Structures of the bacterial ribosome at 3.5 A resolution.

PubWeight™: 12.63‹?› | Rank: Top 0.1% | All-Time Top 10000

🔗 View Article (PMID 16272117)

Published in Science on November 04, 2005

Authors

Barbara S Schuwirth1, Maria A Borovinskaya, Cathy W Hau, Wen Zhang, Antón Vila-Sanjurjo, James M Holton, Jamie H Doudna Cate

Author Affiliations

1: Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Articles citing this

(truncated to the top 100)

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure (2008) 5.97

Structure of the yeast mitochondrial large ribosomal subunit. Science (2014) 4.81

The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science (2009) 4.26

Following translation by single ribosomes one codon at a time. Nature (2008) 4.14

What recent ribosome structures have revealed about the mechanism of translation. Nature (2009) 4.01

Identification of two distinct hybrid state intermediates on the ribosome. Mol Cell (2007) 4.00

The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics. Antimicrob Agents Chemother (2006) 3.94

Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol Cell (2008) 3.58

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature (2010) 3.48

Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid. Mol Microbiol (2007) 3.47

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res (2008) 3.37

The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol (2009) 3.21

Tilt-pair analysis of images from a range of different specimens in single-particle electron cryomicroscopy. J Mol Biol (2011) 3.16

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science (2011) 3.14

Structures of the ribosome in intermediate states of ratcheting. Science (2009) 2.96

The building blocks and motifs of RNA architecture. Curr Opin Struct Biol (2006) 2.94

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol (2007) 2.81

Ribosome biogenesis and the translation process in Escherichia coli. Microbiol Mol Biol Rev (2007) 2.59

Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A (2006) 2.55

Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J (2007) 2.48

The process of mRNA-tRNA translocation. Proc Natl Acad Sci U S A (2007) 2.45

Following movement of the L1 stalk between three functional states in single ribosomes. Proc Natl Acad Sci U S A (2009) 2.40

Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A (2010) 2.38

In vitro activity of TR-700, the antibacterial moiety of the prodrug TR-701, against linezolid-resistant strains. Antimicrob Agents Chemother (2008) 2.38

Unusual biology across a group comprising more than 15% of domain Bacteria. Nature (2015) 2.34

Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell (2011) 2.29

A beginner's guide to radiation damage. J Synchrotron Radiat (2009) 2.26

Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob Agents Chemother (2007) 2.23

Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly. Nature (2008) 2.19

A new system for naming ribosomal proteins. Curr Opin Struct Biol (2014) 2.18

Elongation factor G bound to the ribosome in an intermediate state of translocation. Science (2013) 2.12

Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure (2008) 2.11

Comprehensive molecular structure of the eukaryotic ribosome. Structure (2009) 2.04

Frameshifting RNA pseudoknots: structure and mechanism. Virus Res (2008) 2.02

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc Natl Acad Sci U S A (2010) 1.99

New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA (2007) 1.98

Frequency and isostericity of RNA base pairs. Nucleic Acids Res (2009) 1.88

Irreversible chemical steps control intersubunit dynamics during translation. Proc Natl Acad Sci U S A (2008) 1.88

A hierarchical model for evolution of 23S ribosomal RNA. Nature (2009) 1.87

Structure and dynamics of a processive Brownian motor: the translating ribosome. Annu Rev Biochem (2010) 1.84

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science (2013) 1.84

Intersubunit movement is required for ribosomal translocation. Proc Natl Acad Sci U S A (2007) 1.83

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res (2014) 1.82

Structural dynamics of the ribosome. Curr Opin Chem Biol (2008) 1.79

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning. Proc Natl Acad Sci U S A (2008) 1.78

One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol (2012) 1.77

Navigating the ribosome's metastable energy landscape. Trends Biochem Sci (2009) 1.74

The ribosome uses two active mechanisms to unwind messenger RNA during translation. Nature (2011) 1.74

Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications. ACS Chem Biol (2007) 1.73

Spontaneous formation of the unlocked state of the ribosome is a multistep process. Proc Natl Acad Sci U S A (2009) 1.71

Quantitative proteomic analysis of ribosome assembly and turnover in vivo. J Mol Biol (2010) 1.71

Resistance to linezolid caused by modifications at its binding site on the ribosome. Antimicrob Agents Chemother (2011) 1.70

