6ORE

Release complex 70S

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

  • Deposited: 2019-04-30 Released: 2019-06-19 
  • Deposition Author(s): Fu, Z.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Swedish Research Council

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.

Fu, Z.Indrisiunaite, G.Kaledhonkar, S.Shah, B.Sun, M.Chen, B.Grassucci, R.A.Ehrenberg, M.Frank, J.

(2019) Nat Commun 10: 2579-2579

  • DOI: 10.1038/s41467-019-10608-z
  • Primary Citation of Related Structures:  
    6ORL, 6ORE, 6OT3, 6OST, 6OSK, 6OSQ, 6OUO

  • PubMed Abstract: 
  • When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of ...

    When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. jf2192@cumc.columbia.edu.



Macromolecules

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Entity ID: 6
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FME-PHE-PHEA3Escherichia coliMutation(s): 0 
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50S ribosomal protein L2B271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3C209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4D201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5E177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6F175Escherichia coliMutation(s): 0 
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50S ribosomal protein L9G149Escherichia 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 L17N119Escherichia 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 L23T94Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U103Escherichia coliMutation(s): 0 
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50S ribosomal protein L25V94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W76Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29Y62Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Z58Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L31a66Escherichia coliMutation(s): 0 
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50S ribosomal protein L32b56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33c52Escherichia coliMutation(s): 0 
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50S ribosomal protein L34d46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35e64Escherichia coliMutation(s): 0 
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50S ribosomal protein L36f38Escherichia coliMutation(s): 0 
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30S ribosomal protein S2g225Escherichia coliMutation(s): 0 
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Entity ID: 37
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30S ribosomal protein S3h208Escherichia coliMutation(s): 0 
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Entity ID: 38
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30S ribosomal protein S4i205Escherichia coliMutation(s): 0 
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Entity ID: 39
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30S ribosomal protein S5j156Escherichia coliMutation(s): 0 
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30S ribosomal protein S6k104Escherichia coliMutation(s): 0 
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Entity ID: 41
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30S ribosomal protein S7l151Escherichia coliMutation(s): 0 
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Entity ID: 42
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30S ribosomal protein S8m129Escherichia coliMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S9n127Escherichia coliMutation(s): 0 
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Entity ID: 44
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30S ribosomal protein S10o99Escherichia coliMutation(s): 0 
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30S ribosomal protein S11p117Escherichia coliMutation(s): 0 
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Entity ID: 46
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30S ribosomal protein S12q123Escherichia coliMutation(s): 0 
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Entity ID: 47
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30S ribosomal protein S13r116Escherichia coliMutation(s): 0 
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Entity ID: 48
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30S ribosomal protein S14s100Escherichia coliMutation(s): 0 
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Entity ID: 49
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30S ribosomal protein S15t88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16u82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17v80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18w66Escherichia coliMutation(s): 0 
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Entity ID: 53
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30S ribosomal protein S19x83Escherichia coliMutation(s): 0 
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Entity ID: 54
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30S ribosomal protein S20y86Escherichia coliMutation(s): 0 
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Entity ID: 55
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30S ribosomal protein S21z70Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNA12903Escherichia coli
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Entity ID: 2
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16S ribosomal RNA21534Escherichia coli
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5S ribosomal RNA3120Escherichia coli
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(P*UP*UP*CP*UP*UP*CP*UP*AP*A)-3')49Escherichia coli
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    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    P-tRNA576Escherichia coli
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    a, f
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    1, 2, 3, 5, B, C, Q, b, f, i, r
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  2 Unique
    IDChainsTypeFormula2D DiagramParent
    FME
    Query on FME
    AL-PEPTIDE LINKINGC6 H11 N O3 SMET
    0TD
    Query on 0TD
    qL-PEPTIDE LINKINGC5 H9 N O4 SASP
    Experimental Data & Validation

    Experimental Data

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

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2019-04-30 
    • Released Date: 2019-06-19 
    • Deposition Author(s): Fu, Z.

    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM55440
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169
    Swedish Research CouncilSweden--

    Revision History 

    • Version 1.0: 2019-06-19
      Type: Initial release
    • Version 1.1: 2019-06-26
      Changes: Data collection, Database references
    • Version 1.2: 2019-12-18
      Changes: Author supporting evidence, Other