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Volumn 113, Issue 6, 2003, Pages 789-801

Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; RIBOSOME PROTEIN; RNA;

EID: 0038275890     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(03)00427-6     Document Type: Article
Times cited : (253)

References (51)
  • 1
    • 0032568584 scopus 로고    scopus 로고
    • Visualization of elongation factor G on the Escherichia coli 70S ribosome: The mechanism of translocation
    • Agrawal R.K., Penczek P., Grassucci R.A., Frank J. Visualization of elongation factor G on the Escherichia coli 70S ribosome. the mechanism of translocation Proc. Natl. Acad. Sci. USA. 95:1998;6134-6138.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6134-6138
    • Agrawal, R.K.1    Penczek, P.2    Grassucci, R.A.3    Frank, J.4
  • 2
    • 0032982866 scopus 로고    scopus 로고
    • EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
    • a
    • Agrawal R.K., Heagle A.B., Penczek P., Grassucci R.A., Frank J. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nat. Struct. Biol. 6:1999;643-647. a.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 643-647
    • Agrawal, R.K.1    Heagle, A.B.2    Penczek, P.3    Grassucci, R.A.4    Frank, J.5
  • 3
    • 0033605751 scopus 로고    scopus 로고
    • Effect of buffer conditions on the position of tRNA on the 70S ribosome as visualized by cryoelectron microscopy
    • b
    • Agrawal R.K., Penczek P., Grassucci R.A., Burkhardt N., Nierhaus K.H., Frank J. Effect of buffer conditions on the position of tRNA on the 70S ribosome as visualized by cryoelectron microscopy. J. Biol. Chem. 274:1999;8723-8729. b.
    • (1999) J. Biol. Chem. , vol.274 , pp. 8723-8729
    • Agrawal, R.K.1    Penczek, P.2    Grassucci, R.A.3    Burkhardt, N.4    Nierhaus, K.H.5    Frank, J.6
  • 4
    • 0035943352 scopus 로고    scopus 로고
    • Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation
    • Agrawal R.K., Linde J., Sengupta J., Nierhaus K.H., Frank J. Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation. J. Mol. Biol. 311:2001;777-787.
    • (2001) J. Mol. Biol. , vol.311 , pp. 777-787
    • Agrawal, R.K.1    Linde, J.2    Sengupta, J.3    Nierhaus, K.H.4    Frank, J.5
  • 6
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
    • Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science. 289:2000;905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 7
    • 0036303417 scopus 로고    scopus 로고
    • Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16S RNA
    • Brodersen D.E., Clemons W.M., Carter A.P., Wimberly B.T., Ramakrishnan V. Crystal structure of the 30S ribosomal subunit from Thermus thermophilus. structure of the proteins and their interactions with 16S RNA J. Mol. Biol. 316:2002;725-768.
    • (2002) J. Mol. Biol. , vol.316 , pp. 725-768
    • Brodersen, D.E.1    Clemons, W.M.2    Carter, A.P.3    Wimberly, B.T.4    Ramakrishnan, V.5
  • 10
    • 0001832403 scopus 로고
    • Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron density function
    • Chapman M.S. Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron density function. Acta Crystallogr. A. 51:1995;69-80.
    • (1995) Acta Crystallogr. A , vol.51 , pp. 69-80
    • Chapman, M.S.1
  • 11
    • 0035783170 scopus 로고    scopus 로고
    • Real space refinement of acto-myosin structure from sectioned muscle
    • Chen L.F., Blanc E., Chapman M.S., Taylor K.A. Real space refinement of acto-myosin structure from sectioned muscle. J. Struct. Biol. 133:2001;221-232.
    • (2001) J. Struct. Biol. , vol.133 , pp. 221-232
    • Chen, L.F.1    Blanc, E.2    Chapman, M.S.3    Taylor, K.A.4
  • 12
    • 0029402170 scopus 로고
    • Histidine 229 in protein L2 is apparently essential for 50S peptidyl transferase activity
    • Cooperman B.S., Wooten T., Romero D.P., Traut R.R. Histidine 229 in protein L2 is apparently essential for 50S peptidyl transferase activity. Biochem. Cell Biol. 73:1995;1087-1094.
    • (1995) Biochem. Cell Biol. , vol.73 , pp. 1087-1094
    • Cooperman, B.S.1    Wooten, T.2    Romero, D.P.3    Traut, R.R.4
  • 16
    • 0029975088 scopus 로고    scopus 로고
    • Spider and web: Processing and visualization of images in 3D electron microscopy and related fields
    • Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. Spider and web. processing and visualization of images in 3D electron microscopy and related fields J. Struct. Biol. 116:1996;190-199.
    • (1996) J. Struct. Biol. , vol.116 , pp. 190-199
    • Frank, J.1    Radermacher, M.2    Penczek, P.3    Zhu, J.4    Li, Y.5    Ladjadj, M.6    Leith, A.7
  • 17
    • 0034691576 scopus 로고    scopus 로고
    • A ratchet-like inter-subunit reorganization of the ribosome during translocation
    • Frank J., Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 406:2000;318-322.
