6GXP

Cryo-EM structure of a rotated E. coli 70S ribosome in complex with RF3-GDPCP(RF3-only)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1.

Graf, M.Huter, P.Maracci, C.Peterek, M.Rodnina, M.V.Wilson, D.N.

(2018) Nat Commun 9: 3053-3053

  • DOI: 10.1038/s41467-018-05465-1
  • Primary Citation of Related Structures:  
    6GWT, 6GXP, 6GXO, 6GXN, 6GXM

  • PubMed Abstract: 
  • During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 me ...

    During translation termination in bacteria, the release factors RF1 and RF2 are recycled from the ribosome by RF3. While high-resolution structures of the individual termination factors on the ribosome exist, direct structural insight into how RF3 mediates dissociation of the decoding RFs has been lacking. Here we have used the ApidaecinĀ 137 peptide to trap RF1 together with RF3 on the ribosome and visualize an ensemble of termination intermediates using cryo-electron microscopy. Binding of RF3 to the ribosome induces small subunit (SSU) rotation and swivelling of the head, yielding intermediate states with shifted P-site tRNAs and RF1 conformations. RF3 does not directly eject RF1 from the ribosome, but rather induces full rotation of the SSU that indirectly dislodges RF1 from its binding site. SSU rotation is coupled to the accommodation of the GTPase domain of RF3 on the large subunit (LSU), thereby promoting GTP hydrolysis and dissociation of RF3 from the ribosome.


    Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany. daniel.wilson@chemie.uni-hamburg.de.



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50S ribosomal protein L6G176Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W75Escherichia coliMutation(s): 0 
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50S ribosomal protein L28X77Escherichia 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 L105131Escherichia 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 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 S11k112Escherichia 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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Peptide chain release factor RF3w529Escherichia coliMutation(s): 0 
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Entity ID: 55
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Apidaecinz14Apis melliferaMutation(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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

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w
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 FoundationGermanyFOR-1805
German Research FoundationGermanyWI3285/6-1
Ministry of Education (Czech Republic)Czech RepublicCIISB project number LM2015043
European UnionCzech RepubliciNext project number 2992

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release