Eukaryotic Ribosome (80S)
- 1 Overview
- 2 Composition
- 3 Structure Determination
- 4 Architecture of the Eukaryotic Ribosome
- 5 Functional Aspects
- 6 References
- 7 Notes
The Ribosome is a large and complex molecular machine that catalyzes the synthesis of proteins, referred to as translation. Herein, the ribosome selects aminoacylated transfer RNAs (tRNAs) based on the sequence of a protein encoding messenger RNA (mRNA) and covalently links the amino acids into a polypeptide chain. Ribosomes from all organisms share a highly conserved catalytic center. However, the ribosomes of eukaryotes (animals, plants, fungi and many unicellular organisms with a nucleus) are much larger than prokaryotic (bacterial and archaeal) ribosomes and subject to more complex regulation and biogenesis pathways. These Eukaryotic ribosomes are also known as 80S ribosomes, referring to their sedimentation coefficients in Svedberg units, because they sediment faster than the prokaryotic (70S) ribosomes. Eukaryotic ribosomes have two unequal subunits, designated small subunit (40S) and large subunit (60S) according to their sedimentation coefficients. Both subunits contain dozens of ribosomal proteins arranged on a scaffold composed of ribosomal RNA (rRNA). The small subunit monitors the complementarity between tRNA anticodon and mRNA, while the large subunit catalyzes peptide bond formation.
Compared to their prokaryotic homologs, many of the eukaryotic ribosomal proteins are enlarged by insertions or extensions to the converved core. Furthermore, several additional proteins are found in the small and large subunits of eukaryotic ribosomes, which do not have prokaryotic homologs. The 40S subunit contains a 18S ribosomal RNA (abbreviated 18S rRNA), which is homologous to the prokaryotic 16S rRNA. The 60S subunit contains a 26S rRNA that is homologous to the prokaryotic 23S ribosomal RNA. In addition, it contains a 5.8S rRNA that corresponds to the 5'end of the 23S rRNA, and a short 5S rRNA. Both 18S and 26S have multiple insertions to the core rRNA fold of their prokaryotic counterparts, which are called expansion segments. For a detailed list of proteins, including archaeal and bacterial homologs please refer to the separate articles on the 40S and 60S subunits.
|Ribosome||Sedimentation coefficient||80 S||70 S|
|Molecular mass||~3.2*106 Da||~2.0*106 Da|
|Diameter||~250-300 Å||~200 Å|
|Large subunit||Sedimentation coefficient||60 S||50 S|
|Molecular mass||~2.0*106 Da||~1.3*106 Da|
|Small subunit||Sedimentation coefficient||40 S||30 S|
|Molecular mass||~1.2*106 Da||~0.7*106 Da|
Initial structures of eukaryotic ribosomes were determined by electron microscopy. First 3D structures were obtained at 30-40 Å resolution for yeast  and mammalian ribosomes.   Higher resolution structures of the yeast ribosome by cryo-electron microscopy allowed the identification of protein and RNA structural elements.  More recently structures at sub-nanometer resolution were obtained for complexes of ribosomes and factors involved in translation, for example see.    After the determination of the first bacterial    and archaeal  ribosome structures at atomic resolution in the 1990s it took another decade until high resolution structures of the eukaryotic ribosome were obtained by X-ray crystallography, mainly because of the difficulties in obtaining crystals of sufficient quality.    Recently, the first complete atomic structure of the eukaryotic 80S ribosome from the yeast Saccharomyces cerevisiae was obtained by crystallography.  The model reveals the precise architecture of eukaryote-specific elements, their interaction with the universally conserved core and all eukaryote-specific bridges between the two ribosomal subunits. Shortly after, the complete model of a eukaryotic 40S ribosomal structure in Tetrahymena thermophila was published and described the structure of the 40S subunit as well as much about the 40S subunit's interaction with eIF1 during translation initiation.  Similarly, the eukaryotic 60S subunit structure was also determined from Tetrahymena thermophila in complex with eIF6. 
