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Grant TD, Luft JR, Wolfley JR, Tsuruta H, Martel A, Montelione GT, Snell EH. Small angle X-ray scattering as a complementary tool for high-throughput structural studies. Biopolymers 2011; 95:517-30. [PMID: 21462184 DOI: 10.1002/bip.21630] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 11/07/2022]
Abstract
Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures.
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Affiliation(s)
- Thomas D Grant
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA
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2
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Luft JR, Wolfley JR, Snell EH. What's in a drop? Correlating observations and outcomes to guide macromolecular crystallization experiments. CRYSTAL GROWTH & DESIGN 2011; 11:651-663. [PMID: 21643490 PMCID: PMC3106348 DOI: 10.1021/cg1013945] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Observations of crystallization experiments are classified as specific outcomes and integrated through a phase diagram to visualize solubility and thereby direct subsequent experiments. Specific examples are taken from our high-throughput crystallization laboratory which provided a broad scope of data from 20 million crystallization experiments on 12,500 different biological macromolecules. The methods and rationale are broadly and generally applicable in any crystallization laboratory. Through a combination of incomplete factorial sampling of crystallization cocktails, standard outcome classifications, visualization of outcomes as they relate chemically and application of a simple phase diagram approach we demonstrate how to logically design subsequent crystallization experiments.
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Affiliation(s)
- Joseph R. Luft
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA
- Department of Computational and Structural Biology, SUNY Buffalo, 700 Ellicott St., Buffalo, NY 14203, USA
| | - Jennifer R. Wolfley
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA
- Department of Computational and Structural Biology, SUNY Buffalo, 700 Ellicott St., Buffalo, NY 14203, USA
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3
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Steitz TA. From the structure and function of the ribosome to new antibiotics (Nobel Lecture). Angew Chem Int Ed Engl 2010; 49:4381-98. [PMID: 20509130 DOI: 10.1002/anie.201000708] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University and the Howard Hughes Medical Institute, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
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4
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Steitz T. Von der Struktur und Funktion des Ribosoms zu neuen Antibiotika (Nobel-Aufsatz). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000708] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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5
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Abstract
Since the mid-1990s, insights obtained from electron microscopy and X-ray crystallography have transformed our understanding of how the most important ribozyme in the cell, the ribosome, catalyzes protein synthesis. This review provides a brief account of how this structural revolution came to pass, and the impact it has had on our understanding of how the ribosome decodes messenger RNAs.
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Affiliation(s)
- Peter B Moore
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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6
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Abstract
The determination of the high-resolution structures of ribosomal subunits in the year 2000 and of the entire ribosome a few years later are revolutionizing our understanding of the role of the ribosome in translation. In the present article, I summarize the main contributions from our laboratory to this worldwide effort. These include the determination of the structure of the 30S ribosomal subunit and its complexes with antibiotics, the role of the 30S subunit in decoding, and the high-resolution structure of the entire 70S ribosome complexed with mRNA and tRNA.
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7
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Abstract
The ribosome crystal structures published in the past two years have revolutionized our understanding of ribonucleoprotein structure, and more specifically, the structural basis of the peptide bonding forming activity of the ribosome. This review concentrates on the crystallographic developments that made it possible to solve these structures. It also discusses the information obtained from these structures about the three-dimensional architecture of the large ribosomal subunit, the mechanism by which it facilitates peptide bond formation, and the way antibiotics inhibit large subunit function. The work reviewed, taken as a whole, proves beyond doubt that the ribosome is an RNA enzyme, as had long been surmised on the basis of less conclusive evidence.
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Affiliation(s)
- Peter B Moore
- Departments of Molecular Biophysics and Biochemistry, Chemistry, Yale University, New Haven, Connecticut 06520, USA.
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Brodersen DE, Carter AP, Clemons WM, Morgan-Warren RJ, Murphy FV, Ogle JM, Tarry MJ, Wimberly BT, Ramakrishnan V. Atomic structures of the 30S subunit and its complexes with ligands and antibiotics. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:17-32. [PMID: 12762005 DOI: 10.1101/sqb.2001.66.17] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- D E Brodersen
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom
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9
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Clemons WM, Brodersen DE, McCutcheon JP, May JL, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination. J Mol Biol 2001; 310:827-43. [PMID: 11453691 DOI: 10.1006/jmbi.2001.4778] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 A resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 A resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.
