4V6T

Structure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

The complex of tmRNA-SmpB and EF-G on translocating ribosomes.

Ramrath, D.J.Yamamoto, H.Rother, K.Wittek, D.Pech, M.Mielke, T.Loerke, J.Scheerer, P.Ivanov, P.Teraoka, Y.Shpanchenko, O.Nierhaus, K.H.Spahn, C.M.

(2012) Nature 485: 526-529

  • DOI: 10.1038/nature11006
  • Primary Citation of Related Structures:  
    4V6T

  • PubMed Abstract: 
  • Bacterial ribosomes stalled at the 3' end of malfunctioning messenger RNAs can be rescued by transfer-messenger RNA (tmRNA)-mediated trans-translation. The SmpB protein forms a complex with the tmRNA, and the transfer-RNA-like domain (TLD) of the tmR ...

    Bacterial ribosomes stalled at the 3' end of malfunctioning messenger RNAs can be rescued by transfer-messenger RNA (tmRNA)-mediated trans-translation. The SmpB protein forms a complex with the tmRNA, and the transfer-RNA-like domain (TLD) of the tmRNA then enters the A site of the ribosome. Subsequently, the TLD-SmpB module is translocated to the P site, a process that is facilitated by the elongation factor EF-G, and translation is switched to the mRNA-like domain (MLD) of the tmRNA. Accurate loading of the MLD into the mRNA path is an unusual initiation mechanism. Despite various snapshots of different ribosome-tmRNA complexes at low to intermediate resolution, it is unclear how the large, highly structured tmRNA is translocated and how the MLD is loaded. Here we present a cryo-electron microscopy reconstruction of a fusidic-acid-stalled ribosomal 70S-tmRNA-SmpB-EF-G complex (carrying both of the large ligands, that is, EF-G and tmRNA) at 8.3 Å resolution. This post-translocational intermediate (TI(POST)) presents the TLD-SmpB module in an intrasubunit ap/P hybrid site and a tRNA(fMet) in an intrasubunit pe/E hybrid site. Conformational changes in the ribosome and tmRNA occur in the intersubunit space and on the solvent side. The key underlying event is a unique extra-large swivel movement of the 30S head, which is crucial for both tmRNA-SmpB translocation and MLD loading, thereby coupling translocation to MLD loading. This mechanism exemplifies the versatile, dynamic nature of the ribosome, and it shows that the conformational modes of the ribosome that normally drive canonical translation can also be used in a modified form to facilitate more complex tasks in specialized non-canonical pathways.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany.



Macromolecules

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Entity ID: 2
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30S ribosomal protein S2AB218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3AC206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4AD205Escherichia coliMutation(s): 0 
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Entity ID: 5
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30S ribosomal protein S5AE150Escherichia coliMutation(s): 0 
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30S ribosomal protein S6AF100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7AG151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8AH129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9AI127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10AJ98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11AK117Escherichia coliMutation(s): 0 
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30S ribosomal protein S12AL123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13AM114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14AN100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15AO88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16AP82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17AQ80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18AR55Escherichia coliMutation(s): 0 
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30S ribosomal protein S19AS79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20AT85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21AU51Escherichia coliMutation(s): 0 
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SsrA-binding proteinAW123Escherichia coliMutation(s): 0 
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elongation factor GAY691Escherichia coliMutation(s): 0 
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50S ribosomal protein L2BC271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BD209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4BE201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5BF177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6BG176Escherichia coliMutation(s): 0 
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50S ribosomal protein L9BH149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11BI141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13BJ142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14BK122Escherichia coliMutation(s): 0 
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50S ribosomal protein L15BL143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16BM136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17BN120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18BO116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19BP114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20BQ117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21BR103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22BS110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23BT93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24BU102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25BV94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27BW76Escherichia coliMutation(s): 0 
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50S ribosomal protein L28BX77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29BY63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30BZ58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32B056Escherichia coliMutation(s): 0 
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50S ribosomal protein L33B150Escherichia coliMutation(s): 0 
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50S ribosomal protein L34B246Escherichia coliMutation(s): 0 
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50S ribosomal protein L35B364Escherichia coliMutation(s): 0 
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50S ribosomal protein L36B438Escherichia coliMutation(s): 0 
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16S ribosomal RNAAA1539Escherichia coli
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Entity ID: 22
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full length transfer messenger RNA (tmRNA)AV363Escherichia coli
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Entity ID: 24
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formyl-methionine specific initiator transfer RNAAX77Escherichia coli
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Entity ID: 26
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23S ribosomal RNABA2903Escherichia coli
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5S ribosomal RNABB119Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-01
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 2.0: 2019-12-18
    Changes: Atomic model, Data collection, Derived calculations, Other