The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 Å resolution

Journal of Molecular Biology

Volumn 298, Issue 1, 2000, Pages 35-59

  Mueller, Florian ^a   Sommer, Ingolf ^a   Baranov, Pavel ^b   Matadeen, Rishi ^c   Stoldt, Matthias ^d   Wöhnert, Jens ^d   Görlach, Matthias ^d   Van Heel, Marin ^c   Brimacombe, Richard ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

Atomic structures of ribosomal components; Computer modelling; Cross links and foot prints; Cryo electron microscopy; Functional sites on rRNA

Indexed keywords

AMINO ACID; PEPTIDE; PEPTIDYLTRANSFERASE; RIBOSOME PROTEIN; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; CROSS LINKING; CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; RIBOSOME SUBUNIT;

ESCHERICHIA COLI;

EID: 0034696756     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3635     Document Type: Article

References (102)

1. Ribosomal protein L9 interacts with 23 S rRNA: The use of a translational bypass assay to study the effect of amino acid substitutions
2. Direct visualization of A-, P- and E-site transfer RNAs in the E. coli ribosome
3. Visualization of elongation factor G on the E. coli 70 S ribosome: The mechanism of translocation
4. Effect of buffer conditions on the position of tRNA on the 70 S ribosome as visualized by cryoelectron microscopy
5. A 9 Å resolution X-ray crystallographic map of the large ribosomal subunit
6. Placement of protein and RNA structures into a 5 Å-resolution map of the 50 S ribosomal subunit
7. New features of 23 S ribosomal RNA folding: The long helix 41-42 makes a 'U-turn' inside the ribosome
8. The database of ribosomal cross-links: An update
9. Alignment of conduits for the nascent polypeptide in the ribosome-Sec61 complex
10. Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: Immune mapping of the nascent chain
11. The structure of ribosomal RNA: A three-dimensional jigsaw puzzle
12. The structure of ribosomal RNA
13. A detailed model for the three-dimensional structure of E. coli 16 S ribosomal RNA in situ in the 30 S subunit
14. Clustering of modified nucleotides at the fuctional center of bacterial ribosomal RNA
15. Three-dimensional organization of the bacterial ribosome and its subunits: The transition from low-resolution models to high-resolution structures
16. CHARMM: A program for macromolecular energy, minimization and dynamics calculations
17. Regions of 23 S ribosomal RNA proximal to transfer RNA bound at the P and E sites
18. Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of E. coli
19. X-ray crystal structures of 70 S ribosome functional complexes
20. The path of the growing peptide chain through the 23 S rRNA in the 50 S ribosomal subunit; a comparative cross-linking study with three different peptide families
21. Structure of a bacterial 30 S ribosomal subunit at 5.5 Å resolution
22. Crystal structure of a conserved ribosomal protein - RNA complex
23. Metals, motifs and recognition in the crystal structure of a 5 S rRNA domain
24. Crystal structure of the ribosomal RNA domain essential for binding elongation factors
25. Identification of an RNA-protein bridge spanning the ribosomal subunit interface
26. The loop E-loop D region of E. coli 5 S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins
27. The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus
28. Correlation of the expansion segments in mammalian rRNA with the fine structure of the rabbit reticulocyte ribosome at 21 Å resolution
29. The site of action of alpha sarcin on eukaryotic ribosomes
30. The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28 S ribosomal RNA caused by the toxins
31. 5 S RNA secondary structure
32. Secondary structure of the large subunit ribosomal RNA from E. coli, Z. mays chloroplast, and human and mouse mitochondrial ribosomes
33. The allosteric three-site model for the ribosomal elongation cycle: An analysis with a heteropolymeric mRNA
34. Ribosomal protein L6: Structural evidence of gene duplication from a primitive RNA binding protein
35. Ribosomes and translation
36. Ribosomecatalyzed peptide-bond formation with an A-site substrate covalently linked to 23 S ribosomal RNA
37. The cross-link from the upstream region of mRNA to ribosomal protein S7 is located in the C-terminal peptide; experimental verification of a prediction from modelling studies
38. A compilation of large subunit RNA sequences presented in a structural format
39. Lessons from an evolving rRNA: 16 S and 23 S rRNA structures from a comparative perspective
40. Elucidating the structure of ribosomal particles: An interplay between electron cryo-microscopy and X-ray crystallography
41. The RNA binding domain of ribosomal protein L11: Three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA
42. Ribosomal protein L9: A structure determination by the combined use of X-ray crystallography and NMR spectroscopy
43. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA
44. Folding of an enzyme into an active conformation while bound as peptidyl tRNA to the ribosome
45. Evolutionary relationships amongst archaebacteria: A comparative study of 23 S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen
46. Crystal structure of the C-terminal domain of the ribosomal protein L7/L12 from E. coli at 1.7 Å
47. A common motif organizes the structure of multihelix loops in 16 S and 23 S ribosomal RNAs
48. Enzymatic activity of the ribosome bound nascent peptide
