNA, the A-site, P-site and E-site (see article on protein translation for details). The core of the 60S subunit is formed by the 28S ribosomal RNA (abbreviated 28S rRNA), which is homologous to the prokaryotic 23S rRNA, which also contributes the active site (peptidyl transferase center, PTC) of the ribosome. The rRNA core is decorated with dozens of proteins. In the figure "Crystal Structure of the Eukaryotic 60S Ribosomal Subunit from T. thermophila", the ribosomal RNA core is represented as a grey tube and expansion segments are shown in red. Proteins which have homologs in eukaryotes, archaea and bacteria are shown as blue ribbons. Proteins shared only between eukaryotes and archaea are shown as orange ribbons and proteins specific to eukaryotes are shown as red ribbons.

|File:60S_interface_4A17_4A19.png|60S subunit viewed from the subunit interface side, PDB identifiers 4A17, 4A19 |File:60S_solvent_4A17_4A19.png|60S subunit viewed from the solvent-exposed side, PDB identifiers 4A17, 4A19

60S ribosomal proteins

The table "60S ribosomal proteins" shows the individual protein folds of the 60S subunit colored by conservation as above. The eukaryote-specific extensions, ranging from a few residues or loops to very long alpha helices and additional domains, are highlighted in red.

Historically, different nomenclatures have been used for ribosomal proteins. For instance, proteins have been numbered according to their migration properties in gel electrophoresis experiments. Therefore, different names may refer to homologous proteins from different organisms, while identical names do not necessarily denote homologous proteins. The table "60S ribosomal proteins" cross-references the human ribosomal protein names with yeast, bacterial, and archaeal homologs. Further information can be found in the ribosomal protein gene database (RPG).

References

References

1. {{MeshName. 60S+Ribosome+Subunits
2. (2011). "Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6". Science.
3. (Dec 2011). "The structure of the eukaryotic ribosome at 3.0 Å resolution". Science.
4. (Aug 2000). "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution". Science.
5. (Sep 1999). "X-ray crystal structures of 70S ribosome functional complexes". Science.
6. (May 2001). "Crystal structure of the ribosome at 5.5 A resolution". Science.
7. Structure of the 'T. thermophila,' proteins from the structures of the large subunit PDBS 417, 4A19
8. (2004). "RPG: the Ribosomal Protein Gene database". Nucleic Acids Res..
9. Nomenclature according to the ribosomal protein gene database, applies to ''H. sapiens'' and ''T. thermophila''
10. (2014). "A new system for naming ribosomal proteins". Elsevier BV.
11. (2002). "The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes". Genome Research.
12. EAB means conserved in eukaryotes, archaea and bacteria, EA means conserved in eukaryotes and archaea and E means eukaryote-specific protein
13. Traditionally, ribosomal proteins were named according to their apparent molecular weight in gel electrophoresis, leading to different names for homologous proteins from different organisms. The RPG offers a unified nomenclature for ribosomal protein genes based on homology.
14. RPL28 has no detectable homolog in yeast