6GWT

Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State I)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

  • 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 mediates dissociation of the decoding RFs has been lacking ...

    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 Apidaecin 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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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth r]65Escherichia coliMutation(s): 0 
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Entity ID: 52
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30S ribosomal protein S19ZA [auth s]79Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth t]85Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21BB [auth u]65Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor RF1CB [auth v]248Escherichia coliMutation(s): 0 
Gene Names: prfA, sueB, uar, b1211, JW1202
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 3DB [auth w]525Escherichia coliMutation(s): 0 
Gene Names: prfC, EC55989_5036
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
ApidaecinFB [auth z]14Apis melliferaMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA2,903Escherichia coli
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Entity ID: 2
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5S ribosomal RNAB120Escherichia coli
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Entity ID: 33
MoleculeChainsLengthOrganismImage
mRNAGA [auth 7]7Escherichia coli
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Entity ID: 34
MoleculeChainsLengthOrganismImage
16S ribosomal RNAHA [auth a]1,539Escherichia coli
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Entity ID: 57
MoleculeChainsLengthOrganismImage
fMet-tRNAEB [auth x]77Escherichia coli
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP
Download Ideal Coordinates CCD File 
GB [auth w]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
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  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations