5WE4

70S ribosome-EF-Tu wt complex with GppNHp

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-07-07 Released: 2018-04-25 
  • Deposition Author(s): Fislage, M., Brown, Z., Frank, J.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.

Fislage, M.Zhang, J.Brown, Z.P.Mandava, C.S.Sanyal, S.Ehrenberg, M.Frank, J.

(2018) Nucleic Acids Res 46: 5861-5874

  • DOI: 10.1093/nar/gky346
  • Primary Citation of Related Structures:  
    5WFS, 5WFK, 5WE4, 5WE6, 5WDT, 5WF0

  • PubMed Abstract: 
  • The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognit ...

    The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, USA.



Macromolecules

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Entity ID: 3
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50S ribosomal protein L2C271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3D208Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L4E200Escherichia coliMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L5F177Escherichia coliMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L6G174Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L9H149Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L11I141Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L13J141Escherichia coliMutation(s): 0 
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50S ribosomal protein L14K122Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L15L143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16M136Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L17N119Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L18O116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19P114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20Q115Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L21R102Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L22S109Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L23T92Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L24U102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25V92Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W75Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X77Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L29Y60Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L30Z56Escherichia coliMutation(s): 0 
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50S ribosomal protein L32055Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L33151Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L34245Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L35364Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L36438Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L105131Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L31666Escherichia coliMutation(s): 0 
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Entity ID: 35
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30S ribosomal protein S2b218Escherichia coliMutation(s): 0 
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Entity ID: 36
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30S ribosomal protein S3c206Escherichia coliMutation(s): 0 
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Entity ID: 37
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30S ribosomal protein S4d205Escherichia coliMutation(s): 0 
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Entity ID: 38
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30S ribosomal protein S5e157Escherichia coliMutation(s): 0 
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Entity ID: 39
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30S ribosomal protein S6f100Escherichia coliMutation(s): 0 
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Entity ID: 40
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30S ribosomal protein S7g151Escherichia coliMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S8h129Escherichia coliMutation(s): 0 
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Entity ID: 42
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30S ribosomal protein S9i127Escherichia coliMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S10j98Escherichia coliMutation(s): 0 
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Entity ID: 44
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30S ribosomal protein S11k116Escherichia coliMutation(s): 0 
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Entity ID: 45
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30S ribosomal protein S12l121Escherichia coliMutation(s): 0 
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Entity ID: 46
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30S ribosomal protein S13m115Escherichia coliMutation(s): 0 
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Entity ID: 47
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30S ribosomal protein S14n101Escherichia coliMutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S15o88Escherichia coliMutation(s): 0 
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Entity ID: 49
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30S ribosomal protein S16p82Escherichia coliMutation(s): 0 
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Entity ID: 50
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30S ribosomal protein S17q80Escherichia coliMutation(s): 0 
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Entity ID: 51
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30S ribosomal protein S18r65Escherichia coliMutation(s): 0 
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Entity ID: 52
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30S ribosomal protein S19s79Escherichia coliMutation(s): 0 
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Entity ID: 53
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30S ribosomal protein S20t85Escherichia coliMutation(s): 0 
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Entity ID: 54
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30S ribosomal protein S21u65Escherichia coliMutation(s): 0 
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Entity ID: 58
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Elongation factor Tu 2z393Escherichia coliMutation(s): 0 
Gene Names: tufBb3980JW3943
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23S rRNAA2903Escherichia coli
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5S rRNAB120Escherichia coli
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Entity ID: 34
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16S rRNAa1540Escherichia coli
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Entity ID: 55
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tRNA-fMetv, w77Escherichia coli
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  • Entity ID: 56
    MoleculeChainsLengthOrganismImage
    mRNAx12Escherichia coli
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    Entity ID: 57
    MoleculeChainsLengthOrganismImage
    Phe-tRNA-Phey76Escherichia coli
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

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    z
    PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    FME
    Query on FME

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    v
    N-FORMYLMETHIONINE
    C6 H11 N O3 S
    PYUSHNKNPOHWEZ-YFKPBYRVSA-N
     Ligand Interaction
    PHE
    Query on PHE

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    z
    PHENYLALANINE
    C9 H11 N O2
    COLNVLDHVKWLRT-QMMMGPOBSA-N
     Ligand Interaction
    K
    Query on K

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    A
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    0, 1, 3, 4, A, B, C, K, L, M, Q, R, S, T, a, d, h, i, s, u, v, w, y, z
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.10 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Howard Hughes Medical Institute (HHMI)United States--
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM29169

    Revision History 

    • Version 1.0: 2018-04-25
      Type: Initial release
    • Version 1.1: 2018-05-23
      Changes: Data collection, Database references
    • Version 1.2: 2018-07-04
      Changes: Data collection, Database references
    • Version 1.3: 2018-07-18
      Changes: Data collection, Experimental preparation
    • Version 2.0: 2019-07-03
      Changes: Data collection, Non-polymer description, Structure summary
    • Version 2.1: 2019-11-20
      Changes: Author supporting evidence