|Complex||Source Organism||Resolution||PDB Identifier|
|80S:Stm1||S. cerevisiae||3.0 Å|
|40S:eIF1||T. thermophila||3.9 Å|
|60S:eIF6||T. thermophila||3.5 Å|
Architecture of the Eukaryotic Ribosome
General Architectural Features
Some general architectural features of the ribosome are conserved across kingdoms: 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. In the characteristic "crown view" of the large subunit, structural landmarks include the central protuberance, the L1-stalk and the P-stalk. The majority of the eukaryote-specific RNA and protein elements are found on the solvent-exposed sides of the 40S  and 60S subunits. The subunit interface, as well as important functional regions such as the peptidyl transferase center and the decoding site are mostly conserved, with some differences observed in the surrounding regions. In stark contrast to prokaryotic ribosomal proteins, which interact primarily with RNA, the eukaryote-specific protein segments engage in a multitude of protein-protein interactions. Long distance interactions are mediated by eukaryote-specific helical extensions of ribosomal proteins, and several eukaryotic ribosomal proteins jointly to form inter-protein beta-sheets.
|Crystal Structures of the Eukaryotic Ribosomal Subunits from T. thermophila|
The ribosomal RNA core is represented as a grey tube, expansion segments are shown in red. Universally conserved proteins are shown in blue. These proteins have homologs in eukaryotes, archaea and bacteria. Proteins Shared only between eukaryotes and archaea are shown in orange, and proteins specific to eukaryotes are shown in red.
Co-evolution of rRNA and Proteins
The structure of the 40S subunit revealed that the eukaryote-specific proteins (rpS7, rpS10, rpS12 and RACK1), as well as numerous eukaryote-specific extensions of proteins, are located on the solvent-exposed side of the small subunit. Here, they participate in the stabilization of rRNA expansion segments. Moreover, the beak of the 40S subunit is remodeled, as rRNA has been replaced by proteins rpS10 and rpS12. As observed for the 40S subunit, all eukaryote-specific proteins of the 60S subunit (RPL6, RPL22, RPL27, RPL28, RPL29 and RPL36) and many extensions are located at the solvent-exposed side, forming an intricate network of interactions with eukaryotic-specific RNA expansion segments. RPL6, RPL27 and RPL29 mediate contacts between the ES sets ES7–ES39, ES31–ES20–ES26 and ES9–ES12, respectively and RPL28 stabilized expansion segment ES7A.
Ubiquitin Fusion Proteins
In eukaryotes, the small subunit protein rpS27A(S31) and the large subunit protein RPL40 are processed polypeptides, which are translated as fusion proteins carrying N-terminal Ubiquitin domains. Both proteins are located next to important functional centers of the ribosome: The uncleaved ubiquitin domains of rpS27A(S31) and RPL40 would be positioned in the decoding site and near the translation factor binding site, respectively. These positions suggest that proteolytic cleavage is an essential step in the production of functional ribosomes. Indeed, mutations of the linker between the core of rpS27A(S31) and the ubiquitin domain are lethal in yeast.
Active Site Region
Comparisons between bacterial, archaeal and eukaryotic ribosome structures reveal a very high degree of conservation in the active site (PTC) region. None of the eukaryote-specific protein elements is close enough to directly participate in catalysis. However, RPL29 projects to within 18Å of the active site in T. thermophila, and eukaryote-specific extensions interlink several proteins in the vicinity of the PTC of the 60S subunit, while the corresponding 50S proteins are singular entities.
Contacts across the two ribosomal subunits are known as intersubunit bridges. In the eukaryotic ribosome, additional contacts are made by 60S expansion segments and proteins. Specifically, the C-terminal extension of the 60S protein RPL19 interacts with ES6E of the 40S rRNA, and the C-terminal extension of the 60S protein RPL24 interacts with 40S rpS6 and rRNA helix h10. Moreover, the 60S expansion segments ES31 and ES41 interact with rpS3A(S1) and rpS8 of the 40S subunit, respectively, and the basic 25-amino-acid peptide RPL41 is positioned at the subunit interface in the 80S ribosome, interacting with rRNA elements of both subunits.
Ribosomal Proteins with Roles in Signaling
Two 40S ribosomal proteins (RACK1 and rpS6) have been implicated in signaling: RACK1, the Receptor of Activated Protein Kinase C (PKC), is an integral component of the eukaryotic ribosome and is located at the back of the head, in proximity of rpS17. It links signal-transduction pathways directly to the ribosome (reviewed in ). Ribosomal protein rpS6 is located at the right foot of the 40S subunit  and is phosphorylated in response to mammalian target of rapamycin (mTOR) signaling.