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Affiliation(s)
- W M Clemons
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
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10
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Weinstein S, Jahn W, Glotz C, Schlünzen F, Levin I, Janell D, Harms J, Kölln I, Hansen HA, Glühmann M, Bennett WS, Bartels H, Bashan A, Agmon I, Kessler M, Pioletti M, Avila H, Anagnostopoulos K, Peretz M, Auerbach T, Franceschi F, Yonath A. Metal compounds as tools for the construction and the interpretation of medium-resolution maps of ribosomal particles. J Struct Biol 1999; 127:141-51. [PMID: 10527903 DOI: 10.1006/jsbi.1999.4135] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Procedures were developed exploiting organometallic clusters and coordination compounds in combination with heavy metal salts for derivatization of ribosomal crystals. These enabled the construction of multiple isomorphous replacement (MIR) and multiple isomorphous replacement combined with anomalous scattering medium-resolution electron density maps for the ribosomal particles that yield the crystals diffracting to the highest resolution, 3 A, of the large subunit from Haloarcula marismortui and the small subunit from Thermus thermophilus. The first steps in the interpretation of the 7. 3-A MIR map of the small subunit were made with the aid of a tetrairidium cluster that was covalently attached to exposed sulfhydryls on the particle's surface prior to crystallization. The positions of these sulfhydryls were localized in difference Fourier maps that were constructed with the MIR phases.
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Affiliation(s)
- S Weinstein
- Department of Structural Biology, Weizmann Institute, Rehovot, 76100, Israel
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11
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Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallograhy. Structure 1999; 7:931-41. [PMID: 10467138 DOI: 10.1016/s0969-2126(99)80120-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Ribosomes are the universal cellular organelles that accomplish the translation of the genetic code into proteins. Electron cryo-microscopy (cryo-EM) has yielded fairly detailed three-dimensional reconstructions of ribosomes. These were used to assist in the determination of higher resolution structures by X-ray crystallography. RESULTS Molecular replacement studies using cryo-EM reconstructions provided feasible packing schemes for crystals of ribosomes and their two subunits from Thermus thermophilus, and of the large subunits from Haloarcula marismortui. For the large subunits, these studies also confirmed the major heavy-atom sites obtained by single isomorphous replacement combined with anomalous diffraction (SIRAS) and by multiple isomorphous replacement combined with anomalous diffraction (MIRAS) at approximately 10 A. Although adequate starting phases could not be obtained for the small subunits, the crystals of which diffract to 3.0 A, cryo-EM reconstructions were indispensable for analyzing their 7.2 A multiple isomorphous replacement (MIR) map. This work indicated that the conformation of the crystallized small subunits resembles that seen within the 70S ribosomes. Subsequently, crystals of particles trapped in their functionally active state were grown. CONCLUSIONS Single-particle cryo-EM can contribute to the progress of crystallography of non-symmetrical, large and flexible macromolecular assemblies. Besides confirming heavy-atom sites, obtained from flat or overcrowded difference Patterson maps, the cryo-EM reconstructions assisted in elucidating packing arrangements. They also provided tools for the identification of the conformation within the crystals and for the estimation of the level of inherent non-isomorphism.
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Affiliation(s)
- J Harms
- Max-Planck Research Unit for Ribosomal Structure, Hamburg, Germany
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12
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Moore PB. The three-dimensional structure of the ribosome and its components. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:35-58. [PMID: 9646861 DOI: 10.1146/annurev.biophys.27.1.35] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Exciting progress has been made in the last decade by those who use physical methods to study the structure of the ribosome and its components. The structures of 10 ribosomal proteins and three isolated ribosomal protein domains are known, and the conformations of a significant number of rRNA sequences have been determined. Electron microscopists have made major advances in the analysis of images of ribosomes, and microscopically derived ribosome models at resolutions approaching 10A are likely quite soon. Furthermore, ribosome crystallographers are on the verge of phasing the diffraction patterns they have had for several years, and near-atomic resolution models for entire ribosomal subunits could emerge from this source at any time. The literature relevant to these developments is reviewed below.
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Affiliation(s)
- P B Moore
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
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Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA. A 9 A resolution X-ray crystallographic map of the large ribosomal subunit. Cell 1998; 93:1105-15. [PMID: 9657144 DOI: 10.1016/s0092-8674(00)81455-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The 50S subunit of the ribosome catalyzes the peptidyl-transferase reaction of protein synthesis. We have generated X-ray crystallographic electron density maps of the large ribosomal subunit from Haloarcula marismortui at various resolutions up to 9 A using data from crystals that diffract to 3 A. Positioning a 20 A resolution EM image of these particles in the crystal lattice produced phases accurate enough to locate the bound heavy atoms in three derivatives using difference Fourier maps, thus demonstrating the correctness of the EM model and its placement in the unit cell. At 20 A resolution, the X-ray map is similar to the EM map; however, at 9 A it reveals long, continuous, but branched features whose shape, diameter, and right-handed twist are consistent with segments of double-helical RNA that crisscross the subunit.
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Affiliation(s)
- N Ban
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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14
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Benjamin DR, Robinson CV, Hendrick JP, Hartl FU, Dobson CM. Mass spectrometry of ribosomes and ribosomal subunits. Proc Natl Acad Sci U S A 1998; 95:7391-5. [PMID: 9636159 PMCID: PMC22627 DOI: 10.1073/pnas.95.13.7391] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nanoflow electrospray ionization has been used to introduce intact Escherichia coli ribosomes into the ion source of a mass spectrometer. Mass spectra of remarkable quality result from a partial, but selective, dissociation of the particles within the mass spectrometer. Peaks in the spectra have been assigned to individual ribosomal proteins and to noncovalent complexes of up to five component proteins. The pattern of dissociation correlates strongly with predicted features of ribosomal protein-protein and protein-RNA interactions. The spectra allow the dynamics and state of folding of specific proteins to be investigated in the context of the intact ribosome. This study demonstrates a potentially general strategy to probe interactions within complex biological assemblies.
