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.



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60S ribosomal protein L1A [auth L1]217Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2B [auth L2]254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3C [auth L3]387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4D [auth L4]362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5E [auth L5]297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6F [auth L6]176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7G [auth L7]244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9I [auth L9]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10J [auth 60]221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11K [auth 61]174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L12L [auth 62]165Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13M [auth 63]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18R [auth 68]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19S [auth 69]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20T [auth 70]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22V [auth 72]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23W [auth 73]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24X [auth 74]155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25Y [auth 75]142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26Z [auth 76]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27AA [auth 77]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28BA [auth 78]149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29CA [auth 79]59Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30DA [auth 80]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31EA [auth 81]113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32FA [auth 82]130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33GA [auth 83]107Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34HA [auth 84]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35IA [auth 85]120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36JA [auth 86]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37KA [auth 87]88Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38LA [auth 88]78Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39MA [auth 89]51Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L40NA [auth 90]128Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41OA [auth 91]25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42PA [auth 92]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43QA [auth 93]92Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein P0RA [auth P0]312Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinSA [auth RC]319Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0TA [auth S0]252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1UA [auth S1]255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2VA [auth S2]254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3WA [auth S3]240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4XA [auth S4]261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5YA [auth S5]225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6ZA [auth S6]236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7AB [auth S7]190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8BB [auth S8]200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9CB [auth S9]197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10DB [auth 10]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11EB [auth 11]156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12FB [auth 12]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13GB [auth 13]151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14HB [auth 14]137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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40S ribosomal protein S15IB [auth 15]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S16JB [auth 16]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17KB [auth 17]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18LB [auth 18]146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19MB [auth 19]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20NB [auth 20]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S21OB [auth 21]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22PB [auth 22]130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23QB [auth 23]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S24RB [auth 24]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S25SB [auth 25]108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S26TB [auth 26]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S27UB [auth 27]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S28VB [auth 28]67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S29WB [auth 29]56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S30XB [auth 30]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S31YB [auth 31]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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18S ribosomal RNAZB [auth 1S]1798Saccharomyces cerevisiae
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Entity ID: 79
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25S ribosomal RNAAC [auth 2S]3395Saccharomyces cerevisiae
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Entity ID: 80
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5.8S ribosomal RNABC [auth 8S]158Saccharomyces cerevisiae
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Entity ID: 81
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5S ribosomal RNACC [auth 5S]121Saccharomyces cerevisiae
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Entity ID: 82
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P/E-site initiator transfer RNAfMetDC [auth ET], FC [auth PT]77Escherichia coli
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  • Entity ID: 83
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    messenger RNAEC [auth MR]14Saccharomyces cerevisiae
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    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