The three-dimensional structure of the ribosome and its components.

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.

[1]  C. Merryman,et al.  Structure and function of ribosomal RNA. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[2]  M. W. Gray,et al.  Sixteen discrete RNA components in the cytoplasmic ribosome of Euglena gracilis. , 1990, Journal of molecular biology.

[3]  G. Varani,et al.  Structure of an unusually stable RNA hairpin. , 1991, Biochemistry.

[4]  P. Moore,et al.  The sarcin/ricin loop, a modular RNA. , 1995, Journal of molecular biology.

[5]  J. Lake,et al.  Mapping evolution with ribosome structure: intralineage constancy and interlineage variation. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[6]  H. Heus,et al.  Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. , 1991, Science.

[7]  B. Wittmann-Liebold Ribosomal Proteins: Their Structure and Evolution , 1986 .

[8]  J. Feigon,et al.  Solution structure of the conserved 16 S-like ribosomal RNA UGAA tetraloop. , 1997, Journal of molecular biology.

[9]  V. Ramakrishnan,et al.  The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus. , 1996, Structure.

[10]  Nobutoshi Ito,et al.  Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin , 1994, Nature.

[11]  J. Frank,et al.  A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome , 1995, Nature.

[12]  R. Brimacombe,et al.  Loop IV of 5S ribosomal RNA has contacts both to domain II and to domain V of the 23S RNA. , 1996, RNA.

[13]  Mark Proctor,et al.  The Solution Structure of the S1 RNA Binding Domain: A Member of an Ancient Nucleic Acid–Binding Fold , 1997, Cell.

[14]  H. Noller,et al.  Site-Directed Hydroxyl Radical Probing of the rRNA Neighborhood of Ribosomal Protein S5 , 1996, Science.

[15]  D. Engelman,et al.  Neutron-scattering studies of the ribosome of Escherichia coli: a provisional map of the locations of proteins S3, S4, S5, S7, S8 and S9 in the 30 S subunit. , 1978, Journal of molecular biology.

[16]  H. Bartels,et al.  Characterization and preliminary attempts for derivatization of crystals of large ribosomal subunits from Haloarcula marismortui diffracting to 3 A resolution. , 1991, Journal of molecular biology.

[17]  J. Frank,et al.  Native 3D structure of eukaryotic 80s ribosome: morphological homology with E. coli 70S ribosome , 1996, The Journal of cell biology.

[18]  J. Frank,et al.  Direct Visualization of A-, P-, and E-Site Transfer RNAs in the Escherichia coli Ribosome , 1996, Science.

[19]  R. Brimacombe,et al.  The structure of ribosomal RNA: a three-dimensional jigsaw puzzle. , 1995, European journal of biochemistry.

[20]  J. Lake,et al.  Mapping the three-dimensional locations of ribosomal RNA and proteins. , 1992, Biochimie.

[21]  G. Varani,et al.  Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCC , 1990, Nature.

[22]  V. Ramakrishnan,et al.  Crystal structure of prokaryotic ribosomal protein L9: a bi‐lobed RNA‐binding protein. , 1994, The EMBO journal.

[23]  I. Tanaka,et al.  Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor. , 1997, Structure.

[24]  D. Draper,et al.  High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA , 1997, Nature Structural Biology.

[25]  M van Heel,et al.  A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. III. The topography of the functional centre. , 1997, Journal of molecular biology.

[26]  C. Kundrot,et al.  Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing , 1996, Science.

[27]  J. Lake,et al.  Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: immune mapping of the nascent chain. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[28]  M. Cannon Structure, function, and genetics of ribosomes , 1988 .

[29]  J. Frank,et al.  Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. , 1997, Journal of structural biology.

[30]  A. Liljas,et al.  Crystal structure of the RNA binding ribosomal protein L1 from Thermus thermophilus. , 1996, The EMBO journal.

[31]  R. Brimacombe,et al.  A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A. , 1997, Journal of molecular biology.

