Eukaryotic large ribosomal subunit (60S)

Ribosomal particles are denoted according to their sedimentation coefficients in Svedberg units. The 60S subunit is the large subunit of eukaryotic 80S ribosomes. It is structurally and functionally related to the 50S subunit of 70S prokaryotic ribosomes.[1][2][3][4][5][6] However, the 60S subunit is much larger than the prokaryotic 50S subunit and contains many additional protein segments, as well as ribosomal RNA expansion segments.

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.[2][4] 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.

Crystal Structure of the Eukaryotic 60S Ribosomal Subunit from T. thermophila
60S subunit viewed from the subunit interface side, PDB identifiers 4A17, 4A19 
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.[2]

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.[7] Further information can be found in the ribosomal protein gene database (RPG).[7]

60S ribosomal proteins
Structure (Eukaryotic)[8] H. sapiens[7][9] Amino acids[10] Conservation[11] S. cerevisiae[12] Bacterial homolog (E. coli) Archaeal homolog
 RPLP0 318EABP0L10L10
 RPL3 404 EABL3L3L3
 RPL4 428 EABL4L4L4
 RPL5 298 EABL5L18L18p
 RPL6 289 EL6n/an/a
 RPL7 254 EABL7L30L30
 RPL7A 267EAL8n/aL7Ae
 RPL8 258 EABL2L2L2
 RPL9 193 EABL9L6L6
 RPL10 215EABL10L16L10e
 RPL11 EABL11L5L5
 RPL13 EAL13n/aL13e
RPL13A 204EABL16L13L13
 RPL14 221EAL14n/aL14e
 RPL15 205EAL15n/aL15e
 RPL17 185EABL17L22L22
 RPL18 189EAL18n/aL18e
RPL18A 177EAL20n/aLx
 RPL19 197EAL19n/aL19
 RPL21 161EAL21n/aL21e
 RPL22 129EL22n/an/a
 RPL23 141EABL23L14 L14p
RPL23A 157EABL25L23 L23
 RPL24 158EAL24n/aL24e
 RPL26 146EABL26L24L24
 RPL27 137EL27n/an/a
RPL27A 149EABL28L15 L15
 RPL28 En/a[2][3][13]n/an/a
 RPL29 EL29n/an/a
 RPL30 116EAL30n/aL30e
 RPL31 126EAL31n/aL31e
 RPL32 136EAL32n/aL32e
 RPL34 118EAL34n/aL34e
 RPL35 124EABL35L29 L29
RPL35A EAL33n/aL35Ae
 RPL36 106EL36n/an/a
RPL36A 107EAL42n/aL44e
 RPL37 98EAL37n/aL37e
RPL37A EAL43n/aL37Ae
 RPL38 EAL38n/aL38e
 RPL39 52EAL39n/aL37Ae
 RPL40 129EAL40n/aL40e

References

  1. ↑ 60S Ribosome Subunits at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. 1 2 3 4 Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science. 2011 Nov 18;334(6058):941-8. doi:10.1126/science.1211204. Epub 2011 Nov 3. PMID 22052974.
  3. 1 2 Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. The structure of the eukaryotic ribosome at 3.0 Å resolution. Science. 2011 Dec 16;334(6062):1524-9. doi:10.1126/science.1212642. Epub 2011 Nov 17. PMID 22096102.
  4. 1 2 Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905-20. PMID 10937989.
  5. ↑ Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF. X-ray crystal structures of 70S ribosome functional complexes. Science. 1999 Sep 24;285(5436):2095-104. PMID 10497122.
  6. ↑ Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF. Crystal structure of the ribosome at 5.5 A resolution. Science. 2001 May 4;292(5518):883-96. Epub 2001 Mar 29. PMID 11283358.
  7. 1 2 3 Nakao A, Yoshihama M, Kenmochi N. RPG: the Ribosomal Protein Gene database. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D168-70. PMID 14681386; PMC 308739.
  8. ↑ Structure of the T. thermophila,' proteins from the structures of the large subunit PDBS 417, 4A19
  9. ↑ Nomenclature according to the ribosomal protein gene database, applies to H. sapiens and T. thermophila
  10. ↑ Yoshihama, Maki; Uechi, Tamayo; Asakawa, Shuichi; Kawasaki, Kauhiko (2002). "The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes". Genome Research. 12: 379–390. PMC 155282 Freely accessible. doi:10.1101/gr.214202.
  11. ↑ EAB means conserved in eukaryotes, archaea and bacteria, EA means conserved in eukaryotes and archaea and E means eukaryote-specific protein
  12. ↑ 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.
  13. ↑ RPL28 has no detectable homolog in yeast
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