4V4B

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.

Spahn, C.M.Gomez-Lorenzo, M.G.Grassucci, R.A.Jorgensen, R.Andersen, G.R.Beckmann, R.Penczek, P.A.Ballesta, J.P.Frank, J.

(2004) EMBO J 23: 1008-1019

  • DOI: 10.1038/sj.emboj.7600102
  • Primary Citation of Related Structures:  
    4V4B

  • PubMed Abstract: 
  • An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges ...

    An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.


    Related Citations: 
    • EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
      Agrawal, R.K., Heagle, A.B., Penczek, P., Grassucci, R.A., Frank, J.
      (1999) Nat Struct Biol 6: 643
    • The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery.
      Ballesta, J.P., Remacha, M.
      (1996) Prog Nucleic Acid Res Mol Biol 55: 157
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
      Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A.
      (2000) Science 289: 905

    Organizational Affiliation

    Wadsworth Center, Health Research Inc., Howard Hughes Medical Institute, Albany, NY 12201-0509, USA. christian.spahn@charite.de



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Elongation factor 2B [auth AT]842Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-AC [auth AB]185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3D [auth AC]192Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AE [auth AD]179Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2F [auth AE]149Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5G [auth AG]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22H [auth AH]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16I [auth AI]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20J [auth AJ]100Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-AK [auth AK]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23L [auth AL]118Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18M [auth AM]132Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-BN [auth AN]36Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13O [auth AO]65Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11P [auth AQ]76Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15Q [auth AS]80Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L1T [auth BA]217Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2U [auth BB]253Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3V [auth BC]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-BW [auth BD]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5X [auth BE]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AY [auth BF]162Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AZ [auth BG]119Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AAA [auth BH]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10BA [auth BI]168Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11CA [auth BJ]173Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L12DA [auth BK]131Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AEA [auth BL]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AFA [auth BM]146Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AGA [auth BN]183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18HA [auth BO]120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19IA [auth BP]142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AJA [auth BQ]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23KA [auth BR]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-ALA [auth BS]56Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25MA [auth BT]83Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-ANA [auth BU]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28OA [auth BV]148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32PA [auth B0]130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31QA [auth BW]112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35RA [auth BX]120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-ASA [auth BY]87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42TA [auth BZ]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43UA [auth B9]91Saccharomyces cerevisiaeMutation(s): 0 
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18S ribosomal RNAA [auth AA]1507Saccharomyces cerevisiae
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5.8S/25S ribosomal RNAR [auth B3]2999Saccharomyces cerevisiae
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5S RIBOSOMAL RNAS [auth B4]125Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-18
    Changes: Other
  • Version 1.3: 2019-12-18
    Changes: Data collection, Database references, Other