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

Overall Structure

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 contibutes 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] 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	EAB	P0	L10	L10
	RPL3	EAB	L3	L3	L3
	RPL4	EAB	L4	L4	L4
	RPL5	EAB	L5	L18	L18p
	RPL6	E	L6	n/a	n/a
	RPL7	EAB	L7	L30	L30
	RPL7A	EA	L8	n/a	L7Ae
	RPL8	EAB	L2	L2	L2
	RPL9	EAB	L9	L6	L6
	RPL10	EAB	L10	L16	L10e
	RPL11	EAB	L11	L5	L5
	RPL13	EA	L13	n/a	L13e
	RPL13A	EAB	L16	L13	L13
	RPL14	EA	L14	n/a	L14e
	RPL15	EA	L15	n/a	L15e
	RPL17	EAB	L17	L22	L22
	RPL18	EA	L18	n/a	L18e
	RPL18A	EA	L20	n/a	Lx
	RPL19	EA	L19	n/a	L19
	RPL21	EA	L21	n/a	L21e
	RPL22	E	L22	n/a	n/a
	RPL23	EAB	L23	L14	L14p
	RPL23A	EAB	L25	L23	L23
	RPL24	EA	L24	n/a	L24e
	RPL26	EAB	L26	L24	L24
	RPL27	E	L27	n/a	n/a
	RPL27A	EAB	L28	L15	L15
	RPL28	E	n/a[2][3][12]	n/a	n/a
	RPL29	E	L29	n/a	n/a
	RPL30	EA	L30	n/a	L30e
	RPL31	EA	L31	n/a	L31e
	RPL32	EA	L32	n/a	L32e
	RPL34	EA	L34	n/a	L34e
	RPL35	EAB	L35	L29	L29
	RPL35A	EA	L33	n/a	L35Ae
	RPL36	E	L36	n/a	n/a
	RPL36A	EA	L42	n/a	L44e
	RPL37	EA	L37	n/a	L37e
	RPL37A	EA	L43	n/a	L37Ae
	RPL38	EA	L38	n/a	L38e
	RPL39	EA	L39	n/a	L37Ae
	RPL40	EA	L40	n/a	L40e

External links

• Ribosomal Protein Gene Database (RPG)

References

1. ↑ 60S Ribosome Subunits at the US National Library of Medicine Medical Subject Headings (MeSH)
2. ↑ 2.0 2.1 2.2 2.3 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. ↑ 3.0 3.1 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. ↑ 4.0 4.1 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. ↑ 7.0 7.1 7.2 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