Literature DB >> 18400176

Structure of the mammalian 80S ribosome at 8.7 A resolution.

Preethi Chandramouli1, Maya Topf, Jean-François Ménétret, Narayanan Eswar, Jamie J Cannone, Robin R Gutell, Andrej Sali, Christopher W Akey.   

Abstract

In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.

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Year:  2008        PMID: 18400176      PMCID: PMC2775484          DOI: 10.1016/j.str.2008.01.007

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  57 in total

Review 1.  Regulation of eukaryotic translation by the RACK1 protein: a platform for signalling molecules on the ribosome.

Authors:  Jakob Nilsson; Jayati Sengupta; Joachim Frank; Poul Nissen
Journal:  EMBO Rep       Date:  2004-12       Impact factor: 8.807

2.  Software extensions to UCSF chimera for interactive visualization of large molecular assemblies.

Authors:  Thomas D Goddard; Conrad C Huang; Thomas E Ferrin
Journal:  Structure       Date:  2005-03       Impact factor: 5.006

Review 3.  The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer.

Authors:  Joachim Frank; Jayati Sengupta; Haixiao Gao; Wen Li; Mikel Valle; Andrey Zavialov; Måns Ehrenberg
Journal:  FEBS Lett       Date:  2005-02-07       Impact factor: 4.124

4.  Localization and dynamic behavior of ribosomal protein L30e.

Authors:  Mario Halic; Thomas Becker; Joachim Frank; Christian M T Spahn; Roland Beckmann
Journal:  Nat Struct Mol Biol       Date:  2005-05-01       Impact factor: 15.369

5.  Architecture of the ribosome-channel complex derived from native membranes.

Authors:  Jean-François Ménétret; Ramanujan S Hegde; Sven U Heinrich; Preethi Chandramouli; Steven J Ludtke; Tom A Rapoport; Christopher W Akey
Journal:  J Mol Biol       Date:  2005-04-29       Impact factor: 5.469

Review 6.  Structural insights into translational fidelity.

Authors:  James M Ogle; V Ramakrishnan
Journal:  Annu Rev Biochem       Date:  2005       Impact factor: 23.643

7.  Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker.

Authors:  E ter Haar; A Musacchio; S C Harrison; T Kirchhausen
Journal:  Cell       Date:  1998-11-13       Impact factor: 41.582

8.  The cryo-EM structure of a translation initiation complex from Escherichia coli.

Authors:  Gregory S Allen; Andrey Zavialov; Richard Gursky; Måns Ehrenberg; Joachim Frank
Journal:  Cell       Date:  2005-06-03       Impact factor: 41.582

9.  Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis cytosolic ribosomes.

Authors:  Ing-Feng Chang; Kathleen Szick-Miranda; Songqin Pan; Julia Bailey-Serres
Journal:  Plant Physiol       Date:  2005-02-25       Impact factor: 8.340

10.  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.

Authors:  P Dube; G Bacher; H Stark; F Mueller; F Zemlin; M van Heel; R Brimacombe
Journal:  J Mol Biol       Date:  1998-06-05       Impact factor: 5.469

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  79 in total

Review 1.  One core, two shells: bacterial and eukaryotic ribosomes.

Authors:  Sergey Melnikov; Adam Ben-Shem; Nicolas Garreau de Loubresse; Lasse Jenner; Gulnara Yusupova; Marat Yusupov
Journal:  Nat Struct Mol Biol       Date:  2012-06-05       Impact factor: 15.369

2.  Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome.

Authors:  Konstantin N Bulygin; Yulia S Khairulina; Petr M Kolosov; Aliya G Ven'yaminova; Dmitri M Graifer; Yuri N Vorobjev; Ludmila Yu Frolova; Lev L Kisselev; Galina G Karpova
Journal:  RNA       Date:  2010-08-05       Impact factor: 4.942

3.  Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.

Authors:  Jean-Paul Armache; Alexander Jarasch; Andreas M Anger; Elizabeth Villa; Thomas Becker; Shashi Bhushan; Fabrice Jossinet; Michael Habeck; Gülcin Dindar; Sibylle Franckenberg; Viter Marquez; Thorsten Mielke; Michael Thomm; Otto Berninghausen; Birgitta Beatrix; Johannes Söding; Eric Westhof; Daniel N Wilson; Roland Beckmann
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-25       Impact factor: 11.205

4.  Tandem affinity purification combined with inducible shRNA expression as a tool to study the maturation of macromolecular assemblies.

Authors:  Emanuel Wyler; Mirjam Zimmermann; Barbara Widmann; Matthias Gstaiger; Jens Pfannstiel; Ulrike Kutay; Ivo Zemp
Journal:  RNA       Date:  2010-11-19       Impact factor: 4.942

5.  Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.

Authors:  Jean-Paul Armache; Alexander Jarasch; Andreas M Anger; Elizabeth Villa; Thomas Becker; Shashi Bhushan; Fabrice Jossinet; Michael Habeck; Gülcin Dindar; Sibylle Franckenberg; Viter Marquez; Thorsten Mielke; Michael Thomm; Otto Berninghausen; Birgitta Beatrix; Johannes Söding; Eric Westhof; Daniel N Wilson; Roland Beckmann
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-27       Impact factor: 11.205

6.  Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution.

Authors:  Basil J Greber; Daniel Boehringer; Vlatka Godinic-Mikulcic; Ana Crnkovic; Michael Ibba; Ivana Weygand-Durasevic; Nenad Ban
Journal:  J Mol Biol       Date:  2012-01-27       Impact factor: 5.469

7.  Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes.

Authors:  Kelvin Caban; Paul R Copeland
Journal:  J Biol Chem       Date:  2012-02-03       Impact factor: 5.157

Review 8.  Hydroxylation and translational adaptation to stress: some answers lie beyond the STOP codon.

Authors:  M J Katz; L Gándara; A L De Lella Ezcurra; P Wappner
Journal:  Cell Mol Life Sci       Date:  2016-02-13       Impact factor: 9.261

9.  Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.

Authors:  Keren Lasker; Maya Topf; Andrej Sali; Haim J Wolfson
Journal:  J Mol Biol       Date:  2009-02-20       Impact factor: 5.469

Review 10.  Growing with the wind. Ribosomal protein hydroxylation and cell growth.

Authors:  Maximiliano J Katz; Julieta M Acevedo; Pablo Wappner
Journal:  Fly (Austin)       Date:  2014-10-31       Impact factor: 2.160

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