Protein synthesis is primarily regulated at the stage of translation initiation. In eukaryotes, the canonical initiation pathway requires at least 12 protein initiation factors, some of which are themselves large complexes. The structures of the 40S:eIF1  and 60S:eIF6  complexes provide first detailed insights into the atomic interactions between the eukaryotic ribosome and regulatory factors. eIF1 is involved in start codon selection, and eIF6 sterically precludes the joining of subunits. However, strutural information on the eukaryotic initiaion factors and their interactions with the ribosome is limited, and largely derived from homology models or low-resolution analyses. Elucidation of the interactions between the eukaryotic ribosome and initiation factors at an atomic level is essential for a mechanistic understanding of the regulatory processes, but represents a significant technical challenge, because of the inherent dynamics and flexibility of the initiation complexes.
Regulatory Roles of Ribosomal Proteins
Recent evidence suggests that individual proteins of the eukaryotic ribosome may directly contribute to the regulation of translation. Specifically, mutations in RPL38 lead to developmental abnormalities, but not to global translational alterations  Moreover, the specific defects  and the increased cancer susceptibility  that result from mutations in ribosomal proteins may support such a regulatory role.
Protein Translocation and Targeting
To exert their functions in the cell newly synthesized proteins must be targeted to the appropriate location in the cell, which is achieved protein targeting and translocation systems. The growing polypeptide leaves the ribosome through a narrow tunnel in the large subunit. The region around the exit tunnel of the 60S subunit is very similar to the bacterial and archaeal 50S subunits. Additional elements are restricted to the second tier of proteins around the tunnel exit, possibly by conserved interactions with components of the translocation machinery. The targeting and translocation machinery is much more complex in eukaryotes.
Ribosomal Diseases and Cancer
Ribosomopathies are congenital human disorders resulting from defects in ribosomal protein or rRNA genes, or other genes whose products are implicated in ribosome biogenesis. Examples include X-linked Dyskeratosis congenita (X-DC), Diamond–Blackfan anemia, Treacher Collins syndrome (TCS)  and Shwachman–Bodian–Diamond syndrome (SBDS). SBDS is caused by mutations in the SBDS protein that affects its ability to couple GTP hydrolysis by the GTPase EFL1 to the release of eIF6 from the 60S subunit.
The ribosome is a prominent drug target and many antibacterials interfere with translation at different stages of the elongation cycle  Most clinically relevant translation compounds are inhibitors of bacterial translation, but inhibitors of eukaryotic translation may also hold therapeutic potential for application in cancer or antifungal chemotherapy. Elongation inhibitors show antitumor activity 'in vivo' and 'in vitro'. One inhibitor of eukaryotic translation elongation is the glutarimide antibiotic cycloheximide (CHX), which was co-crystallized with the eukaryotic 60S subunit  and binds in the ribosomal E-site. The structural characterization of the eukaryotic ribosome  enables the use of structure based methods for the design of novel therapeutics, and allows the structural differences to the bacterial ribosome to be exploited, improving the selectivity and drug and therefore reducing adverse effects.
- "Difference Between 70S Ribosomes and 80S Ribosomes, RNA, Micromolecules". www.microbiologyprocedure.com. Retrieved 2009-08-06.
- "80S Ribosomes, Eukaryotic Ribosomes, Prokaryotic Ribosomes, Nucleic Acids, Sedimentation Coefficient". www.microbiologyprocedure.com. Retrieved 2009-08-06.
- Values are based on the ribosomes of T. thermophila (PDB:4A17,4A19) and Thermus thermophilus (PDB 2WDL, 2WDK). The exact size, weight and number of proteins varies from organism to organism.
- Verschoor A, Warner JR, Srivastava S, Grassucci RA, Frank J. Three-dimensional structure of the yeast ribosome. Nucleic Acids Res. 1998 Jan 15;26(2):655-61.PubMed PMID 9421530; PubMed Central PMCID: PMC147289
- Verschoor A, Frank J. Three-dimensional structure of the mammalian cytoplasmic ribosome. J Mol Biol. 1990 Aug 5;214(3):737-49. PubMed PMID 2388265
- Dube P, Wieske M, Stark H, Schatz M, Stahl J, Zemlin F, Lutsch G, van Heel M.The 80S rat liver ribosome at 25 Å resolution by electron cryomicroscopy and angular reconstitution. Structure. 1998 Mar 15;6(3):389-99. PubMed PMID 9551559
- Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell. 2001 Nov 2;107(3):373-86. PubMed PMID 11701127.