Heterogeneity of large macromolecular complexes revealed by 3D cryo-EM variance analysis. Structure (2008) 1.70

SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center. PLoS Biol (2011) 1.68

Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proc Natl Acad Sci U S A (2010) 1.68

alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel. Nat Struct Mol Biol (2010) 1.68

The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly. J Bacteriol (2006) 1.67

Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol Cell (2011) 1.65

A steric block in translation caused by the antibiotic spectinomycin. ACS Chem Biol (2007) 1.64

Initiation of ribosome degradation during starvation in Escherichia coli. RNA (2009) 1.61

Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing. Nucleic Acids Res (2009) 1.61

Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy. Structure (2015) 1.61

The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA (2007) 1.60

GTP hydrolysis by IF2 guides progression of the ribosome into elongation. Mol Cell (2009) 1.59

Chain dynamics of nascent polypeptides emerging from the ribosome. ACS Chem Biol (2008) 1.59

An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. BMC Biol (2006) 1.58

Optimization of ribosome structure and function by rRNA base modification. PLoS One (2007) 1.57

Following the intersubunit conformation of the ribosome during translation in real time. Nat Struct Mol Biol (2010) 1.56

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol (2007) 1.53

Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain. Proc Natl Acad Sci U S A (2009) 1.53

Structural analysis of kasugamycin inhibition of translation. Nat Struct Mol Biol (2006) 1.51

From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. RNA (2008) 1.48

Origin and evolution of the ribosome. Cold Spring Harb Perspect Biol (2010) 1.47

Structure of the human 80S ribosome. Nature (2015) 1.47

Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. J Mol Biol (2012) 1.46

Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. Proc Natl Acad Sci U S A (2007) 1.46

The interaction networks of structured RNAs. Nucleic Acids Res (2006) 1.45

Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu. Q Rev Biophys (2009) 1.45

Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43

Changes produced by bound tryptophan in the ribosome peptidyl transferase center in response to TnaC, a nascent leader peptide. Proc Natl Acad Sci U S A (2006) 1.43

Structural characterization of mRNA-tRNA translocation intermediates. Proc Natl Acad Sci U S A (2012) 1.42

mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Nat Struct Mol Biol (2011) 1.42

The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome. Nat Struct Mol Biol (2010) 1.42

Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol (2013) 1.41

Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J (2008) 1.41

U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome. J Mol Biol (2009) 1.39

Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome. RNA (2011) 1.39

Correlated conformational events in EF-G and the ribosome regulate translocation. Nat Struct Mol Biol (2010) 1.39

Forespore engulfment mediated by a ratchet-like mechanism. Cell (2006) 1.38

Structure of a mitochondrial ribosome with minimal RNA. Proc Natl Acad Sci U S A (2009) 1.38

Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3. Proc Natl Acad Sci U S A (2011) 1.37

Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex. Mol Cell (2008) 1.37

Rotation of the head of the 30S ribosomal subunit during mRNA translocation. Proc Natl Acad Sci U S A (2012) 1.36

The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol (2010) 1.35

The ribosome as a conveying thermal ratchet machine. J Biol Chem (2009) 1.34

Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem (2006) 1.33

Ribosomal translocation: one step closer to the molecular mechanism. ACS Chem Biol (2009) 1.33

Deconstructing ribosome construction. Trends Biochem Sci (2009) 1.31

Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. EMBO J (2007) 1.31

Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit. J Cell Biol (2010) 1.30

Articles by these authors

Femtosecond X-ray protein nanocrystallography. Nature (2011) 14.34

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol (2010) 9.01

The first metal-organic framework (MOF) of Imazethapyr and its SHG, piezoelectric and ferroelectric properties. Dalton Trans (2008) 8.86

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell (2008) 7.93

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell (2004) 7.32

Hydrogen-bonded ferroelectrics based on metal-organic coordination. J Am Chem Soc (2009) 6.69

Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21

Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91

Supramolecular bola-like ferroelectric: 4-methoxyanilinium tetrafluoroborate-18-crown-6. J Am Chem Soc (2011) 4.73

Diisopropylammonium chloride: a ferroelectric organic salt with a high phase transition temperature and practical utilization level of spontaneous polarization. Adv Mater (2011) 4.30

