Eukaryotic Large Ribosomal Subunit (60S)

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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 rRNA expansion segments. More general information can be found in the article on the eukaryotic ribosome.

Overall Structure[edit]

Characteristic features of the large subunit, shown in the "Crown View" (as seen below) 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[edit]

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] For a details, refer to the article on the eukaryotic ribosome. 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 organism, while identical names not necessarily denote homologous proteins. The table "60S ribosomal proteins" crossreferences 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] Conservation[10] S. cerevisiae[11] Bacterial homolog (E. coli) Archaeal homolog
RPLP0.png
RPLP0 EAB P0 L10 L10
RPL3.png
RPL3 EAB L3 L3 L3
RPL4.png
RPL4 EAB L4 L4 L4
RPL5.png
RPL5 EAB L5 L18 L18p
RPL6.png
RPL6 E L6 n/a n/a
RPL7.png
RPL7 EAB L7 L30 L30
RPL7A.png
RPL7A EA L8 n/a L7Ae
RPL8.png
RPL8 EAB L2 L2 L2
RPL9.png
RPL9 EAB L9 L6 L6
RPL10.png
RPL10 EAB L10 L16 L10e
RPL11.png
RPL11 EAB L11 L5 L5
RPL13.png
RPL13 EA L13 n/a L13e
RPL13A.png
RPL13A EAB L16 L13 L13
RPL14.png
RPL14 EA L14 n/a L14e
RPL15.png
RPL15 EA L15 n/a L15e
RPL17.png
RPL17 EAB L17 L22 L22
RPL18.png
RPL18 EA L18 n/a L18e
RPL18A.png
RPL18A EA L20 n/a Lx
RPL19.png
RPL19 EA L19 n/a L19
RPL21.png
RPL21 EA L21 n/a L21e
RPL22.png
RPL22 E L22 n/a n/a
RPL23.png
RPL23 EAB L23 L14 L14p
RPL23A.png
RPL23A EAB L25 L23 L23
RPL24.png
RPL24 EA L24 n/a L24e
RPL26.png
RPL26 EAB L26 L24 L24
RPL27.png
RPL27 E L27 n/a n/a
RPL27A.png
RPL27A EAB L28 L15 L15
RPL28.png
RPL28 E n/a[2][3][12] n/a n/a
RPL29.png
RPL29 E L29 n/a n/a
RPL30.png
RPL30 EA L30 n/a L30e
RPL31.png
RPL31 EA L31 n/a L31e
RPL32.png
RPL32 EA L32 n/a L32e
RPL34.png
RPL34 EA L34 n/a L34e
RPL35.png
RPL35 EAB L35 L29 L29
RPL35A.png
RPL35A EA L33 n/a L35Ae
RPL36.png
RPL36 E L36 n/a n/a
RPL36A.png
RPL36A EA L42 n/a L44e
RPL37.png
RPL37 EA L37 n/a L37e
RPL37A.png
RPL37A EA L43 n/a L37Ae
RPL38.png
RPL38 EA L38 n/a L38e
RPL39.png
RPL39 EA L39 n/a L37Ae
RPL40.png
RPL40 EA L40 n/a L40e

External links[edit]

References[edit]

  1. ^ 60S Ribosome Subunits at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ a b c d 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. PubMed PMID 22052974.
  3. ^ a b 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. PubMed PMID 22096102.
  4. ^ a b 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. PubMed 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. PubMed 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. PubMed PMID 11283358.
  7. ^ a b c Nakao A, Yoshihama M, Kenmochi N. RPG: the Ribosomal Protein Gene database. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D168-70. PubMed PMID 14681386; PubMed Central PMCID: PMC308739.
  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. ^ EAB means conserved in eukaryotes, archaea and bacteria, EA means conserved in eukaryotes and archaea and E means eukaryote-specific protein
  11. ^ 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.
  12. ^ RPL28 has no detectable homolog in yeast