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 subunit interface side, PDB identifiers 4A17, 4A19
  • 60S subunit viewed from the solvent-exposed 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] Universal name [10] Amino acids[11] Conservation[12] S. cerevisiae[13] Bacterial homolog (E. coli) Archaeal homolog
RPLP0uL10318EABP0L10L10
RPL3uL3404EABL3L3L3
RPL4uL4428EABL4L4L4
RPL5uL18298EABL5L18L18p
RPL6eL6289EL6n/an/a
RPL7uL30254EABL7L30L30
RPL7AeL8267EAL8n/aL7Ae
RPL8uL2258EABL2L2L2
RPL9uL6193EABL9L6L6
RPL10uL16215EABL10L16L10e
RPL11uL5EABL11L5L5
RPL13eL13EAL13n/aL13e
RPL13AuL13204EABL16L13L13
RPL14eL14221EAL14n/aL14e
RPL15eL15205EAL15n/aL15e
RPL17uL22185EABL17L22L22
RPL18eL18189EAL18n/aL18e
RPL18AeL20177EAL20n/aLx
RPL19eL19197EAL19n/aL19
RPL21eL21161EAL21n/aL21e
RPL22, RPL22L1eL22129EL22n/an/a
RPL23uL14141EABL23L14L14p
RPL23AuL23157EABL25L23L23
RPL24eL24158EAL24n/aL24e
RPL26uL24146EABL26L24L24
RPL27eL27137EL27n/an/a
RPL27AuL15149EABL28L15L15
RPL28eL28En/a[2][3][14]n/an/a
RPL29eL29EL29n/an/a
RPL30eL30116EAL30n/aL30e
RPL31eL31126EAL31n/aL31e
RPL32eL32136EAL32n/aL32e
RPL34eL34118EAL34n/aL34e
RPL35uL29124EABL35L29L29
RPL35AeL33EAL33n/aL35Ae
RPL36eL36106EL36n/an/a
RPL36AeL42107EAL42n/aL44e
RPL37eL3798EAL37n/aL37e
RPL37AeL43EAL43n/aL37Ae
RPL38eL38EAL38n/aL38e
RPL39eL3952EAL39n/aL37Ae
RPL40eL40129EAL40n/aL40e

See also

References
  1. 60S+Ribosome+Subunits at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
  2. 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. Bibcode:2011Sci...334..941K. doi:10.1126/science.1211204. PMID 22052974. S2CID 206536444.
  3. Ben-Shem, A; Garreau; de Loubresse, N; Melnikov, S; Jenner, L; Yusupova, G; Yusupov, M (Dec 2011). "The structure of the eukaryotic ribosome at 3.0 Å resolution". Science. 334 (6062): 1524–1529. Bibcode:2011Sci...334.1524B. doi:10.1126/science.1212642. PMID 22096102. S2CID 9099683.
  4. Ban, N; Nissen, P; Hansen, J; Moore, PB; Steitz, TA (Aug 2000). "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution". Science. 289 (5481): 905–920. doi:10.1126/science.289.5481.905. PMID 10937989.
  5. Cate, JH; Yusupov, MM; Yusupova, GZ; Earnest, TN; Noller, HF (Sep 1999). "X-ray crystal structures of 70S ribosome functional complexes". Science. 285 (5436): 2095–2104. doi:10.1126/science.285.5436.2095. PMID 10497122.
  6. Yusupov, MM; Yusupova, GZ; Baucom, A; Lieberman, K; Earnest, TN; Cate, JH; Noller, HF (May 2001). "Crystal structure of the ribosome at 5.5 A resolution". Science. 292 (5518): 883–896. doi:10.1126/science.1060089. PMID 11283358. S2CID 39505192.
  7. Nakao, A; Yoshihama, M; Kenmochi, N (2004). "RPG: the Ribosomal Protein Gene database". Nucleic Acids Res. 32 (90001): D168–70. doi:10.1093/nar/gkh004. PMC 308739. PMID 14681386.
  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. Ban, Nenad; Beckmann, Roland; Cate, Jamie HD; Dinman, Jonathan D; Dragon, François; Ellis, Steven R; Lafontaine, Denis LJ; Lindahl, Lasse; Liljas, Anders; Lipton, Jeffrey M; McAlear, Michael A; Moore, Peter B; Noller, Harry F; Ortega, Joaquin; Panse, Vikram Govind; Ramakrishnan, V; Spahn, Christian MT; Steitz, Thomas A; Tchorzewski, Marek; Tollervey, David; Warren, Alan J; Williamson, James R; Wilson, Daniel; Yonath, Ada; Yusupov, Marat (2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology. Elsevier BV. 24: 165–169. doi:10.1016/j.sbi.2014.01.002. ISSN 0959-440X. PMC 4358319. PMID 24524803.
  11. Yoshihama, Maki; Uechi, Tamayo; Asakawa, Shuichi; Kawasaki, Kauhiko (2002). "The Human Ribosomal Protein Genes: Sequencing and Comparative Analysis of 73 Genes". Genome Research. 12 (3): 379–390. doi:10.1101/gr.214202. PMC 155282. PMID 11875025.
  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
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