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 1.4 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: https://doi.org/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 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11141Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7J7
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7J7
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12J [auth I]123Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7S3
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UniProt GroupP0A7S3
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-recycling factorK [auth J]185Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q9WX76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q9WX76 
Go to UniProtKB:  Q9WX76
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WX76
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Entity ID: 1
MoleculeChains LengthOrganismImage
ribosomal 23S RNA50Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
ribosomal 23S RNA22Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
ribosomal 23S RNA17Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
ribosomal 23S RNA13Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
ribosomal 23S RNA19Escherichia coli
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Entity ID: 6
MoleculeChains LengthOrganismImage
ribosomal 23S RNA19Escherichia coli
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Entity ID: 8
MoleculeChains LengthOrganismImage
ribosomal 16S RNA18Escherichia coli
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Entity ID: 9
MoleculeChains LengthOrganismImage
ribosomal 16S RNAI [auth h]19Escherichia coli
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Refinement description