- Halic M, Gartmann M, Schlenker O, Mielke T, Pool MR, Sinning I, Beckmann R. Signal recognition particle receptor exposes the ribosomal translocon binding site. Science. 2006 May 5;312(5774):745-7. PubMed PMID 16675701
- Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J,Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon EC, Beckmann R. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science. 2009 Dec 4;326(5958):1369-73. doi:10.1126/science.1178535. Epub 2009 Oct 29. PubMed PMID 19933108; PubMed Central PMCID: PMC2920595
- Schüler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat Struct Mol Biol. 2006 Dec;13(12):1092-6. Epub 2006 Nov 19. PubMed PMID 17115051
- Clemons WM Jr, May JL, Wimberly BT, McCutcheon JP, Capel MS, Ramakrishnan V. Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature. 1999 Aug 26;400(6747):833-40. PubMed PMID 10476960.
- 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.
- 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.
- 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.
- 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.
- 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.
- Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. (February 2011). "The structure of the eukaryotic ribosome at 3.0 Å resolution.". Science 334 (6062): 1524–1529. doi:10.1126/science.1212642. PMID 22096102.
- Rabl, Leibundgut, Ataide, Haag, Ban (February 2010). "Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1". Science 331 (6018): 730–736. doi:10.1126/science.1198308. PMID 21205638.
- Klinge, Voigts-Hoffmann, Leibundgut, Arpagaus, Ban (November 2011). "Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6". Science 334 (6058): 941–948. doi:10.1126/science.1211204. PMID 22052974.
- Due to size limitations, ribosome structures are often split into several coordinate files
- Melnikov S, Ben-Shem A, Garreau de Loubresse N, Jenner L, Yusupova G, Yusupov M. One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol. 2012 Jun 5;19(6):560-7. doi: 10.1038/nsmb.2313. Review. PubMed PMID 22664983.
- Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N. Atomic structures of the eukaryotic ribosome. Trends Biochem Sci. 2012 May;37(5):189-98. doi:10.1016/j.tibs.2012.02.007. Epub 2012 Mar 20. Review. PubMed PMID 22436288.
- Jenner L, Melnikov S, de Loubresse NG, Ben-Shem A, Iskakova M, Urzhumtsev A, Meskauskas A, Dinman J, Yusupova G, Yusupov M. Crystal structure of the 80S yeast ribosome. Curr Opin Struct Biol. 2012 Dec;22(6):759-67. doi: 10.1016/j.sbi.2012.07.013. Epub 2012 Aug 8. PubMed PMID 22884264.
- Lacombe T, García-Gómez JJ, de la Cruz J, Roser D, Hurt E, Linder P, Kressler D. Linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits. Mol Microbiol. 2009 Apr;72(1):69-84. doi: 10.1111/j.1365-2958.2009.06622.x. Epub 2009 Feb 4. PubMed PMID 19210616.
- Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. The structure of the eukaryotic ribosome at 3.0 Ã resolution. Science. 2011 Dec 16;334(6062):1524-9. doi: 10.1126/science.1212642. Epub 2011 Nov 17. PubMed PMID 22096102.
- Regulation of eukaryotic translation by the RACK1 protein: a platform for signalling molecules on the ribosome. Nilsson J, Sengupta J, Frank J, Nissen P. EMBO Rep. 2004 Dec;5(12):1137-41. Review.
- Palm L, Andersen J, Rahbek-Nielsen H, Hansen TS, Kristiansen K, Højrup P. The phosphorylated ribosomal protein S7 in Tetrahymena is homologous with mammalian S4 and the phosphorylated residues are located in the C-terminal region. Structural characterization of proteins separated by two-dimensional polyacrylamide gel electrophoresis. J Biol Chem. 1995 Mar 17;270(11):6000-5. PubMed PMID 7890730.
- Hinnebusch AG, Lorsch JR. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb Perspect Biol. 2012 Oct 1;4(10).doi:pii: a011544. 10.1101/cshperspect.a011544. Review. PubMed PMID 22815232.
- Voigts-Hoffmann F, Klinge S, Ban N. Structural insights into eukaryotic ribosomes and the initiation of translation. Curr Opin Struct Biol. 2012 Dec;22(6):768-77. doi: 10.1016/j.sbi.2012.07.010. Epub 2012 Aug 10. PubMed PMID 22889726.
