Structures of the human and Drosophila 80S ribosome (original) (raw)

• Schmeing, T. M. & Ramakrishnan, V. What recent ribosome structures have revealed about the mechanism of translation. Nature 461, 1234–1242 (2009)
  Article CAS ADS PubMed Google Scholar
• Wilson, D. N. & Cate, J. H. D. The structure and function of the eukaryotic ribosome. Cold Spring Harb. Perspect. Biol. 4, a011536 (2012)
  Article CAS PubMed PubMed Central Google Scholar
• Klinge, S., Voigts-Hoffmann, F., Leibundgut, M. & Ban, N. Atomic structures of the eukaryotic ribosome. Trends Biochem. Sci. 37, 189–198 (2012)
  Article CAS PubMed Google Scholar
• Melnikov, S. et al. One core, two shells: bacterial and eukaryotic ribosomes. Nature Struct. Mol. Biol. 19, 560–567 (2012)
  Article CAS Google Scholar
• Taylor, D. J. et al. Comprehensive molecular structure of the eukaryotic ribosome. Structure 17, 1591–1604 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Armache, J. P. et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc. Natl Acad. Sci. USA 107, 19748–19753 (2010)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Armache, J. P. et al. Localization of eukaryote-specific ribosomal proteins in a 5.5-A cryo-EM map of the 80S eukaryotic ribosome. Proc. Natl Acad. Sci. USA 107, 19754–19759 (2010)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Rabl, J., Leibundgut, M., Ataide, S. F., Haag, A. & Ban, N. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science 331, 730–736 (2011)
  Article CAS ADS PubMed Google Scholar
• 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 334, 941–948 (2011)
  Article CAS ADS PubMed Google Scholar
• Ben-Shem, A. et al. The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334, 1524–1529 (2011)
  Article CAS ADS PubMed Google Scholar
• Dube, P. et al. Correlation of the expansion segments in mammalian rRNA with the fine structure of the 80 S ribosome; a cryoelectron microscopic reconstruction of the rabbit reticulocyte ribosome at 21 A resolution. J. Mol. Biol. 279, 403–421 (1998)
  Article CAS PubMed Google Scholar
• Spahn, C. M. et al. Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes; the IRES functions as an RNA-based translation factor. Cell 118, 465–475 (2004)
  Article CAS PubMed Google Scholar
• Boehringer, D., Thermann, R., Ostareck-Lederer, A., Lewis, J. D. & Stark, H. Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES. Structure 13, 1695–1706 (2005)
  Article CAS PubMed Google Scholar
• Chandramouli, P. et al. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure 16, 535–548 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Ruvinsky, I. & Meyuhas, O. Ribosomal protein S6 phosphorylation: from protein synthesis to cell size. Trends Biochem. Sci. 31, 342–348 (2006)
  Article CAS PubMed Google Scholar
• Koyama, Y., Katagiri, S., Hanai, S., Uchida, K. & Miwa, M. Poly(ADP-ribose) polymerase interacts with novel Drosophila ribosomal proteins, L22 and l23a, with unique histone-like amino-terminal extensions. Gene 226, 339–345 (1999)
  Article CAS PubMed Google Scholar
• Ramakrishnan, V. Histone structure and the organization of the nucleosome. Annu. Rev. Biophys. Biomol. Struct. 26, 83–112 (1997)
  Article CAS PubMed Google Scholar
• Taylor, D. J. et al. Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J. 26, 2421–2431 (2007)
  Article CAS PubMed PubMed Central Google Scholar
• Harms, J. M. et al. Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Mol. Cell 30, 26–38 (2008)
  Article CAS PubMed Google Scholar
• Gao, Y. G. et al. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326, 694–699 (2009)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Dever, T. E. & Green, R. The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harb. Perspect. Biol. 4, a013706 (2012)
  Article CAS PubMed PubMed Central Google Scholar
• Ogle, J. M. & Ramakrishnan, V. Structural insights into translational fidelity. Annu. Rev. Biochem. 74, 129–177 (2005)
  Article CAS PubMed Google Scholar
