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, with the other major component being the eukaryotic small ribosomal subunit (40S). 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
RPLP0 uL10 318 EAB P0 L10 L10
RPL3 uL3 404 EAB L3 L3 L3
RPL4 uL4 428 EAB L4 L4 L4
RPL5 uL18 298 EAB L5 L18 L18p
RPL6 eL6 289 E L6 n/a n/a
RPL7 uL30 254 EAB L7 L30 L30
RPL7A eL8 267 EA L8 n/a L7Ae
RPL8 uL2 258 EAB L2 L2 L2
RPL9 uL6 193 EAB L9 L6 L6
RPL10 uL16 215 EAB L10 L16 L10e
RPL11 uL5 EAB L11 L5 L5
RPL13 eL13 EA L13 n/a L13e
RPL13A uL13 204 EAB L16 L13 L13
RPL14 eL14 221 EA L14 n/a L14e
RPL15 eL15 205 EA L15 n/a L15e
RPL17 uL22 185 EAB L17 L22 L22
RPL18 eL18 189 EA L18 n/a L18e
RPL18A eL20 177 EA L20 n/a Lx
RPL19 eL19 197 EA L19 n/a L19
RPL21 eL21 161 EA L21 n/a L21e
RPL22, RPL22L1 eL22 129 E L22 n/a n/a
RPL23 uL14 141 EAB L23 L14 L14p
RPL23A uL23 157 EAB L25 L23 L23
RPL24 eL24 158 EA L24 n/a L24e
RPL26 uL24 146 EAB L26 L24 L24
RPL27 eL27 137 E L27 n/a n/a
RPL27A uL15 149 EAB L28 L15 L15
RPL28 eL28 E n/a[2][3][14] n/a n/a
RPL29 eL29 E L29 n/a n/a
RPL30 eL30 116 EA L30 n/a L30e
RPL31 eL31 126 EA L31 n/a L31e
RPL32 eL32 136 EA L32 n/a L32e
RPL34 eL34 118 EA L34 n/a L34e
RPL35 uL29 124 EAB L35 L29 L29
RPL35A eL33 EA L33 n/a L35Ae
RPL36 eL36 106 E L36 n/a n/a
RPL36A eL42 107 EA L42 n/a L44e
RPL37 eL37 98 EA L37 n/a L37e
RPL37A eL43 EA L43 n/a L37Ae
RPL38 eL38 EA L38 n/a L38e
RPL39 eL39 52 EA L39 n/a L37Ae
RPL40 eL40 129 EA L40 n/a L40e

See also

References

  1. ^ 60S+Ribosome+Subunits at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ a b c d 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. ^ a b 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. ^ a b 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. Bibcode:2000Sci...289..905B. 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. Bibcode:2001Sci...292..883Y. doi:10.1126/science.1060089. PMID 11283358. S2CID 39505192.
  7. ^ a b c 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. 24. Elsevier BV: 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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