6OT3

RF2 accommodated state bound Release complex 70S at 24 ms


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 hydrolysis in the peptidyl transfer center 70 Å away ...

    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.



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30S ribosomal protein S15UA [auth t]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16VA [auth u]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17WA [auth v]80Escherichia coliMutation(s): 0 
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30S ribosomal protein S21AB [auth z]70Escherichia coliMutation(s): 0 
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Peptide chain release factor 2CB [auth A]357Escherichia coliMutation(s): 0 
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FME-PHE-PHEDB [auth 6]3Escherichia coliMutation(s): 0 
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23S ribosomal RNAA [auth 1]2903Escherichia coli
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16S ribosomal RNAB [auth 2]1534Escherichia coli
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5S ribosomal RNAC [auth 3]120Escherichia coli
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    mRNAD [auth 4]9Escherichia coli
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    P-tRNABB [auth 5]76Escherichia coli
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    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    PB [auth a], QB [auth f]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    EB [auth 1] , FB [auth 1] , GB [auth 2] , HB [auth 3] , IB [auth 3] , JB [auth 3] , KB [auth 3] , LB [auth 3] , 
    EB [auth 1],  FB [auth 1],  GB [auth 2],  HB [auth 3],  IB [auth 3],  JB [auth 3],  KB [auth 3],  LB [auth 3],  MB [auth 3],  NB [auth 3],  OB [auth 3],  RB [auth i]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    FME
    Query on FME
    DB [auth 6]L-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 & Funding Information

    Deposition Data


    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  (Full details and data files)

    • 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