49. A quantitative model of the E. coli 16 S RNA in the 30 S ribosomal subunit
50. E. coli 70 S ribosome at 15 Å resolution by cryo-electron microscopy: Localization of fMet-tRNA(fMet) and fitting of L1 protein
51. High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA
52. The E. coli large ribosomal subunit at 7.5 Å resolution
53. Interprotein distances within the large subunit from E. coli ribosomes
54. Selective isolation and detailed analysis of intra-RNA cross-links induced in the large ribosomal subunit of E. coli; a model for the tertiary structure of the tRNA binding domain in 23 S RNA
55. Identification of intermolecular cross-links at the subunit interface of the E. coli ribosome
56. Site-directed cross-linking studies on the E. coli tRNA-ribosome complex; determination of sites labelled with an aromatic azide attached to the variable loop or aminoacyl group of tRNA
57. Interaction of tRNA with 23 S rRNA in the ribosomal A, P and E sites
58. Sites of interaction of the CCA end of peptidyl-tRNA with 23 S rRNA
59. Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23 S RNA
60. A new model for the three-dimensional folding of E. coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 Å
61. A new model for the three-dimensional folding of E. coli 16 S ribosomal RNA. II. The RNA-protein interaction data
62. A new model for the three-dimensional folding of E. coli 16 S ribosomal RNA. III. The topography of the functional centre
63. The ribosome-in-pieces: Binding of elongation factor EF-G to oligo-ribonucleotides that mimic the sarcin/ricin and thiostrepton domains of 23 S ribosomal RNA
64. Prediction of three-dimensional structure of E. coli ribosomal RNA
65. The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome
66. Crystal structure of the RNA binding ribosomal protein L1 from Thermus thermophilus
67. Crystal structure of the ternary complex of Phe-tRNA(Phe), EF-Tu and a GTP analog
68. Secondary structure model for 23 S ribosomal RNA
69. The pseudouridine residues of rRNA: Number, location, biosynthesis, and function
70. The environment of 5 S rRNA in the ribosome: Cross-links to 23 S rRNA from sites within helices II and III of the 5 S molecule
71. The ribosomal neighbourhood of the central fold of tRNA; cross-links from position 47 of tRNA located at the A, P or E site
72. Structure of a conserved RNA component of the peptidyl transferase centre
73. The ribosomal environment of tRNA: Cross-links to rRNA from positions 8 and 20:1 in the central fold of tRNA located at the A, P or E site
74. Does the channel for nascent peptide exist inside the ribosome? Immune electron microscopy study
75. A base-pair between tRNA and 23 S rRNA in the peptidyl transferase centre of the ribosome
76. The environment of 5 S rRNA in the ribosome: Cross-links to the GTPase-associated area of 23 S rRNA
77. Methylation sites in E. coli ribosomal RNA: Localization and identification of four new sites of methylation in 23 S rRNA
78. Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryoelectron microscopy
79. Contacts between the growing peptide chain and the 23 S RNA in the 50 S ribosomal subunit
80. Mapping the path of the nascent peptide chain through the 23 S RNA in the 50 S ribosomal subunit
81. The 70 S E. coli ribosome at 23 Å resolution; fitting the ribosomal RNA
82. Arrangement of tRNAs in pre- and post-translocational ribosomes revealed by electron cryomicroscopy
83. Visualization of elongation factor Tu on the E. coli ribosome
84. Photo-affinity labelling at the peptidyl transferase centre reveals two different positions for the A- and P-sites in domain V of 23 S rRNA
85. Model for the three-dimensional folding of 16 S ribosomal RNA
86. Topography of the ribosomal proteins from E. coli within the intact subunits as determined by immunoelectron microscopy and protein-protein cross-linking
87. The NMR structure of E. coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases
88. The NMR structure of the 5S rRNA E-domain-protein L25 complex shows pre-formed and induced recognition
89. The sarcin/ricin loop, a modular RNA
90. Matching the crystallographic structure of ribosomal protein S7 to a three-dimensional model of the 16 S ribosomal RNA
91. Precise determination of RNA-protein contact sites in the 50 S ribosomal subunit of E. coli
92. Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton
93. The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution. Pattern fittings and the identification of a functional site
94. The crystal structure of ribosomal protein L22 from Thermus thermophilus: Insights into the mechanism of erythromycin resistance
95. The importance of highly conserved nucleotides in the binding region of chloramphenicol at the peptidyl transferase centre of E. coli 23 S ribosomal RNA
96. Three-dimensional reconstruction of the ribosome from E. coli
97. A model for the spatial arrangement of the proteins in the large subunit of the E. coli ribosome
98. Molecular movement inside the translational engine
99. Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing
100. Crystal structure of a prokaryotic ribosomal protein
101. A detailed view of a ribosomal active site: The structure of the GTPase center at 2.6 Å resolution
102. Labeling the peptidyl transferase center of the E. coli ribosome with photoreactive tRNA(Phe) derivatives containing azidoadenosine at the 3' end of the acceptor arm; a new model of the tRNA-ribosome complex