    • (2000) Nature , vol.406 , pp. 318-322
    • Frank, J.1    Agrawal, R.K.2
  • 18
    • 0035787732 scopus 로고    scopus 로고
    • Ratchet-like movements between the two ribosomal subunits: Their implications in elongation factor recognition and tRNA translocation
    • Cold Spring, NY: Cold Spring Harbor Laboratory Press
    • Frank, J., and Agrawal, R.K. (2001). Ratchet-like movements between the two ribosomal subunits: their implications in elongation factor recognition and tRNA translocation. In Cold Spring Harbor Symposia on Quantitative Biology. (Cold Spring, NY: Cold Spring Harbor Laboratory Press), pp. 67-75.
    • (2001) Cold Spring Harbor Symposia on Quantitative Biology , pp. 67-75
    • Frank, J.1    Agrawal, R.K.2
  • 19
    • 0002726944 scopus 로고    scopus 로고
    • Cryo-electron microscopy of the translational apparatus: Experimental evidence for the paths of mRNA, tRNA, and the polypeptide chain
    • Antibiotics Function, Cellular Interactions, R.A. Garrett, S.R. Douthwaite, A. Liljas, A.T. Matheson, P.B. Moore, & H.F. Noller. Washington, DC: ASM Press. 45-51.pp
    • Frank J., Penczek P., Grassucci R.A., Heagle A.B., Spahn C.M.T., Agrawal R.K. Cryo-electron microscopy of the translational apparatus. experimental evidence for the paths of mRNA, tRNA, and the polypeptide chain Function Antibiotics, Cellular Interactions, Garrett R.A., Douthwaite S.R., Liljas A., Matheson A.T., Moore P.B., Noller H.F. The Ribosome. Structure:2000;ASM Press, Washington, DC. 45-51.pp.
    • (2000) The Ribosome: Structure
    • Frank, J.1    Penczek, P.2    Grassucci, R.A.3    Heagle, A.B.4    Spahn, C.M.T.5    Agrawal, R.K.6
  • 20
    • 0033571249 scopus 로고    scopus 로고
    • Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA
    • Gabashvili I.S., Agrawal R., Grassucci R., Squires C.L., Dahlberg A.E., Frank J. Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA. EMBO J. 18:1999;6501-6507.
    • (1999) EMBO J. , vol.18 , pp. 6501-6507
    • Gabashvili, I.S.1    Agrawal, R.2    Grassucci, R.3    Squires, C.L.4    Dahlberg, A.E.5    Frank, J.6
  • 25
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
    • (1991) Acta Crystallogr. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 26
    • 0017388322 scopus 로고
    • Physical properties of ribosomal protein S1 and its interaction with the 30S ribosomal subunit of Escherichia coli
    • Laughrea M., Moore P.B. Physical properties of ribosomal protein S1 and its interaction with the 30S ribosomal subunit of Escherichia coli. J. Mol. Biol. 112:1977;399-421.
    • (1977) J. Mol. Biol. , vol.112 , pp. 399-421
    • Laughrea, M.1    Moore, P.B.2
  • 29
    • 0037062958 scopus 로고    scopus 로고
    • The involvement of RNA in ribosome function
    • Moore P.B., Steitz T.A. The involvement of RNA in ribosome function. Nature. 418:2002;229-235.
    • (2002) Nature , vol.418 , pp. 229-235
    • Moore, P.B.1    Steitz, T.A.2
  • 30
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A. The structural basis of ribosome activity in peptide bond synthesis. Science. 289:2000;920-930.
    • (2000) Science , vol.289 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.B.4    Steitz, T.A.5
  • 32
    • 0036089481 scopus 로고    scopus 로고
    • MODBASE, a database of annotated comparative protein structure models
    • Pieper U., Eswar N., Stuart A.C., Ilyin V.A., Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30:2002;255-259.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 255-259
    • Pieper, U.1    Eswar, N.2    Stuart, A.C.3    Ilyin, V.A.4    Sali, A.5
  • 33
    • 0033776245 scopus 로고    scopus 로고
    • Docking structures of domains into maps from cryo-electron microscopy using local correlation
    • Roseman A.M. Docking structures of domains into maps from cryo-electron microscopy using local correlation. Acta Crystallogr. D. 56:2000;1332-1340.
    • (2000) Acta Crystallogr. D , vol.56 , pp. 1332-1340
    • Roseman, A.M.1
  • 34
    • 0033780164 scopus 로고    scopus 로고
    • Fitting atomic models into electron-microscopy maps
    • Rossmann M.G. Fitting atomic models into electron-microscopy maps. Acta Crystallogr. D. 56:2000;1341-1349.
