6GZ5

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Flis, J.Holm, M.Rundlet, E.J.Loerke, J.Hilal, T.Dabrowski, M.Burger, J.Mielke, T.Blanchard, S.C.Spahn, C.M.T.Budkevich, T.V.

(2018) Cell Rep 25: 2676-2688.e7

  • DOI: 10.1016/j.celrep.2018.11.040
  • Primary Citation of Related Structures:  
    6GZ4, 6GZ3, 6GZ5

  • PubMed Abstract: 
  • Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA subst ...

    Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA 2 ⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: tetyana.budkevych@charite.de.



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eukaryotic elongation factor 2 (eEF2)Ct853Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS12BM120Oryctolagus cuniculusMutation(s): 0 
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28S ribosomal RNAA23612Oryctolagus cuniculus
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P/P-site-tRNABv76Oryctolagus cuniculus
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    mRNABx11Salmonella virus SP6
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    18S ribosomal RNAB11708Oryctolagus cuniculus
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    5.8S ribosomal RNAA3157Oryctolagus cuniculus
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    5S ribosomal RNAA4119Oryctolagus cuniculus
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    Ligands 3 Unique
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    GNP
    Query on GNP

    Download CCD File 
    Ct
    PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download CCD File 
    Aj, Ao, Ap, Ba, Bd
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A2, A3, A4, AA, AC, AL, AO, AP, AY, An, B1, BD, Ba, Bx
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    DDE
    Query on DDE
    CtL-PEPTIDE LINKINGC13 H24 N5 O3HIS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.50 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermanyDFG SFB 740
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079238
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM115327-Tan

    Revision History 

    • Version 1.0: 2018-12-05
      Type: Initial release
    • Version 1.1: 2018-12-19
      Changes: Data collection, Database references