Eukaryotic Small Ribosomal Subunit (40S)

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Ribosomal particles are denoted according to their sedimentation coefficients in Svedberg units. The 40S subunit is the small subunit of eukaryotic 80S ribosomes. It is structurally and functionally related to the 30S subunit of 70S prokaryotic ribosomes.[1][2][3][4][5] However, the 40S subunit is much larger than the prokaryotic 30S subunit and contains many additional protein segments, as well as rRNA expansion segments.

Function[edit]

The 40S subunit contains the decoding center which monitors the complementarity of tRNA and mRNA in protein translation. It is the target of most eukaryotic initiation factors and also interacts with the internal ribosome entry site of the hepatitis C virus.[6] More information can be found in the articles on the 80S eukaryotic ribosome, the ribosome in general and the article on protein translation.

Overall Structure[edit]

The shape of the small subunit can be subdivided into two large segments, the head and the body. Characteristic features of the body include the left and right feet, the shoulder and the platform. The head features a pointed protrusion reminiscent of a bird's beak. The mRNA binds in the cleft between the head and the body, and 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 40S subunit is formed by the 18S ribosomal RNA (abbreviated 18S rRNA), which is homologous to the prokaryotic 16S rRNA. This rRNA core is decorated with dozens of proteins. In the figure "Crystal Structure of the Eukaryotic 40S 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 40S Ribosomal Subunit from T. thermophila
40S subunit viewed from the subunit interface side, PDB identifier 2XZM 
40S subunit viewed from the solvent-exposed side, PDB identifier 2XZM 

40S Ribosomal Proteins[edit]

The table "40S ribosomal proteins" shows the individual protein folds of the 40S subunit colored by conservation. Proteins which have homologs in eukaryotes, archaea and bacteria (EAB) are shown as blue ribbons. Proteins shared only between eukaryotes and archaea (EA) are shown as orange ribbons and proteins specific to eukaryotes (E) are shown as red ribbons. Eukaryote-specific extensions of conserved proteins, 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 "40S 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]

40S ribosomal proteins
Structure (Eukaryotic)[8] H. sapiens[7][9] Conservation[10] S. cerevisiae[11] Bacterial homolog (E. coli) Archaeal homolog
RpSA.png
RPSA EAB S0 S2p S2
RpS2.png
RPS2 EAB S2 S5p S5p
RpS3.png
RPS3 EAB S3 S3p S3p
RpS3A.png
RPS3A EA S1 n/a S3Ae
RpS4.png
RPS4 EA S4 n/a S4e
RpS5.png
RPS5 EAB S5 S7p S5p
RpS6.png
RPS6 EA S6 n/a S6e
RpS7.png
RPS7 E S7 n/a n/a
RpS8.png
RPS8 EA S8 n/a S8e
RpS9.png
RPS9 EAB S9 S4p S4p
RpS10.png
RPS10 E S10 n/a n/a
RpS11.png
RPS11 EAB S11 S17p S17p
RpS12.png
RPS12 E S12 n/a n/a
RpS13.png
RPS13 EAB S13 S15p S15p
RpS14.png
RPS14 EAB S14 S11p S11p
RpS15.png
RPS15 EAB S15 S19p S19p
RpS15A.png
RPS15A EAB S22 S8p S8p
RpS16.png
RPS16 EAB S16 S9p S9p
RpS17.png
RPS17 EA S17 n/a S17e
RpS18.png
RPS18 EAB S18 S13p S13p
RpS19.png
RPS19 EA S19 n/a S19e
RpS20.png
RPS20 EAB S20 S10p S10p
RpS21.png
RPS21 E S21 n/a n/a
RpS23.png
RPS23 EAB S23 S12p S12p
RpS24.png
RPS24 EA S24 n/a S24e
RpS25.png
RPS25 EA S25 n/a S25e
RpS26.png
RPS26 EA S26 n/a S26e
RpS27.png
RPS27 EA S27 n/a S27e
RpS27A.png
RPS27A EA S31 n/a S27ae
RpS28.png
RPS28 EA S28 n/a S28e
2000px.png
RPS29 EAB S29 S14p S14p
RpS30.png
RPS30 EA S30 n/a S30e
RACK1.png
RACK1 E Asc1 n/a n/a

External links[edit]

References[edit]

  1. ^ 40S Ribosomal Subunits at the US National Library of Medicine Medical Subject Headings (MeSH)
  2. ^ a b Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science. 2011 Feb 11;331(6018):730-6. doi: 10.1126/science.1198308. Epub 2010 Dec 23. PubMed PMID 21205638.
  3. ^ 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. ^ Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327-39. PubMed PMID 11014182.
  5. ^ Schmeing TM, Ramakrishnan V. What recent ribosome structures have revealed about the mechanism of translation. Nature. 2009 Oct 29;461(7268):1234-42. doi:10.1038/nature08403. Epub 2009 Oct 18. Review. PubMed PMID 19838167.
  6. ^ Lytle JR, Wu L, Robertson HD (August 2002). "Domains on the hepatitis C virus internal ribosome entry site for 40s subunit binding". RNA 8 (8): 1045–55. doi:10.1017/S1355838202029965. PMC 1370315. PMID 12212848. 
  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 and small subunit PDB 2XZM
  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.