    • (2000) Acta Crystallogr. D , vol.56 , pp. 1341-1349
    • Rossmann, M.G.1
  • 35
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali A., Blundell T.L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 36
    • 0032506030 scopus 로고    scopus 로고
    • Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
    • Sanchez R., Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. USA. 95:1998;13597-13602.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 13597-13602
    • Sanchez, R.1    Sali, A.2
  • 37
    • 0038438514 scopus 로고    scopus 로고
    • Impala: Matching a protein sequence against a collection of psi-blast-constructed position-specific score matrices
    • Schaffer A.A., Wolf Y.I., Ponting C.P., Koonin E.V., Aravind L., Altschul S.F. Impala. matching a protein sequence against a collection of psi-blast-constructed position-specific score matrices Bioinformatics. 15:1999;1000-1011.
    • (1999) Bioinformatics , vol.15 , pp. 1000-1011
    • Schaffer, A.A.1    Wolf, Y.I.2    Ponting, C.P.3    Koonin, E.V.4    Aravind, L.5    Altschul, S.F.6
  • 39
    • 0035834062 scopus 로고    scopus 로고
    • Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA
    • Sengupta J., Agrawal R.K., Frank J. Visualization of protein S1 within the 30S ribosomal subunit and its interaction with messenger RNA. Proc. Natl. Acad. Sci. USA. 98:2001;11991-11996.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 11991-11996
    • Sengupta, J.1    Agrawal, R.K.2    Frank, J.3
  • 41
    • 0035798380 scopus 로고    scopus 로고
    • Structure of the 80S ribosome from Saccharomyces cerevisiae - TRNA-ribosome and subunit-subunit interactions
    • Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J. Structure of the 80S ribosome from Saccharomyces cerevisiae - tRNA-ribosome and subunit-subunit interactions. Cell. 107:2001;373-386.
    • (2001) Cell , vol.107 , pp. 373-386
    • Spahn, C.M.T.1    Beckmann, R.2    Eswar, N.3    Penczek, P.A.4    Sali, A.5    Blobel, G.6    Frank, J.7
  • 42
  • 43
    • 84913050729 scopus 로고
    • An efficient general-purpose least-squares refinement program for macromolecular structures
    • Tronrud D.E., Ten Eyck L.F., Matthews B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallogr. A. 43:1987;489-501.
    • (1987) Acta Crystallogr. A , vol.43 , pp. 489-501
    • Tronrud, D.E.1    Ten Eyck, L.F.2    Matthews, B.W.3
  • 44
    • 0036786684 scopus 로고    scopus 로고
    • All-atom homology model of the Escherichia coli 30S ribosomal subunit
    • Tung C.S., Joseph S., Sanbonmatsu K.Y. All-atom homology model of the Escherichia coli 30S ribosomal subunit. Nat. Struct. Biol. 9:2002;750-755.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 750-755
    • Tung, C.S.1    Joseph, S.2    Sanbonmatsu, K.Y.3
  • 45
    • 0032522579 scopus 로고    scopus 로고
    • Functional implications of ribosomal protein L2 in protein biosynthesis as shown by in vivo replacement studies
    • Uhlein M., Weglohner W., Urlaub H., Wittmann-Liebold B. Functional implications of ribosomal protein L2 in protein biosynthesis as shown by in vivo replacement studies. Biochem. J. 331:1998;423-430.
    • (1998) Biochem. J. , vol.331 , pp. 423-430
    • Uhlein, M.1    Weglohner, W.2    Urlaub, H.3    Wittmann-Liebold, B.4
  • 47
    • 0032779888 scopus 로고    scopus 로고
    • Quantitative fitting of atomic models into observed densities derived by electron microscopy
    • Volkmann N., Hanein D. Quantitative fitting of atomic models into observed densities derived by electron microscopy. J. Struct. Biol. 125:1999;176-184.
    • (1999) J. Struct. Biol. , vol.125 , pp. 176-184
    • Volkmann, N.1    Hanein, D.2
  • 49
    • 0035783173 scopus 로고    scopus 로고
    • Using Situs for flexible and rigid-body fitting of multi resolution single-molecule data
    • Wriggers W., Birmanns S. Using Situs for flexible and rigid-body fitting of multi resolution single-molecule data. J. Struct. Biol. 133:2001;193-202.
    • (2001) J. Struct. Biol. , vol.133 , pp. 193-202
    • Wriggers, W.1    Birmanns, S.2
  • 51
    • 0035958587 scopus 로고    scopus 로고
    • The path of messenger RNA through the ribosome
    • Yusupova G.Z., Yusupov M.M., Cate J.H., Noller H.F. The path of messenger RNA through the ribosome. Cell. 106:2001;233-241.
    • (2001) Cell , vol.106 , pp. 233-241
    • Yusupova, G.Z.1    Yusupov, M.M.2    Cate, J.H.3    Noller, H.F.4


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