• Demeshkina, N., Jenner, L., Westhof, E., Yusupov, M. & Yusupova, G. A new understanding of the decoding principle on the ribosome. Nature 484, 256–259 (2012)
  Article CAS ADS PubMed Google Scholar
• Lu, H., Li, W., Noble, W. S., Payan, D. & Anderson, D. C. Riboproteomics of the hepatitis C virus internal ribosomal entry site. J. Proteome Res. 3, 949–957 (2004)
  Article CAS PubMed Google Scholar
• Spahn, C. M. et al. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science 291, 1959–1962 (2001)
  Article CAS ADS PubMed Google Scholar
• Balagopal, V. & Parker, R. Stm1 modulates translation after 80S formation in Saccharomyces cerevisiae. RNA 17, 835–842 (2011)
  Article CAS PubMed PubMed Central Google Scholar
• Gerbi, S. A. in Ribosomal RNA—Structure, Evolution, Processing, and Function in Protein Synthesis (eds Zimmermann, R. A. & Dahlberg, A. E.) 71–87 (CRC Press, 1996)
  Google Scholar
• Haga, J. Y., Hamilton, M. G. & Petermann, M. L. Electron microscopic observations on the large subunit of the rat liver ribosome. J. Cell Biol. 47, 211–221 (1970)
  Article CAS PubMed PubMed Central Google Scholar
• Cannone, J. J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 (2002)
  Article PubMed PubMed Central Google Scholar
• Fields, D. S. & Gutell, R. R. An analysis of large rRNA sequences folded by a thermodynamic method. Fold. Des. 1, 419–430 (1996)
  Article CAS PubMed Google Scholar
• Alkemar, G. & Nygard, O. Probing the secondary structure of expansion segment ES6 in 18S ribosomal RNA. Biochemistry 45, 8067–8078 (2006)
  Article CAS PubMed Google Scholar
• Andersen, C. B. et al. Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature 443, 663–668 (2006)
  Article CAS ADS PubMed Google Scholar
• Srivastava, S., Verschoor, A. & Frank, J. Eukaryotic initiation factor-3 does not prevent association through physical blockage of the ribosomal subunit-subunit interface. J. Mol. Biol. 226, 301–304 (1992)
  Article CAS PubMed Google Scholar
• Siridechadilok, B., Fraser, C. S., Hall, R. J., Doudna, J. A. & Nogales, E. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science 310, 1513–1515 (2005)
  Article CAS ADS PubMed Google Scholar
• Yu, Y., Abaeva, I. S., Marintchev, A., Pestova, T. V. & Hellen, C. U. Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors. Nucleic Acids Res. 39, 4851–4865 (2011)
  Article CAS PubMed PubMed Central Google Scholar
• Beckmann, R. et al. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361–372 (2001)
  Article CAS PubMed Google Scholar
• Becker, T. et al. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science 326, 1369–1373 (2009)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Sweeney, R., Chen, L. H. & Yao, M. C. An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence. Mol. Cell. Biol. 14, 4203–4215 (1994)
  Article CAS PubMed PubMed Central Google Scholar
• Bradatsch, B. et al. Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Nature Struct. Mol. Biol. 19, 1234–1241 (2012)
  Article CAS Google Scholar
• Greber, B. J., Boehringer, D., Montellese, C. & Ban, N. Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Nature Struct. Mol. Biol. 19, 1228–1233 (2012)
  Article CAS Google Scholar
• Leidig, C. et al. Structural characterization of a eukaryotic chaperone—the ribosome-associated complex. Nature Struct. Mol. Biol. 20, 23–28 (2013)
  Article CAS Google Scholar
• Blau, M. et al. ERj1p uses a universal ribosomal adaptor site to coordinate the 80S ribosome at the membrane. Nature Struct. Mol. Biol. 12, 1015–1016 (2005)
  Article CAS Google Scholar
• Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996)
  Article CAS PubMed Google Scholar
• Jossinet, F. & Westhof, E. Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 21, 3320–3321 (2005)
  Article CAS PubMed Google Scholar
• Jossinet, F., Ludwig, T. E. & Westhof, E. Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26, 2057–2059 (2010)
  Article CAS PubMed PubMed Central Google Scholar
• Eswar, N., Eramian, D., Webb, B., Shen, M. Y. & Sali, A. Protein structure modeling with MODELLER. Methods Mol. Biol. 426, 145–159 (2008)
