3J9Y

Cryo-EM structure of tetracycline resistance protein TetM bound to a translating E.coli ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Cryo-EM structure of the tetracycline resistance protein TetM in complex with a translating ribosome at 3.9- angstrom resolution.

Arenz, S.Nguyen, F.Beckmann, R.Wilson, D.N.

(2015) Proc Natl Acad Sci U S A 112: 5401-5406

  • DOI: 10.1073/pnas.1501775112
  • Primary Citation of Related Structures:  
    3J9Y

  • PubMed Abstract: 
  • Ribosome protection proteins (RPPs) confer resistance to tetracycline by binding to the ribosome and chasing the drug from its binding site. Current models for RPP action are derived from 7.2- to 16-Å resolution structures of RPPs bound to vacant or ...

    Ribosome protection proteins (RPPs) confer resistance to tetracycline by binding to the ribosome and chasing the drug from its binding site. Current models for RPP action are derived from 7.2- to 16-Å resolution structures of RPPs bound to vacant or nontranslating ribosomes. Here we present a cryo-electron microscopy reconstruction of the RPP TetM in complex with a translating ribosome at 3.9-Å resolution. The structure reveals the contacts of TetM with the ribosome, including interaction between the conserved and functionally critical C-terminal extension of TetM with a unique splayed conformation of nucleotides A1492 and A1493 at the decoding center of the small subunit. The resolution enables us to unambiguously model the side chains of the amino acid residues comprising loop III in domain IV of TetM, revealing that the tyrosine residues Y506 and Y507 are not responsible for drug-release as suggested previously but rather for intrafactor contacts that appear to stabilize the conformation of loop III. Instead, Pro509 at the tip of loop III is located directly within the tetracycline binding site where it interacts with nucleotide C1054 of the 16S rRNA, such that RPP action uses Pro509, rather than Y506/Y507, to directly dislodge and release tetracycline from the ribosome.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany; and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany wilson@genzentrum.lmu.de.



Macromolecules

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Entity ID: 3
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30S ribosomal protein S4d206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5e167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6f135Escherichia coliMutation(s): 0 
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30S ribosomal protein S8h130Escherichia 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 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 S20t87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21u71Escherichia coliMutation(s): 0 
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Tetracycline resistance protein TetMw639Enterococcus faecalisMutation(s): 0 
Gene Names: tetMtet(M)
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30S ribosomal protein S3c233Escherichia coliMutation(s): 0 
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30S ribosomal protein S7g179Escherichia 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 S13m118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14n102Escherichia coliMutation(s): 0 
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30S ribosomal protein S19s92Escherichia 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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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 L105165Escherichia coliMutation(s): 0 
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50S ribosomal protein L31670Escherichia coliMutation(s): 0 
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50S ribosomal protein L7/L12769Escherichia coliMutation(s): 0 
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30S ribosomal protein S2b240Escherichia coliMutation(s): 0 
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50S ribosomal protein L36438Escherichia coliMutation(s): 0 
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16S ribosomal RNAa1539Escherichia coli
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Entity ID: 15
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P-site fMet-tRNAfMetv78Escherichia coli
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    MoleculeChainsLengthOrganismImage
    mRNAx11Escherichia coli
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    Entity ID: 25
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    23S ribosomal RNAA2903Escherichia coli
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    Entity ID: 26
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    5S ribosomal RNAB120Escherichia coli
    Small Molecules
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    FME
    Query on FME
    vL-PEPTIDE LINKINGC6 H11 N O3 SMET
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2015-04-15
      Type: Initial release
    • Version 1.1: 2015-04-29
      Changes: Database references
    • Version 1.2: 2015-05-13
      Changes: Database references
    • Version 2.0: 2018-07-18
      Changes: Data collection, Polymer sequence