[32]  M. Wabl Electron microscopic localization of two proteins on the surface of the 50 S ribosomal subunit of Escherichia coli using specific antibody markers. , 1974, Journal of molecular biology.

[33]  H. Noller,et al.  Unusual resistance of peptidyl transferase to protein extraction procedures. , 1992, Science.

[34]  E. Nikonowicz,et al.  Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[35]  V. Erdmann Structure and function of 5S and 5.8 S RNA. , 1976, Progress in nucleic acid research and molecular biology.

[36]  A. Yonath,et al.  Cryocrystallography of ribosomal particles. , 1989, Acta crystallographica. Section B, Structural science.

[37]  Y. Ohsumi,et al.  Initiation of Protein Synthesis in E. coli , 1969 .

[38]  G. Varani,et al.  The conformation of loop E of eukaryotic 5S ribosomal RNA. , 1993, Biochemistry.

[39]  Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy. , 1996, Biochemistry.

[40]  M. Nilges,et al.  NMR analysis of helix I from the 5S RNA of Escherichia coli. , 1992, Biochemistry.

[41]  Triangulation of proteins in the 30 S ribosomal subunit of Exherichia coli. , 1977, Journal of molecular biology.

[42]  N. Volkmann,et al.  A milestone in ribosomal crystallography: the construction of preliminary electron density maps at intermediate resolution. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[43]  R P May,et al.  Inter‐protein distances within the large subunit from Escherichia coli ribosomes. , 1992, The EMBO journal.

[44]  B. Golden,et al.  Ribosomal protein L6: structural evidence of gene duplication from a primitive RNA binding protein. , 1993, The EMBO journal.

[45]  R. Nazar A 5.8 S rRNA‐like sequence in prokaryotic 23 S rRNA , 1980, FEBS letters.

[46]  R. Brimacombe,et al.  Arrangement of tRNAs in Pre- and Posttranslocational Ribosomes Revealed by Electron Cryomicroscopy , 1997, Cell.

[47]  A Yonath,et al.  A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction. , 1987, Science.

[48]  J Frank,et al.  Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. , 1996, Journal of molecular biology.

[49]  I. Wool,et al.  The site of action of alpha-sarcin on eukaryotic ribosomes. The sequence at the alpha-sarcin cleavage site in 28 S ribosomal ribonucleic acid. , 1982, The Journal of biological chemistry.

[50]  T. Steitz,et al.  Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain , 1997, Cell.

[51]  C R Woese,et al.  Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[52]  R. Brimacombe,et al.  A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. II. The RNA-protein interaction data. , 1997, Journal of molecular biology.

[53]  Walter E. Hill,et al.  The Ribosome : structure, function, and evolution , 1990 .

[54]  D. Draper,et al.  Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs. , 1996, Journal of molecular biology.

[55]  Y. Xing,et al.  The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains , 1997, Nature Structural Biology.

[56]  Helena Berglund,et al.  Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus , 1997, Nature Structural Biology.

[57]  R. Brimacombe,et al.  Getting closer to an understanding of the three-dimensional structure of ribosomal RNA. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[58]  R. Roberts,et al.  Microsomal particles and protein synthesis , 1958 .

[59]  I. Tanaka,et al.  Crystal structure of a prokaryotic ribosomal protein. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[60]  J A Lake,et al.  Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes. , 1976, Journal of molecular biology.

[61]  M van Heel,et al.  The 70S Escherichia coli ribosome at 23 A resolution: fitting the ribosomal RNA. , 1995, Structure.

[62]  I. Wool,et al.  Structure and evolution of mammalian ribosomal proteins. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[63]  J A Langer,et al.  A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. , 1987, Science.

[64]  I. Wool Extraribosomal functions of ribosomal proteins. , 1996, Trends in biochemical sciences.

[65]  W. Hoppe A New X‐Ray Method for the Determination of the Quaternary Structure of Protein Complexes , 1972 .

