5AFI

2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 3.1 of the entry. See complete history


Literature

Structure of the E. coli ribosome-EF-Tu complex at <3 angstrom resolution by Cs-corrected cryo-EM.

Fischer, N.Neumann, P.Konevega, A.L.Bock, L.V.Ficner, R.Rodnina, M.V.Stark, H.

(2015) Nature 520: 567-570

  • DOI: 10.1038/nature14275
  • Primary Citation of Related Structures:  
    5AFI

  • PubMed Abstract: 
  • Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analys ...

    Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes.


    Organizational Affiliation

    1] 3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany [2] Department of 3D Electron Cryomicroscopy, Institute of Microbiology and Genetics, Georg-August Universität, 37077 Göttingen, Germany.



Macromolecules

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Entity ID: 2
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30S ribosomal protein S2b240Escherichia coliMutation(s): 0 
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30S ribosomal protein S3c233Escherichia coliMutation(s): 0 
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Entity ID: 4
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30S ribosomal protein S4d206Escherichia coliMutation(s): 0 
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Entity ID: 5
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30S ribosomal protein S5e167Escherichia coliMutation(s): 0 
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Entity ID: 6
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30S ribosomal protein S6f135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7g179Escherichia coliMutation(s): 0 
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30S ribosomal protein S8h130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9i130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10j103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11k129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12l124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13m118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14n102Escherichia coliMutation(s): 0 
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30S ribosomal protein S15o89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16p82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17q84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18r75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19s92Escherichia coliMutation(s): 0 
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30S ribosomal protein S20t87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21u71Escherichia coliMutation(s): 0 
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Elongation factor Tu 2z393Escherichia coliMutation(s): 0 
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50S ribosomal protein L2C273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3D209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4E201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5F179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6G177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9H149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11I142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13J142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14K123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15L144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16M136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17N127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18O117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19P115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20Q118Escherichia coliMutation(s): 0 
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Entity ID: 43
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50S ribosomal protein L21R103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22S110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23T100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25V94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29Y63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Z59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32057Escherichia coliMutation(s): 0 
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50S ribosomal protein L33155Escherichia coliMutation(s): 0 
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50S ribosomal protein L34246Escherichia coliMutation(s): 0 
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50S ribosomal protein L35365Escherichia coliMutation(s): 0 
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50S ribosomal protein L36438Escherichia coliMutation(s): 0 
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50S ribosomal protein L105165Escherichia coliMutation(s): 0 
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50S ribosomal protein L31670Escherichia coliMutation(s): 0 
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Entity ID: 1
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16S ribosomal RNAa1539Escherichia coli
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Entity ID: 22
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P-site fMet-tRNAfMetv, w77Escherichia coli
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    mRNAx11Escherichia coli
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    A/T-site Phe-tRNAPhey77Escherichia coli
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    23S ribosomal RNAA2903Escherichia coli
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    Entity ID: 27
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    5S ribosomal RNAB120Escherichia coli
    Small Molecules
    Ligands 7 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    KIR
    Query on KIR

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    z
    KIRROMYCIN
    C43 H60 N2 O12
    HMSYAPGFKGSXAJ-PAHGNTJYSA-N
     Ligand Interaction
    GDP
    Query on GDP

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    z
    GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-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
    ZN
    Query on ZN

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    4, 6
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    CL
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    A, a
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
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    0, 4, A, B, N, a, v, z
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

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    A, B
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2015-03-11
      Type: Initial release
    • Version 1.1: 2017-06-07
      Changes: Atomic model, Derived calculations
    • Version 1.2: 2017-08-02
      Changes: Advisory, Data collection, Derived calculations
    • Version 1.3: 2017-08-09
      Changes: Structure summary
    • Version 2.0: 2019-02-20
      Changes: Data collection, Database references, Derived calculations, Polymer sequence
    • Version 3.0: 2019-06-26
      Changes: Data collection, Non-polymer description, Structure summary
    • Version 3.1: 2019-12-18
      Changes: Other