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 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.



Macromolecules

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Entity ID: 6
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ribosomal protein uS3BD220Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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Ribosomal protein S5BF190Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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ribosomal protein eS10BK98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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40S ribosomal protein S12BM120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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ribosomal protein uS19BP120Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS9BQ139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS17BR125Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS13BS139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS19BT143Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS10BU97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS25BZ86Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS14Bd51Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein RACK 1Bg314Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS2BA215Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S3aBB212Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS5BC222Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS4BE257Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6BG232Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS8BI207Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15BN149Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS11BO136Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS21BV81Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S15aBW129Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S23BX141Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS24BY125Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS26Ba97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS27Bb80Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS30Be55Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L8AA252Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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ribosomal protein uL3AB394Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL4AC363Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL18AD294Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL6AE194Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL30AF234Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL8AG234Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL6AH191Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)AI211Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Ribosomal protein L11AJ169Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL13AL205Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL14AM139Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL13AO195Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL22AP153Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL19AR181Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL20AS175Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL22AU99Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L23AV129Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL24AW121Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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ribosomal protein uL23AX117Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L26AY127Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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60S ribosomal protein L27AZ134Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL15Aa147Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL29Ab68Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL30Ac103Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL31Ad106Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL32Ae129Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL33Af109Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL34Ag114Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL29Ah122Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL36Ai97Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL38Ak69Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL39Al50Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL40Am50Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL41An25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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ribosomal protein eL42Ao105Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43Ap91Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL28At122Oryctolagus cuniculusMutation(s): 0 
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Ribosomal proteinAu217Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L12Aq151Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL10AK202Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
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eukaryotic elongation factor 2 (eEF2)Ct853Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S27aBf73Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 28
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Ribosomal protein S9 (Predicted)BJ179Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 53
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Ribosomal protein L15AN203Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 56
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ribosomal protein eL18AQ187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
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ribosomal protein eL21AT157Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 75
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Ribosomal protein L37Aj84Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 1
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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
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    18S ribosomal RNAB11708Oryctolagus cuniculus
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    Entity ID: 39
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    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 CCD File 
    Ct
    		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N    		 Ligand Interaction
    ZN
    Query on ZN
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    Aj, Ao, Ap, Ba, Bd
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    MG
    Query on MG
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    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 

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