[66]  D. Glitz,et al.  Tracing the path of messenger RNA on the Escherichia coli small ribosomal subunit. Immune electron microscopy using defined oligodeoxynucleotide analogs of mRNA. , 1994, The Journal of biological chemistry.

[67]  V. Ramakrishnan,et al.  Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution. , 1996, Structure.

[68]  G. Stöffler,et al.  Immunoelectron microscopy of ribosomes. , 1984, Annual review of biophysics and bioengineering.

[69]  G G Brownlee,et al.  The sequence of 5 s ribosomal ribonucleic acid. , 1968, Journal of molecular biology.

[70]  V. Ramakrishnan,et al.  The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA , 1992, Nature.

[71]  R. Gutell,et al.  Secondary structure model for 23S ribosomal RNA. , 1981, Nucleic acids research.

[72]  P. Zamecnik,et al.  Studies on cytoplasmic ribonucleoprotein particles from the liver of the rat. , 1955, The Journal of biological chemistry.

[73]  H. Noller,et al.  Secondary structure of 16S ribosomal RNA. , 1981, Science.

[74]  P. Moore,et al.  The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. , 1997, Structure.

[75]  A. Murzin A ribosomal protein module in EF-G and DNA gyrase , 1995, Nature Structural Biology.

[76]  D. Engelman,et al.  Neutron-scattering studies of the ribosome. , 1976, Scientific American.

[77]  V. Ramakrishnan,et al.  The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids. , 1997, Structure.

[78]  H. Heus,et al.  A network of heterogeneous hydrogen bonds in GNRA tetraloops. , 1996, Journal of molecular biology.

[79]  A. Liljas,et al.  Crystal structure of a ribosomal component at 2.6 Å resolution , 1980, Nature.

[80]  J. Frank,et al.  Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA , 1991, The Journal of cell biology.

[81]  A. Pardi,et al.  Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif. , 1995, Biochemistry.

[82]  S Weinstein,et al.  The suitability of multi-metal clusters for phasing in crystallography of large macromolecular assemblies. , 1996, Structure.

[83]  K. Nierhaus,et al.  The determination of the in situ structure by nuclear spin contrast variation. , 1996, Basic life sciences.

[84]  D. Engelman,et al.  A new method for the determination of biological quarternary structure by neutron scattering. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[85]  S. Harvey,et al.  Modeling the structure of the ribosome. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[86]  G. Stormo,et al.  CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[87]  B. Schoenborn,et al.  Neutron scattering measurements of separation and shape of proteins in 30S ribosomal subunit of Escherichia coli: S2-S5, S5-S8, S3-S7. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[88]  H. Noller,et al.  Structure of a conserved RNA component of the peptidyl transferase centre , 1997, Nature Structural Biology.

[89]  D. Turner,et al.  Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA. , 1996, Biochemistry.

[90]  J. Puglisi,et al.  Structure of the A Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic , 1996, Science.

[91]  C. Woese,et al.  5S RNA secondary structure , 1975, Nature.

[92]  G. Stöffler,et al.  Immuno Electron Microscopy on Escherichia coli Ribosomes , 1986 .

[93]  K. Tsurugi,et al.  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. , 1987, The Journal of biological chemistry.

[94]  M. Eisenstein,et al.  Ribosomal crystallography: from crystal growth to initial phasing , 1996 .

[95]  D. Svergun,et al.  Structural model of the 50S subunit of E. coli ribosomes from solution scattering. , 1996, Basic life sciences.

[96]  Volker A. Erdmann,et al.  The Translational Apparatus , 1993, Springer US.

[97]  C. Betzel,et al.  Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure , 1994, FEBS letters.

[98]  J Frank,et al.  Computer averaging of electron micrographs of 40S ribosomal subunits. , 1981, Science.

[99]  A. Liljas,et al.  Three‐dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. , 1994, The EMBO journal.

[100]  M Kjeldgaard,et al.  Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli. , 1988, Journal of molecular biology.