5U9F

3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure II)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanism of ribosome rescue by ArfA and RF2.

Demo, G.Svidritskiy, E.Madireddy, R.Diaz-Avalos, R.Grant, T.Grigorieff, N.Sousa, D.Korostelev, A.A.

(2017) Elife 6

  • DOI: 10.7554/eLife.23687
  • Primary Citation of Related Structures:  
    5U9F, 5U9G

  • PubMed Abstract: 
  • ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures - determined from a single sample - of the 70S ribosom ...

    ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures - determined from a single sample - of the 70S ribosome with ArfA•RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA 'senses' the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Alternative ribosome-rescue factor AY72Escherichia coli K-12Mutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
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50S ribosomal protein L103234Escherichia coliMutation(s): 0 
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50S ribosomal protein L204273Escherichia coliMutation(s): 0 
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50S ribosomal protein L305209Escherichia coliMutation(s): 0 
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50S ribosomal protein L406201Escherichia coliMutation(s): 0 
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50S ribosomal protein L507179Escherichia coliMutation(s): 0 
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50S ribosomal protein L608177Escherichia coliMutation(s): 0 
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50S ribosomal protein L909149Escherichia coliMutation(s): 0 
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50S ribosomal protein L1010165Escherichia coliMutation(s): 0 
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50S ribosomal protein L1111142Escherichia coliMutation(s): 0 
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50S ribosomal protein L1312142Escherichia coliMutation(s): 0 
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50S ribosomal protein L1413123Escherichia coliMutation(s): 0 
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50S ribosomal protein L1615136Escherichia coliMutation(s): 0 
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50S ribosomal protein L1716127Escherichia coliMutation(s): 0 
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50S ribosomal protein L1817117Escherichia coliMutation(s): 0 
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50S ribosomal protein L1918115Escherichia coliMutation(s): 0 
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50S ribosomal protein L2019118Escherichia coliMutation(s): 0 
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50S ribosomal protein L2120103Escherichia coliMutation(s): 0 
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50S ribosomal protein L2221110Escherichia coliMutation(s): 0 
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50S ribosomal protein L2322100Escherichia coliMutation(s): 0 
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50S ribosomal protein L2423104Escherichia coliMutation(s): 0 
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50S ribosomal protein L252494Escherichia coliMutation(s): 0 
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50S ribosomal protein L272585Escherichia coliMutation(s): 0 
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50S ribosomal protein L282678Escherichia coliMutation(s): 0 
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50S ribosomal protein L292763Escherichia coliMutation(s): 0 
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50S ribosomal protein L302859Escherichia coliMutation(s): 0 
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50S ribosomal protein L312970Escherichia coliMutation(s): 0 
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50S ribosomal protein L323057Escherichia coliMutation(s): 0 
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50S ribosomal protein L333155Escherichia coliMutation(s): 0 
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50S ribosomal protein L343246Escherichia coliMutation(s): 0 
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50S ribosomal protein L353365Escherichia coliMutation(s): 0 
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50S ribosomal protein L363438Escherichia coliMutation(s): 0 
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Entity ID: 39
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Peptide chain release factor RF2Z365Escherichia coli K-12Mutation(s): 0 
Gene Names: prfBsupKb2891JW5847
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30S ribosomal protein S2B241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3C233Escherichia coliMutation(s): 0 
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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 S6F131Escherichia coliMutation(s): 0 
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30S ribosomal protein S7G156Escherichia 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 S14N101Escherichia 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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16S ribosomal RNAA1539Escherichia coli
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23S ribosomal RNA012903Escherichia coli
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5S ribosomal RNA02119Escherichia coli
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fMet-tRNA (P- and E-site)W, X77Escherichia coli
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  • Entity ID: 38
    MoleculeChainsLengthOrganismImage
    truncated mRNAV14Escherichia coli
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    34
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    01, 02, 17, 19, 30, 31, 34, A, I, V, W, X
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.20 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 StatesGM106105
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107465

    Revision History 

    • Version 1.0: 2017-03-22
      Type: Initial release
    • Version 1.1: 2017-03-29
      Changes: Database references
    • Version 1.2: 2017-09-27
      Changes: Author supporting evidence, Data collection, Experimental preparation
    • Version 1.3: 2018-07-18
      Changes: Data collection
    • Version 1.4: 2020-01-01
      Changes: Author supporting evidence