- Topisirovic I, Sonenberg N. Translational control by the eukaryotic ribosome. Cell. 2011 Apr 29;145(3):333-4. doi: 10.1016/j.cell.2011.04.006. PubMed PMID 21529706
- Kondrashov N, Pusic A, Stumpf CR, Shimizu K, Hsieh AC, Xue S, Ishijima J, Shiroishi T, Barna M. Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Cell. 2011 Apr 29;145(3):383-97. doi:10.1016/j.cell.2011.03.028. PubMed PMID 21529712.
- Narla A, Ebert BL. Translational medicine: ribosomopathies. Blood. 2011 Oct 20;118(16):4300-1. doi: 10.1182/blood-2011-08-372250
- Stumpf CR, Ruggero D. The cancerous translation apparatus. Curr Opin Genet Dev. 2011 Aug;21(4):474-83. doi: 10.1016/j.gde.2011.03.007. Epub 2011 May 3. Review. PubMed PMID 21543223; PubMed Central PMCID: PMC3481834.
- Boehringer, Daniel, Greber, Basil, Ban, Nenad. Mechanistic insight into co-translational protein processing, folding, targeting, and membrane insertion. Ribosomes, 405-418. 2011, http://dx.doi.org/10.1007/978-3-7091-0215-2_32
- Markus T. Bohnsack, Enrico Schleiff, The evolution of protein targeting and translocation systems, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Volume 1803, Issue 10, October 2010, Pages 1115-1130, ISSN 0167-4889, 10.1016/j.bbamcr.2010.06.005.
- Narla A, Ebert BL. Ribosomopathies: human disorders of ribosome dysfunction. Blood. 2010 Apr 22;115(16):3196-205. doi: 10.1182/blood-2009-10-178129. Epub 2010 Mar 1. Review. PubMed PMID 20194897; PubMed Central PMCID: PMC2858486.
- Dauwerse JG, Dixon J, Seland S, Ruivenkamp CA, van Haeringen A, Hoefsloot LH, Peters DJ, Boers AC, Daumer-Haas C, Maiwald R, Zweier C, Kerr B, Cobo AM, Toral JF, Hoogeboom AJ, Lohmann DR, Hehr U, Dixon MJ, Breuning MH, Wieczorek D. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nat Genet. 2011 Jan;43(1):20-2. doi: 10.1038/ng.724. Epub 2010 Dec 5. PubMed PMID 21131976.
- Finch AJ, Hilcenko C, Basse N, Drynan LF, Goyenechea B, Menne TF, González Fernández A, Simpson P, D'Santos CS, Arends MJ, Donadieu J, Bellanné-Chantelot C, Costanzo M, Boone C, McKenzie AN, Freund SM, Warren AJ. Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. Genes Dev. 2011 May 1;25(9):917-29. doi: 10.1101/gad.623011. PubMed PMID 21536732; PubMed Central PMCID: PMC3084026.
- Blanchard SC, Cooperman BS, Wilson DN. Probing translation with small-molecule inhibitors. Chem Biol. 2010 Jun 25;17(6):633-45. doi:10.1016/j.chembiol.2010.06.003. Review. PubMed PMID 20609413; PubMed Central PMCID: PMC2914516.
- Pelletier,J. & Peltz,S.W.,2007.Therapeutic Opportunities in Translation. Cold Spring Harbor Monograph Archive, 48(0), pp.855–895.
- Schneider-‐Poetsch, T., Usui, T., et al., 2010a. Garbled messages and corrupted translations. Nature Methods, 6(3), pp.189–198.
- Schneider-‐Poetsch, T., Ju, J., et al., 2010b. Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin. Nat Chem Biol, 6(3), pp.209–217.
- Dang, Y. et al., 2011. Inhibition of eukaryotic translation elongation by the antitumor natural product Mycalamide B. RNA (New York, N.Y.), 17(8), pp.1578–1588.
- "EMDB-1067: Ribosomal 80S-eEF2-sordarin complex from S. cerevisiae - EM Navigator". emnavi.protein.osaka-u.ac.jp. Retrieved 2009-08-06.
- Giavalisco P, Wilson D, Kreitler T, et al. (March 2005). "High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome". Plant Mol. Biol. 57 (4): 577–91. doi:10.1007/s11103-005-0699-3. PMID 15821981.
- "Ribosomes". www.cs.stedwards.edu. Retrieved 2009-08-06.