6GZ3

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated ...

    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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Entity ID: 6
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ribosomal protein uS3 BD220Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S5 BF190Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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ribosomal protein eS10 BK98Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S12 BM120Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS19 BP120Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS9 BQ139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS17 BR125Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS13 BS139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS19 BT143Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS10 BU97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS25 BZ86Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS14 Bd51Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS4 BE257Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6 BG232Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS8 BI207Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15 BN149Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS11 BO136Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS21 BV81Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S23 BX141Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS24 BY125Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS26 Ba97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS27 Bb80Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS30 Be55Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8 AA252Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL3 AB394Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL4 AC363Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL18 AD294Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL6 AE194Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL30 AF234Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL8 AG234Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL6 AH191Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted) AI211Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11 AJ169Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL13 AL205Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL14 AM139Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L15 AN203Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL22 AP153Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL18 AQ187Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL19 AR181Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL20 AS175Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL21 AT157Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL22 AU99Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L23 AV129Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL24 AW121Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL23 AX117Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26 AY127Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L27 AZ134Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL29 Ab68Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL30 Ac103Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL31 Ad106Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL32 Ae129Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL33 Af109Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL34 Ag114Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL29 Ah122Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL36 Ai97Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37 Aj84Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL38 Ak69Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL39 Al50Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL40 Am50Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL41 An25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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ribosomal protein eL42 Ao105Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43 Ap91Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL28 At122Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein Au217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L12 Aq151Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Go to UniProtKB:  G1SMR7
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL10 AK202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
eukaryotic elongation factor 2 (eEF2) Ct853Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA23612Oryctolagus cuniculus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
ap/P-site tRNABv76Oryctolagus cuniculus
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    • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    mRNABx12Salmonella virus SP6
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    Entity ID: 4
    MoleculeChainsLengthOrganismImage
    pe/E-site-tRNABw76Saccharomyces cerevisiae
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    18S ribosomal RNAB11708Oryctolagus cuniculus
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    Entity ID: 39
    MoleculeChainsLengthOrganismImage
    5.8S ribosomal RNAA3157Oryctolagus cuniculus
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    Entity ID: 40
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAA4119Oryctolagus cuniculus
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP
    Download Ideal Coordinates CCD File 
    Ct
    		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N    		 Ligand Interaction
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    Aj, Ao, Ap, Ba, Bd
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    A2, A3, A4, AA, AL, AN, AP, AY, Al, An, B1, BD, BS, Ba, Bd, 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: 3.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    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  (Full details and data files)

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