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Affiliation(s)
- D R Benjamin
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QT, United Kingdom
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15
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Nierhaus KH, Stuhrmann HB, Svergun D. The ribosomal elongation cycle and the movement of tRNAs across the ribosome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1998; 59:177-204. [PMID: 9427843 DOI: 10.1016/s0079-6603(08)61032-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ribosome research has reached an exciting state, where two lines of experimental research have considerably improved our understanding of the ribosomal functions. On one hand, functional analysis has elucidated principles of both the decoding process and the tRNA movement on the ribosome during translocation. Experimental data leading to current competing models of the ribosomal elongation cycle can be reconciled by a new model, the alpha-epsilon model, according to which both tRNAs are tightly bound to a movable ribosomal domain. This alpha-epsilon domain carries the tRNA2.mRNA complex from the A and P sites to the P and E sites in the course of translocation maintaining the binding of both tRNAs. On the other hand, the location of tRNAs within the elongating ribosome can be directly determined for the first time by neutron scattering and electron microscopy. Both lines of evidence complement each other and define a frame for the first experimentally sound functional model of the elongating ribosome.
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Affiliation(s)
- K H Nierhaus
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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16
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Liljas A, al-Karadaghi S. Structural aspects of protein synthesis. NATURE STRUCTURAL BIOLOGY 1997; 4:767-71. [PMID: 9334736 DOI: 10.1038/nsb1097-767] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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17
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Svergun DI, Burkhardt N, Pedersen JS, Koch MH, Volkov VV, Kozin MB, Meerwink W, Stuhrmann HB, Diedrich G, Nierhaus KH. Solution scattering structural analysis of the 70 S Escherichia coli ribosome by contrast variation. I. Invariants and validation of electron microscopy models. J Mol Biol 1997; 271:588-601. [PMID: 9281427 DOI: 10.1006/jmbi.1997.1190] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Solutions of selectively deuterated 70 S Escherichia coli ribosomes and of free 30 S and 50 S subunits were studied by neutron scattering using contrast variation. The integrity of the partially deuterated particles was controlled by parallel X-ray measurements. Integral parameters of the entire ribosome, of its subunits and of the protein and rRNA moieties were evaluated. The data allow an experimental validation of the two most recent electron microscopy reconstructions of the 70 S ribosome presented by the groups of J. Frank (Albany) and of M. van Heel & R. Brimacombe (Berlin). For each reconstruction, integral parameters and theoretical scattering curves from the 70 S and its subunits were calculated and compared with the experimental data. Although neither of the two models yields a comprehensive agreement with the experimental data, Frank's model provides a better fit. For the 50 S subunit of van Heel & Brimacombe's model the fit with the experimental data improves significantly when the internal channels and tunnels are filled up. The poorer fit of the latter model is thus caused by its "sponge"-like structure which may partly be due to an enhancement of high frequency contributions in some of the steps of the three-dimensional image reconstruction. It seems therefore unlikely that the ribosome has a "sponge"-like structure with a pronounced network of channels.
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Affiliation(s)
- D I Svergun
- Hamburg Outstation, EMBL, Notkestrasse 85, Hamburg, D-22603, Germany
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Abstract
During the past 18 months, electron microscopists have published two reconstructions of the Escherichia coli ribosome, independently derived from images of unstained particles. The resolutions of their images are 20-25 A-much higher than any previously available. During the same time, NMR spectroscopists have provided an atomic-resolution model for the A-site region of 16S rRNA complexed with paromomycin that explains much of what is known about the interaction of aminoglycoside antibiotics with ribosomes.
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Affiliation(s)
- P B Moore
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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Yonath A, Franceschi F. New RNA recognition features revealed in ancient ribosomal proteins. NATURE STRUCTURAL BIOLOGY 1997; 4:3-5. [PMID: 8989311 DOI: 10.1038/nsb0197-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Abstract
The ribosome is a large multifunctional complex composed of both RNA and proteins. Biophysical methods are yielding low-resolution structures of the overall architecture of ribosomes, and high-resolution structures of individual proteins and segments of rRNA. Accumulating evidence suggests that the ribosomal RNAs play central roles in the critical ribosomal functions of tRNA selection and binding, translocation, and peptidyl transferase. Biochemical and genetic approaches have identified specific functional interactions involving conserved nucleotides in 16S and 23S rRNA. The results obtained by these quite different approaches have begun to converge and promise to yield an unprecedented view of the mechanism of translation in the coming years.
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Affiliation(s)
- R Green
- Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA
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