4V69

Ternary complex-bound E.coli 70S ribosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

Villa, E.Sengupta, J.Trabuco, L.G.LeBarron, J.Baxter, W.T.Shaikh, T.R.Grassucci, R.A.Nissen, P.Ehrenberg, M.Schulten, K.Frank, J.

(2009) Proc Natl Acad Sci U S A 106: 1063-1068

  • DOI: 10.1073/pnas.0811370106
  • Primary Citation of Related Structures:  
    4V69

  • PubMed Abstract: 
  • In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs ...

    In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.


    Related Citations: 
    • Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
      Trabuco, L., Villa, E., Mitra, K., Frank, J., Schulten, K.
      (2008) Structure 16: 673
    • Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome
      LeBarron, J., Grassucci, R.A., Shaikh, T.R., Baxter, W.T., Sengupta, J., Frank, J.
      (2008) J Struct Biol 164: 24

    Organizational Affiliation

    Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10AJ98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11AK117Escherichia coliMutation(s): 0 
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30S ribosomal protein S12AL123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13AM113Escherichia coliMutation(s): 0 
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30S ribosomal protein S14AN96Escherichia coliMutation(s): 0 
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30S ribosomal protein S15AO88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16AP80Escherichia coliMutation(s): 0 
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30S ribosomal protein S17AQ80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18AR55Escherichia coliMutation(s): 0 
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30S ribosomal protein S19AS79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20AT85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21AU51Escherichia coliMutation(s): 0 
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30S ribosomal protein S2AB218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3AC206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4AD205Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S ribosomal protein S5AE150Escherichia coliMutation(s): 0 
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30S ribosomal protein S6AF100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7AG150Escherichia coliMutation(s): 0 
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30S ribosomal protein S8AH129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9AI127Escherichia coliMutation(s): 0 
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Entity ID: 25
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Elongation factor TuAZ393Escherichia coliMutation(s): 0 
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50S ribosomal protein L1B5234Escherichia coliMutation(s): 0 
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50S ribosomal protein L11BI141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13BJ142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14BK121Escherichia coliMutation(s): 0 
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50S ribosomal protein L15BL143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16BM136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17BN120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18BO116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19BP114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20BQ117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21BR103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22BS110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23BT93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24BU102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BV94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27BW79Escherichia coliMutation(s): 0 
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50S ribosomal protein L28BX77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29BY63Escherichia coliMutation(s): 0 
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50S ribosomal protein L2BC271Escherichia coliMutation(s): 0 
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50S ribosomal protein L30BZ58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32B056Escherichia coliMutation(s): 0 
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50S ribosomal protein L33B150Escherichia coliMutation(s): 0 
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50S ribosomal protein L34B246Escherichia coliMutation(s): 0 
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50S ribosomal protein L35B364Escherichia coliMutation(s): 0 
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50S ribosomal protein L36B438Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BD209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4BE201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5BF178Escherichia coliMutation(s): 0 
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50S ribosomal protein L6BG176Escherichia coliMutation(s): 0 
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50S ribosomal protein L9BH149Escherichia coliMutation(s): 0 
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Entity ID: 21
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16S rRNAAA1530Escherichia coli
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Entity ID: 22
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A/T-site tRNA PheAY76N/A
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Entity ID: 23
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P-site tRNA fMet (Unmodified bases except for Thymine 54)AW76Escherichia coli
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  • Entity ID: 24
    MoleculeChainsLengthOrganismImage
    mRNAAX11N/A
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    E-site tRNA PheAV77Escherichia coli
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    Entity ID: 57
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    23S ribosomal RNABB2903Escherichia coli
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    Entity ID: 58
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNABA117Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GDP
    Query on GDP

    Download CCD File 
    AZ
    GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 6.70 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2015-03-25
      Changes: Other
    • Version 1.3: 2018-07-18
      Changes: Data collection
    • Version 1.4: 2019-12-18
      Changes: Database references, Derived calculations, Other