High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell (2004) 4.18

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science (2011) 3.14

Improved virological outcomes in British Columbia concomitant with decreasing incidence of HIV type 1 drug resistance detection. Clin Infect Dis (2010) 3.12

A panoramic view of yeast noncoding RNA processing. Cell (2003) 3.11

Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature (2007) 3.05

Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A (2011) 2.92

A multiferroic perdeutero metal-organic framework. Angew Chem Int Ed Engl (2011) 2.88

DAPK1 interaction with NMDA receptor NR2B subunits mediates brain damage in stroke. Cell (2010) 2.87

Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals. Acta Crystallogr A (2011) 2.86

Net primary production of Chinese croplands from 1950 to 1999. Ecol Appl (2007) 2.61

Structural and mechanistic studies of VPS4 proteins. EMBO J (2005) 2.58

Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A (2006) 2.55

Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Mol Biol (2007) 2.54

Determination of X-ray flux using silicon pin diodes. J Synchrotron Radiat (2009) 2.44

Time-resolved protein nanocrystallography using an X-ray free-electron laser. Opt Express (2012) 2.38

Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol (2004) 2.37

Crystallographic data processing for free-electron laser sources. Acta Crystallogr D Biol Crystallogr (2013) 2.36

Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet (2005) 2.26

Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. Mol Cell (2005) 2.26

The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Mol Cell (2003) 2.25

Ubiquitin recognition by the human TSG101 protein. Mol Cell (2004) 2.17

Automated electron-density sampling reveals widespread conformational polymorphism in proteins. Protein Sci (2010) 2.16

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat Genet (2005) 2.15

Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Phys Rev B Condens Matter Mater Phys (2011) 2.05

Adenomatous polyposis coli (APC) differentially regulates beta-catenin phosphorylation and ubiquitination in colon cancer cells. J Biol Chem (2006) 1.86

IKK mediates ischemia-induced neuronal death. Nat Med (2005) 1.83

Structural insight into KCNQ (Kv7) channel assembly and channelopathy. Neuron (2007) 1.81

Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol (2007) 1.80

Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nat Struct Mol Biol (2008) 1.78

Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histone acetylation. J Biol Chem (2007) 1.78

The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl (2010) 1.76

A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Nat Struct Mol Biol (2004) 1.72

Vascular gene expression in nonneoplastic and malignant brain. Am J Pathol (2004) 1.71

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J Synchrotron Radiat (2004) 1.70

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr (2013) 1.69

Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathways. Mol Cancer Res (2003) 1.67

Azide-bridged one-dimensional Mn(III) polymers: effects of side group of Schiff base ligands on structure and magnetism. Inorg Chem (2007) 1.65

Statistical resynchronization and Bayesian detection of periodically expressed genes. Nucleic Acids Res (2004) 1.64

Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics (2009) 1.61

Diisopropylammonium bromide is a high-temperature molecular ferroelectric crystal. Science (2013) 1.61

Specificity of Distalless repression and limb primordia development by abdominal Hox proteins. Dev Cell (2002) 1.61

Nuclear factor-kappaB contributes to infarction after permanent focal ischemia. Stroke (2004) 1.58

X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci U S A (2003) 1.58

Polymorphism of antigen MPT64 in Mycobacterium tuberculosis strains. J Clin Microbiol (2013) 1.56

Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell (2007) 1.56

X-ray fluorescence microscopy reveals large-scale relocalization and extracellular translocation of cellular copper during angiogenesis. Proc Natl Acad Sci U S A (2007) 1.55

Structural analysis of kasugamycin inhibition of translation. Nat Struct Mol Biol (2006) 1.51

Clinical parameter and Th17 related to lymphocytes infiltrating degree of labial salivary gland in primary Sjögren's syndrome. Clin Rheumatol (2014) 1.47

KLF4 interacts with beta-catenin/TCF4 and blocks p300/CBP recruitment by beta-catenin. Mol Cell Biol (2009) 1.44

Major vascular involvement in Behçet's disease: a retrospective study of 796 patients. Clin Rheumatol (2013) 1.44

A systematic review of the effectiveness of oral health promotion activities among patients with cardiovascular disease. Int J Cardiol (2010) 1.43

Renal involvement and followup of 130 patients with primary Sjögren's syndrome. J Rheumatol (2007) 1.43

