Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes

[1]  V. G. Panse,et al.  Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation , 2016, Cell.

[2]  E. Hurt,et al.  Architecture of the Rix1–Rea1 checkpoint machinery during pre-60S-ribosome remodeling , 2015, Nature Structural &Molecular Biology.

[3]  E. Hurt,et al.  The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins , 2015, Cell.

[4]  N. Leulliot,et al.  Chaperoning 5S RNA assembly , 2015, Genes & development.

[5]  Satyavati Kharde,et al.  The structure of Rpf2–Rrs1 explains its role in ribosome biogenesis , 2015, Nucleic acids research.

[6]  S. Baserga,et al.  A protein interaction map of the LSU processome , 2015, Genes & development.

[7]  I. Tanaka,et al.  Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis , 2015, Nucleic acids research.

[8]  Sarah A. Clark,et al.  A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation , 2014, The Journal of cell biology.

[9]  V. Ramakrishnan,et al.  Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome , 2014, Cell.

[10]  S. Sanyal,et al.  Structural and Functional Insights into the Mode of Action of a Universally Conserved Obg GTPase , 2014, PLoS biology.

[11]  Alan Brown,et al.  Structure of the Yeast Mitochondrial Large Ribosomal Subunit , 2014, Science.

[12]  Christoph Leidig,et al.  60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle , 2014, Nature Communications.

[13]  Hemant D. Tagare,et al.  The Local Resolution of Cryo-EM Density Maps , 2013, Nature Methods.

[14]  D. Tollervey,et al.  Coupled GTPase and remodeling ATPase activities form a checkpoint for ribosome export , 2013, Nature.

[15]  Yang Zhang,et al.  The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.

[16]  R. Henderson,et al.  High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆ , 2013, Ultramicroscopy.

[17]  J. Woolford,et al.  Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae , 2013, Genetics.

[18]  J. Woolford,et al.  Has1 regulates consecutive maturation and processing steps for assembly of 60S ribosomal subunits , 2013, Nucleic acids research.

[19]  Daniel W. A. Buchan,et al.  Scalable web services for the PSIPRED Protein Analysis Workbench , 2013, Nucleic Acids Res..

[20]  D. Agard,et al.  Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM , 2013, Nature Methods.

[21]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[22]  Daniel Boehringer,et al.  Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit , 2012, Nature Structural &Molecular Biology.

[23]  Gernot Fruhmann,et al.  Rlp24 activates the AAA-ATPase Drg1 to initiate cytoplasmic pre-60S maturation , 2012, The Journal of cell biology.

[24]  D. Tollervey,et al.  Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel , 2012, Nature Structural &Molecular Biology.

[25]  J. Woolford,et al.  Ribosomal proteins L7 and L8 function in concert with six A₃ assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits. , 2012, RNA.

[26]  M. Dong,et al.  Identification of cross-linked peptides from complex samples , 2012, Nature Methods.

[27]  J. Woolford,et al.  Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae , 2012, Nucleic acids research.

[28]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[29]  Sergey Melnikov,et al.  The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution , 2011, Science.

[30]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[31]  N. Ban,et al.  Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6 , 2011, Science.

[32]  J. Strahler,et al.  Assembly of Saccharomyces cerevisiae 60S ribosomal subunits: role of factors required for 27S pre‐rRNA processing , 2011, The EMBO journal.

[33]  E. Petfalski,et al.  A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease , 2011, The EMBO journal.

[34]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[35]  Arlen W. Johnson,et al.  Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit , 2010, The Journal of cell biology.

[36]  V. G. Panse,et al.  Maturation of eukaryotic ribosomes: acquisition of functionality. , 2010, Trends in biochemical sciences.

[37]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[38]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[39]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[40]  D. Tollervey,et al.  The Final Step in 5.8S rRNA Processing Is Cytoplasmic in Saccharomyces cerevisiae , 2009, Molecular and Cellular Biology.

[41]  B. Böttcher,et al.  Mechanochemical Removal of Ribosome Biogenesis Factors from Nascent 60S Ribosomal Subunits , 2009, Cell.

[42]  J. Frank,et al.  SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs , 2008, Nature Protocols.

[43]  G. Machado-Santelli,et al.  Nop53p interacts with 5.8S rRNA co‐transcriptionally, and regulates processing of pre‐rRNA by the exosome , 2008, The FEBS journal.

[44]  Micheline Fromont-Racine,et al.  60S ribosomal subunit assembly dynamics defined by semi-quantitative mass spectrometry of purified complexes , 2008, Nucleic acids research.

[45]  Norman Stein,et al.  CHAINSAW: a program for mutating pdb files used as templates in molecular replacement , 2008 .

[46]  T. Hughes,et al.  Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. , 2007, Genes & development.

[47]  I. J. van der Klei,et al.  Cytoplasmic Recycling of 60S Preribosomal Factors Depends on the AAA Protein Drg1 , 2007, Molecular and Cellular Biology.

[48]  Wen Jiang,et al.  EMAN2: an extensible image processing suite for electron microscopy. , 2007, Journal of structural biology.

[49]  Joachim Frank,et al.  Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. , 2005, Journal of structural biology.

[50]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[51]  P. Gleizes,et al.  Sequential Protein Association with Nascent 60S Ribosomal Particles , 2003, Molecular and Cellular Biology.

[52]  N. Grigorieff,et al.  Accurate determination of local defocus and specimen tilt in electron microscopy. , 2003, Journal of structural biology.

[53]  Rupert De Wachter,et al.  RnaViz 2: an improved representation of RNA secondary structure , 2003, Bioinform..

[54]  J. Yates,et al.  DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. , 2002, Journal of proteome research.

[55]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[56]  P. Gleizes,et al.  Nog2p, a putative GTPase associated with pre‐60S subunits and required for late 60S maturation steps , 2001, The EMBO journal.

[57]  Stephen K. Burley,et al.  Crystal structures of ribosome anti-association factor IF6 , 2000, Nature Structural Biology.

[58]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[59]  P. Mitchell,et al.  The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. , 1996, Genes & development.