2RDO

50S subunit with EF-G(GDPNP) and RRF bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.

Gao, N.Zavialov, A.V.Ehrenberg, M.Frank, J.

(2007) J Mol Biol 374: 1345-1358

  • DOI: 10.1016/j.jmb.2007.10.021
  • Primary Citation of Related Structures:  
    2RDO

  • PubMed Abstract: 
  • After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Ba ...

    After termination of protein synthesis, the bacterial ribosome is split into its 30S and 50S subunits by the action of ribosome recycling factor (RRF) and elongation factor G (EF-G) in a guanosine 5'-triphosphate (GTP)-hydrolysis-dependent manner. Based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of EF-G to an RRF-containing posttermination ribosome triggers an interdomain rotation of RRF, which destabilizes two strong intersubunit bridges (B2a and B3) and, ultimately, separates the two subunits. Here, we present a 9-A (Fourier shell correlation cutoff of 0.5) cryo-electron microscopy map of a 50S x EF-G x guanosine 5'-[(betagamma)-imido]triphosphate x RRF complex and a quasi-atomic model derived from it, showing the interaction between EF-G and RRF on the 50S subunit in the presence of the noncleavable GTP analogue guanosine 5'-[(betagamma)-imido]triphosphate. The detailed information in this model and a comparative analysis of EF-G structures in various nucleotide- and ribosome-bound states show how rotation of the RRF head domain may be triggered by various domains of EF-G. For validation of our structural model, all known mutations in EF-G and RRF that relate to ribosome recycling have been taken into account. More importantly, our results indicate a substantial conformational change in the Switch I region of EF-G, suggesting that a conformational signal transduction mechanism, similar to that employed in transfer RNA translocation on the ribosome by EF-G, translates a large-scale movement of EF-G's domain IV, induced by GTP hydrolysis, into the domain rotation of RRF that eventually splits the ribosome into subunits.


    Related Citations: 
    • Structural insights into fusidic acid resistance and sensitivity in EF-G.
      Hansson, S., Singh, R., Gudkov, A.T., Liljas, A., Logan, D.T.
      (2005) J Mol Biol 348: 939
    • Structures of the bacterial ribosome at 3.5 A resolution.
      Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H.
      (2005) Science 310: 827
    • Crystal structure of the ribosome recycling factor from Escherichia coli.
      Kim, K.K., Min, K., Suh, S.W.
      (2000) EMBO J 19: 2362
    • Structure of the L1 protuberance in the ribosome.
      Nikulin, A., Eliseikina, I., Tishchenko, S., Nevskaya, N., Davydova, N., Platonova, O., Piendl, W., Selmer, M., Liljas, A., Drygin, D., Zimmermann, R., Garber, M., Nikonov, S.
      (2003) Nat Struct Mol Biol 10: 104
    • Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
      Gao, N., Zavialov, A.V., Li, W., Sengupta, J., Valle, M., Gursky, R.P., Ehrenberg, M., Frank, J.
      (2005) Mol Cell 18: 663

    Organizational Affiliation

    Howard Hughes Medical Institute, Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.



Macromolecules

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Entity ID: 3
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50S ribosomal protein L2C272Escherichia coliMutation(s): 0 
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50S ribosomal protein L16M136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17N127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18O117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21R103Escherichia coliMutation(s): 0 
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50S ribosomal protein L23T100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24U103Escherichia coliMutation(s): 0 
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50S ribosomal protein L27W84Escherichia coliMutation(s): 0 
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50S ribosomal protein L29X63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30Y58Escherichia coliMutation(s): 0 
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50S ribosomal protein L31Z70Escherichia coliMutation(s): 0 
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50S ribosomal protein L32056Escherichia coliMutation(s): 0 
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50S ribosomal protein L33154Escherichia coliMutation(s): 0 
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Entity ID: 27
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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 L11I141Escherichia coliMutation(s): 0 
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50S ribosomal protein L9H149Escherichia coliMutation(s): 0 
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50S ribosomal protein L19233Escherichia coliMutation(s): 0 
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Entity ID: 33
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Elongation factor G7704Escherichia coliMutation(s): 0 
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Entity ID: 34
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Ribosome recycling factor8185Escherichia coliMutation(s): 0 
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Entity ID: 1
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5S RIBOSOMAL RNAA120Escherichia coli
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23S RIBOSOMAL RNAB2904Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Data collection