Distinct functions of homeodomain-containing and homeodomain-less isoforms encoded by homothorax. Genes Dev (2006) 1.42

Associations between salivary gland histopathologic diagnoses and phenotypic features of Sjögren's syndrome among 1,726 registry participants. Arthritis Rheum (2011) 1.42

Monitoring G-protein-coupled receptor signaling with DNA microarrays and real-time polymerase chain reaction. Methods Enzymol (2002) 1.41

Bim and Noxa are candidates to mediate the deleterious effect of the NF-kappa B subunit RelA in cerebral ischemia. J Neurosci (2006) 1.40

Development of gene silencing pyrrole-imidazole polyamide targeting the TGF-beta1 promoter for treatment of progressive renal diseases. J Am Soc Nephrol (2005) 1.39

Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature (2010) 1.36

A combined 1H-NMR spectroscopy- and mass spectrometry-based metabolomic study of the PPAR-alpha null mutant mouse defines profound systemic changes in metabolism linked to the metabolic syndrome. Physiol Genomics (2006) 1.34

Mechanism of photogenerated reactive oxygen species and correlation with the antibacterial properties of engineered metal-oxide nanoparticles. ACS Nano (2012) 1.33

Predicting progression of IgA nephropathy: new clinical progression risk score. PLoS One (2012) 1.30

Supranormal myocardial creatine and phosphocreatine concentrations lead to cardiac hypertrophy and heart failure: insights from creatine transporter-overexpressing transgenic mice. Circulation (2005) 1.30

Profilin 1 obtained by proteomic analysis in all-trans retinoic acid-treated hepatocarcinoma cell lines is involved in inhibition of cell proliferation and migration. Proteomics (2006) 1.27

Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis. Antimicrob Agents Chemother (2010) 1.27

NF-kappaB-dependent microRNA-425 upregulation promotes gastric cancer cell growth by targeting PTEN upon IL-1β induction. Mol Cancer (2014) 1.27

Unique evolutionary pattern of numbers of gramineous NBS-LRR genes. Mol Genet Genomics (2010) 1.24

Mycophenolate mofetil in induction and maintenance therapy of severe lupus nephritis: a meta-analysis of randomized controlled trials. Nephrol Dial Transplant (2007) 1.24

Coexistence of magnetic and electric orderings in the metal-formate frameworks of [NH4][M(HCOO)3]. J Am Chem Soc (2011) 1.24

Regulation of the potential marker for intestinal cells, Bmi1, by β-catenin and the zinc finger protein KLF4: implications for colon cancer. J Biol Chem (2011) 1.23

Recombination analysis reveals a double recombination event in hepatitis E virus. Virol J (2010) 1.22

Hydrogencyanamide-bridged one-dimensional polymers built on Mn(III)-Schiff base fragments: synthesis, structure, and magnetism. Chemistry (2007) 1.22

Characterizing IgG4-related disease with ¹⁸F-FDG PET/CT: a prospective cohort study. Eur J Nucl Med Mol Imaging (2014) 1.21

Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res (2010) 1.21

Genomic characterization and high prevalence of bocaviruses in swine. PLoS One (2011) 1.19

A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23. Nat Genet (2013) 1.19

Are CD4+CD25-Foxp3+ cells in untreated new-onset lupus patients regulatory T cells? Arthritis Res Ther (2009) 1.19

In vitro and in vivo evaluation of a melamine dendrimer as a vehicle for drug delivery. Int J Pharm (2004) 1.19

Metabolomics of the interaction between PPAR-alpha and age in the PPAR-alpha-null mouse. Mol Syst Biol (2009) 1.18

Tumor necrosis factor-like weak inducer of apoptosis-induced neurodegeneration. J Neurosci (2004) 1.18

Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. New Phytol (2009) 1.18

Allosteric control of the ribosome by small-molecule antibiotics. Nat Struct Mol Biol (2012) 1.17

Genistein induces pancreatic beta-cell proliferation through activation of multiple signaling pathways and prevents insulin-deficient diabetes in mice. Endocrinology (2010) 1.17

Clinical and prognostic characteristics of 573 cases of primary Sjögren's syndrome. Chin Med J (Engl) (2010) 1.15

Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology. J Clin Microbiol (2013) 1.15