6ENJ

Polyproline-stalled ribosome in the presence of A+P site tRNA and elongation-factor P (EF-P)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.

Huter, P.Arenz, S.Bock, L.V.Graf, M.Frister, J.O.Heuer, A.Peil, L.Starosta, A.L.Wohlgemuth, I.Peske, F.Novacek, J.Berninghausen, O.Grubmuller, H.Tenson, T.Beckmann, R.Rodnina, M.V.Vaiana, A.C.Wilson, D.N.

(2017) Mol Cell 68: 515-527.e6

  • DOI: 10.1016/j.molcel.2017.10.014
  • Primary Citation of Related Structures:  
    6ENU, 6ENJ, 6ENF

  • PubMed Abstract: 
  • Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking ...

    Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation.


    Organizational Affiliation

    Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany; Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany. Electronic address: daniel.wilson@chemie.uni-hamburg.de.



Macromolecules

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50S ribosomal protein L2C271Escherichia 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 L5F177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6G176Escherichia coliMutation(s): 0 
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50S ribosomal protein L13J142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14K122Escherichia coliMutation(s): 0 
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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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50S ribosomal protein L17N120Escherichia coliMutation(s): 0 
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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 L20Q117Escherichia 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 L23T93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25V94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W84Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29Y63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Z58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32056Escherichia coliMutation(s): 0 
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50S ribosomal protein L33150Escherichia coliMutation(s): 0 
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50S ribosomal protein L34246Escherichia coliMutation(s): 0 
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50S ribosomal protein L35364Escherichia coliMutation(s): 0 
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50S ribosomal protein L36438Escherichia coliMutation(s): 0 
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50S ribosomal protein L31666Escherichia coliMutation(s): 0 
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30S ribosomal protein S2b218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3c206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4d205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5e157Escherichia coliMutation(s): 0 
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30S ribosomal protein S6f100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7g151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8h129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9i127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10j98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11k116Escherichia coliMutation(s): 0 
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30S ribosomal protein S12l123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13m114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14n101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15o88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16p82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17q80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18r65Escherichia coliMutation(s): 0 
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30S ribosomal protein S19s79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20t85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21u65Escherichia coliMutation(s): 0 
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Entity ID: 52
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Elongation factor Pw188Escherichia coliMutation(s): 0 
Gene Names: efpb4147JW4107
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50S ribosomal protein L17224Escherichia coliMutation(s): 0 
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23S Ribosomal RNAA2903Escherichia coli
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5S Ribosomal RNAB120Escherichia coli
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16S ribosomal RNAa1539Escherichia coli
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  • Entity ID: 53
    MoleculeChainsLengthOrganismImage
    mRNAv9Escherichia coli
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    Entity ID: 54
    MoleculeChainsLengthOrganismImage
    Proline tRNA9, x77Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PRO
    Query on PRO

    Download CCD File 
    9
    PROLINE
    C5 H9 N O2
    ONIBWKKTOPOVIA-BYPYZUCNSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    KEO
    Query on KEO
    wL-PEPTIDE LINKINGC12 H26 N4 O4LYS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.70 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermanyFOR1805
    German Research FoundationGermanyWI3285/4-1
    iNEXTNetherlands1503

    Revision History 

    • Version 1.0: 2017-11-22
      Type: Initial release
    • Version 1.1: 2018-01-31
      Changes: Author supporting evidence
    • Version 1.2: 2019-10-30
      Changes: Advisory, Data collection, Derived calculations