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


This is version 2.0 of the entry. See complete history


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 tmRNA then enters the A site of the ribosome ...

    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.



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Entity ID: 2
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30S ribosomal protein S2B [auth AB]218Escherichia coliMutation(s): 0 
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30S ribosomal protein S3C [auth AC]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S4D [auth AD]205Escherichia coliMutation(s): 0 
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30S ribosomal protein S5E [auth AE]150Escherichia coliMutation(s): 0 
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30S ribosomal protein S6F [auth AF]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7G [auth AG]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8H [auth AH]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9I [auth AI]127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10J [auth AJ]98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11K [auth AK]117Escherichia coliMutation(s): 0 
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30S ribosomal protein S12L [auth AL]123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13M [auth AM]114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14N [auth AN]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15O [auth AO]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16P [auth AP]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17Q [auth AQ]80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18R [auth AR]55Escherichia coliMutation(s): 0 
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30S ribosomal protein S19S [auth AS]79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20T [auth AT]85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21U [auth AU]51Escherichia coliMutation(s): 0 
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SsrA-binding proteinW [auth AW]123Escherichia coliMutation(s): 0 
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elongation factor GY [auth AY]691Escherichia coliMutation(s): 0 
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50S ribosomal protein L2AA [auth BC]271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3BA [auth BD]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4CA [auth BE]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5DA [auth BF]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6EA [auth BG]176Escherichia coliMutation(s): 0 
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50S ribosomal protein L9FA [auth BH]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11GA [auth BI]141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13HA [auth BJ]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14IA [auth BK]122Escherichia coliMutation(s): 0 
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50S ribosomal protein L15JA [auth BL]143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16KA [auth BM]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17LA [auth BN]120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18MA [auth BO]116Escherichia coliMutation(s): 0 
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50S ribosomal protein L19NA [auth BP]114Escherichia coliMutation(s): 0 
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50S ribosomal protein L20OA [auth BQ]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21PA [auth BR]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22QA [auth BS]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23RA [auth BT]93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24SA [auth BU]102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25TA [auth BV]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27UA [auth BW]76Escherichia coliMutation(s): 0 
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50S ribosomal protein L28VA [auth BX]77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29WA [auth BY]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30XA [auth BZ]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32YA [auth B0]56Escherichia coliMutation(s): 0 
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50S ribosomal protein L33ZA [auth B1]50Escherichia coliMutation(s): 0 
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50S ribosomal protein L34AB [auth B2]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35BB [auth B3]64Escherichia coliMutation(s): 0 
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50S ribosomal protein L36CB [auth B4]38Escherichia coliMutation(s): 0 
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16S ribosomal RNAA [auth AA]1539Escherichia coli
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Entity ID: 22
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full length transfer messenger RNA (tmRNA)V [auth AV]363Escherichia coli
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formyl-methionine specific initiator transfer RNAX [auth AX]77Escherichia coli
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23S ribosomal RNAZ [auth BA]2903Escherichia coli
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5S ribosomal RNADB [auth BB]119Escherichia coli
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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  (Full details and data files)

  • 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