3J78

Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated conformations (Class I - non-rotated ribosome with 2 tRNAs)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of Yeast 80S Ribosome-tRNA Complexes in the Rotated and Nonrotated Conformations.

Svidritskiy, E.Brilot, A.F.Koh, C.S.Grigorieff, N.Korostelev, A.A.

(2014) Structure 22: 1210-1218

  • DOI: 10.1016/j.str.2014.06.003
  • Primary Citation of Related Structures:  
    3J78, 3J77

  • PubMed Abstract: 
  • The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome complexes formed with either one or two tRNAs and bound in response to an mRNA fragment containing the Kozak consensus sequence ...

    The structural understanding of eukaryotic translation lags behind that of translation on bacterial ribosomes. Here, we present two subnanometer resolution structures of S. cerevisiae 80S ribosome complexes formed with either one or two tRNAs and bound in response to an mRNA fragment containing the Kozak consensus sequence. The ribosomes adopt two globally different conformations that are related to each other by the rotation of the small subunit. Comparison with bacterial ribosome complexes reveals that the global structures and modes of intersubunit rotation of the yeast ribosome differ significantly from those in the bacterial counterpart, most notably in the regions involving the tRNA, small ribosomal subunit, and conserved helix 69 of the large ribosomal subunit. The structures provide insight into ribosome dynamics implicated in tRNA translocation and help elucidate the role of the Kozak fragment in positioning an open reading frame during translation initiation in eukaryotes.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address: andrei.korostelev@umassmed.edu.



Macromolecules

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60S ribosomal protein L1 L1217Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2 L2254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 L3387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4 L4362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 L5297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6 L6176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7 L7244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8 L8256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9 L9191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 60221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11 61174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L12 62165Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13 63199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14 64138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15 65204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16 66199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17 67184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18 68186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19 69189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20 70172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21 71160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22 72121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23 73137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24 74155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 75142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26 76127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27 77136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 78149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29 7959Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30 80105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31 81113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32 82130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33 83107Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34 84121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35 85120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36 86100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37 8788Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38 8878Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39 8951Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L40 90128Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41 9125Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42 92106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43 9392Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein P0 P0312Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein RC319Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0 S0252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1 S1255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 S2254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 S3240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4 S4261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5 S5225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6 S6236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7 S7190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8 S8200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9 S9197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10 10105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11 11156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12 12143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 13151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14 14137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 15142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16 16143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17 17136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18 18146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19 19144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S20 20121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S21 2187Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S22 22130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S23 23145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S24 24135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S25 25108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S26 26119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S27 2782Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28 2867Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S29 2956Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S30 3063Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S31 31152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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18S ribosomal RNA1S1798Saccharomyces cerevisiae
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Entity ID: 79
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25S ribosomal RNA2S3395Saccharomyces cerevisiae
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Entity ID: 80
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5.8S ribosomal RNA8S158Saccharomyces cerevisiae
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Entity ID: 81
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5S ribosomal RNA5S121Saccharomyces cerevisiae
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Entity ID: 82
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P/E-site initiator transfer RNAfMetET, PT77Escherichia coli
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  • Entity ID: 83
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    messenger RNAMR14Saccharomyces cerevisiae
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 6.30 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-08-06
      Type: Initial release
    • Version 1.1: 2014-08-20
      Changes: Database references
    • Version 1.2: 2014-12-10
      Changes: Other
    • Version 1.3: 2014-12-17
      Changes: Other
    • Version 1.4: 2018-07-18
      Changes: Data collection