  Article CAS PubMed Google Scholar
• Jenner, L., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural rearrangements of the ribosome at the tRNA proofreading step. Nature Struct. Mol. Biol. 17, 1072–1078 (2010)
  Article CAS Google Scholar
• Gebauer, F., Corona, D. F., Preiss, T., Becker, P. B. & Hentze, M. W. Translational control of dosage compensation in Drosophila by Sex-lethal: cooperative silencing via the 5′ and 3′ UTRs of msl-2 mRNA is independent of the poly(A) tail. EMBO J. 18, 6146–6154 (1999)
  Article CAS PubMed PubMed Central Google Scholar
• Fuss, I. J., Kanof, M. E., Smith, P. D. & Zola, H. Isolation of whole mononuclear cells from peripheral blood and cord blood. Curr. Protoc. Immunol. 85, 7.1.1–7.1.8 (2009)
  Google Scholar
• Becker, T. et al. Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. Nature 482, 501–506 (2012)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003)
  Article PubMed Google Scholar
• Becker, T. et al. Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome. Nature Struct. Mol. Biol. 18, 715–720 (2011)
  Article CAS Google Scholar
• Hirsch, M., Scholkopf, B. & Habeck, M. A blind deconvolution approach for improving the resolution of cryo-EM density maps. J. Comput. Biol. 18, 335–346 (2011)
  Article CAS MathSciNet PubMed Google Scholar
• Lasker, K. et al. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc. Natl Acad. Sci. USA 109, 1380–1387 (2012)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001)
  Article CAS ADS PubMed Google Scholar
• Maden, B. E. et al. Clones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the human ribosomal transcription unit and diversity among clones. Biochem. J. 246, 519–527 (1987)
  Article CAS PubMed PubMed Central Google Scholar
• Tautz, D., Hancock, J. M., Webb, D. A., Tautz, C. & Dover, G. A. Complete sequences of the rRNA genes of Drosophila melanogaster. Mol. Biol. Evol. 5, 366–376 (1988)
  CAS PubMed Google Scholar
• Thompson, J. F., Wegnez, M. R. & Hearst, J. E. Determination of the secondary structure of Drosophila melanogaster 5 S RNA by hydroxymethyltrimethylpsoralen crosslinking. J. Mol. Biol. 147, 417–436 (1981)
  Article CAS PubMed Google Scholar
• Rousset, F., Pelandakis, M. & Solignac, M. Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc. Natl Acad. Sci. USA 88, 10032–10036 (1991)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Dunkle, J. A. et al. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science 332, 981–984 (2011)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Hofacker, I. L. Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429–3431 (2003)
  Article CAS PubMed PubMed Central Google Scholar
• Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673–683 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Humphrey, W., Dalke, A. & Schulten, K. VMD - Visual Molecular Dynamics. J. Mol. Graph. 14, 33–38 (1996)
  Article CAS PubMed Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-Building Tools for Molecular Graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004)
  Article CAS PubMed Google Scholar
• Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007)
  Article CAS PubMed Google Scholar
• Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011)
  Article PubMed PubMed Central Google Scholar
• Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005)
  Article CAS PubMed PubMed Central Google Scholar
• Pettersen, E. F. et al. UCSF Chimera — a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)
  Article CAS PubMed Google Scholar
• Nierhaus, K. H. & Dohme, F. Total reconstitution of functionally active 50S ribosomal subunits from E. coli. Proc. Natl Acad. Sci. USA 71, 4713–4717 (1974)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Márquez, V. et al. Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. J. Mol. Biol. 405, 1215–1232 (2011)
  Article CAS PubMed Google Scholar
• Norousi, R. et al. Automated post-picking using MAPPOS improves particle image detection from cryo-EM micrographs. J. Struct. Biol. http://dx.doi.org/10.1016/j.jsb.2013.02.008 (2013)