3J0D

Models for the T. thermophilus ribosome recycling factor bound to the E. coli post-termination complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into initial and intermediate steps of the ribosome-recycling process.

Yokoyama, T.Shaikh, T.R.Iwakura, N.Kaji, H.Kaji, A.Agrawal, R.K.

(2012) EMBO J 31: 1836-1846

  • DOI: 10.1038/emboj.2012.22
  • Primary Citation of Related Structures:  
    3J0D, 3J0E

  • PubMed Abstract: 
  • The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with ...

    The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven towards the tRNA-exit (E) site, with a large rotational movement of domain II of RRF towards the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adopt hitherto unknown conformations. Furthermore, binding of EF-G to the PoTC·RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC and (ii) the modes of action of EF-G during tRNA translocation and ribosome-recycling steps are markedly different.


    Organizational Affiliation

    Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY, USA.



Macromolecules

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11G141Escherichia coliMutation(s): 0 
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7J7
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  • Reference Sequence
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12I123Escherichia coliMutation(s): 0 
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7S3
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  • Reference Sequence
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factorJ185Thermus thermophilusMutation(s): 0 
Find proteins for Q9WX76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q9WX76 
Go to UniProtKB:  Q9WX76
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
ribosomal 23S RNAA50Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
ribosomal 23S RNAB22Escherichia coli
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    ribosomal 23S RNAC17Escherichia coli
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    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      ribosomal 23S RNAD13Escherichia coli
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      • Entity ID: 5
        MoleculeChainsLengthOrganismImage
        ribosomal 23S RNAE19Escherichia coli
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        • Entity ID: 6
          MoleculeChainsLengthOrganismImage
          ribosomal 23S RNAF19Escherichia coli
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          • Entity ID: 8
            MoleculeChainsLengthOrganismImage
            ribosomal 16S RNAH18Escherichia coli
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            • Entity ID: 9
              MoleculeChainsLengthOrganismImage
              ribosomal 16S RNAh19Escherichia coli
              Experimental Data & Validation

              Experimental Data

              • Method: ELECTRON MICROSCOPY
              • Resolution: 11.1 Å
              • Aggregation State: PARTICLE 
              • Reconstruction Method: SINGLE PARTICLE 

              Structure Validation

              View Full Validation Report



              Entry History 

              Deposition Data

              Revision History 

              • Version 1.0: 2012-04-25
                Type: Initial release
              • Version 1.1: 2013-11-13
                Changes: Database references
              • Version 1.2: 2014-07-23
                Changes: Other
              • Version 1.3: 2018-07-18
                Changes: Data collection