EttA regulates translation by binding to the ribosomal E site and restricting ribosome-tRNA dynamics

[1]  J. Frank,et al.  The ABC-F protein EttA gates ribosome entry into the translation elongation cycle , 2014, Nature Structural &Molecular Biology.

[2]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[3]  Henning Urlaub,et al.  EF-P Is Essential for Rapid Synthesis of Proteins Containing Consecutive Proline Residues , 2013, Science.

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

[5]  Shaoxia Chen,et al.  Prevention of overfitting in cryo-EM structure determination , 2012, Nature Methods.

[6]  Klaus Schulten,et al.  Structural characterization of mRNA-tRNA translocation intermediates , 2012, Proceedings of the National Academy of Sciences.

[7]  Stephan Wickles,et al.  Structural basis of highly conserved ribosome recycling in eukaryotes and archaea , 2012, Nature.

[8]  Sjors H.W. Scheres,et al.  A Bayesian View on Cryo-EM Structure Determination , 2012, 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI).

[9]  J. Gerring A case study , 2011, Technology and Society.

[10]  Jonathan E. Bronson,et al.  Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis , 2011, Nature Structural &Molecular Biology.

[11]  Jue Chen,et al.  Crystal Structure of the Maltose Transporter in a Pretranslocation Intermediate State , 2011, Science.

[12]  Vincent B. Chen,et al.  Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding , 2011, Science.

[13]  R. Tampé,et al.  Ribosome recycling depends on a mechanistic link between the FeS cluster domain and a conformational switch of the twin-ATPase ABCE1 , 2011, Proceedings of the National Academy of Sciences.

[14]  John F Hunt,et al.  Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant. , 2010, Protein engineering, design & selection : PEDS.

[15]  R. Ficner,et al.  The iron–sulphur protein RNase L inhibitor functions in translation termination , 2010, EMBO reports.

[16]  J. M. Sauder,et al.  Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry. , 2010, Journal of molecular biology.

[17]  M. Hentze,et al.  The role of ABCE1 in eukaryotic posttermination ribosomal recycling. , 2010, Molecular cell.

[18]  Yong-Gui Gao,et al.  The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State , 2009, Science.

[19]  V. Ramakrishnan,et al.  What recent ribosome structures have revealed about the mechanism of translation , 2009, Nature.

[20]  Jake M. Hofman,et al.  Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation , 2009, Proceedings of the National Academy of Sciences.

[21]  T. Steitz,et al.  Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome , 2009, Science.

[22]  R. L. Gonzalez,et al.  Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling , 2009, Nature Structural &Molecular Biology.

[23]  Colin Echeverría Aitken,et al.  GTP hydrolysis by IF2 guides progression of the ribosome into elongation. , 2009, Molecular cell.

[24]  V. Ramakrishnan,et al.  Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome , 2009, Nature Structural &Molecular Biology.

[25]  Taekjip Ha,et al.  Following movement of the L1 stalk between three functional states in single ribosomes , 2009, Proceedings of the National Academy of Sciences.

[26]  Klaus Schulten,et al.  Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis , 2009, Proceedings of the National Academy of Sciences.

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

[28]  Jianlin Lei,et al.  Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. , 2008, Molecular cell.

[29]  Y. Mechulam,et al.  A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis , 2008, Nucleic acids research.

[30]  Taekjip Ha,et al.  Spontaneous intersubunit rotation in single ribosomes. , 2008, Molecular cell.

[31]  Jue Chen,et al.  Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems , 2008, Microbiology and Molecular Biology Reviews.

[32]  R. L. Gonzalez,et al.  Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. , 2008, Molecular cell.

[33]  Leonardo G. Trabuco,et al.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. , 2008, Structure.

[34]  K. Hopfner,et al.  X-ray Structure of the Complete ABC Enzyme ABCE1 from Pyrococcus abyssi* , 2008, Journal of Biological Chemistry.

[35]  T. Steitz A structural understanding of the dynamic ribosome machine , 2008, Nature Reviews Molecular Cell Biology.

[36]  Joachim Frank,et al.  Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes , 2008, Nature Protocols.

[37]  O. Uhlenbeck,et al.  [3'-32P]-labeling tRNA with nucleotidyltransferase for assaying aminoacylation and peptide bond formation. , 2008, Methods.

[38]  Joachim Frank,et al.  The process of mRNA–tRNA translocation , 2007, Proceedings of the National Academy of Sciences.

[39]  Steven Chu,et al.  Fluctuations of transfer RNAs between classical and hybrid states. , 2007, Biophysical journal.

[40]  H. Rubin,et al.  Characterization of Nucleotide Pools as a Function of Physiological State in Escherichia coli , 2007, Journal of bacteriology.

[41]  Daniel N. Wilson,et al.  The Weird and Wonderful World of Bacterial Ribosome Regulation , 2007, Critical reviews in biochemistry and molecular biology.

[42]  Thomas Becker,et al.  Structure of eEF3 and the mechanism of transfer RNA release from the E-site , 2006, Nature.

[43]  R. Dawson,et al.  Structure of a bacterial multidrug ABC transporter , 2006, Nature.

[44]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[45]  Anchi Cheng,et al.  Automated molecular microscopy: the new Leginon system. , 2005, Journal of structural biology.

[46]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[47]  Y. Ivanov,et al.  70-S ribosomes of Escherichia coli have an additional site for deacylated tRNA binding. , 2005, European journal of biochemistry.

[48]  B. S. Laursen,et al.  Initiation of Protein Synthesis in Bacteria , 2005, Microbiology and Molecular Biology Reviews.

[49]  Paola Vergani,et al.  CFTR channel opening by ATP-driven tight dimerization of its nucleotide-binding domains , 2005, Nature.

[50]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

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

[52]  Steven Chu,et al.  tRNA dynamics on the ribosome during translation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Rachel Green,et al.  The Active Site of the Ribosome Is Composed of Two Layers of Conserved Nucleotides with Distinct Roles in Peptide Bond Formation and Peptide Release , 2004, Cell.

[54]  Scott M Stagg,et al.  Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy , 2003, Nature Structural Biology.

[55]  Joachim Frank,et al.  Locking and Unlocking of Ribosomal Motions , 2003, Cell.

[56]  John F Hunt,et al.  ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer. , 2002, Molecular cell.

[57]  O. Uhlenbeck,et al.  Modulation of tRNAAla identity by inorganic pyrophosphatase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Alexander D. MacKerell,et al.  CHARMM: The Energy Function and Its Parameterization , 2002 .

[59]  J. Hunt,et al.  Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter. , 2001, Structure.

[60]  Joachim Frank,et al.  Visualization of Trna Movements on the Escherichia coli 70s Ribosome during the Elongation Cycle , 2000, The Journal of cell biology.

[61]  Joachim Frank,et al.  A ratchet-like inter-subunit reorganization of the ribosome during translocation , 2000, Nature.

[62]  John A. Tainer,et al.  Structural Biology of Rad50 ATPase ATP-Driven Conformational Control in DNA Double-Strand Break Repair and the ABC-ATPase Superfamily , 2000, Cell.

[63]  J. Frank,et al.  Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution , 2000, Cell.

[64]  Joachim Frank,et al.  EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome , 1999, Nature Structural Biology.

[65]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[66]  J. Frank Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State , 1996 .

[67]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[68]  D. E. Atkinson,et al.  Adenylate Energy Charge in Escherichia coli During Growth and Starvation , 1971, Journal of bacteriology.

[69]  Margaret M. Elvekrog,et al.  A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis. , 2010, Methods in enzymology.

[70]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[71]  J Frank,et al.  Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study. , 2004, Journal of structural biology.

[72]  Mathias Sprinzl,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 1993, Nucleic Acids Res..

[73]  A. Spirin Ribosomal translocation: facts and models. , 1985, Progress in nucleic acid research and molecular biology.