2OB7

Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.

Gillet, R.Kaur, S.Li, W.Hallier, M.Felden, B.Frank, J.

(2007) J Biol Chem 282: 6356-6363

  • DOI: https://doi.org/10.1074/jbc.M609658200
  • Primary Citation of Related Structures:  
    2OB7

  • PubMed Abstract: 

    A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger RNA, small protein B, and ribosome protein S1. By means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein B, which appears near the decoding center. This result suggests that, when lacking a codon, the A-site on the small subunit is a target for small protein B. To investigate the role of S1 played in trans-translation, we obtained a cryo-electron microscopic map, including a stalled ribosome, transfer-messenger RNA, and small protein Bs but in the absence of S1. In this complex, several connections between the 30 S subunit and transfer-messenger RNA that appear in the +S1 complex are no longer found. We propose the unifying concept of scaffolding for the roles of small protein B and S1 in binding of transfer-messenger RNA to the ribosome during trans-translation, and we infer a pathway of sequential binding events in the initial phase of trans-translation.


  • Organizational Affiliation

    Université de Rennes I, IFR 140, UPRES JE 2311, INSERM U835 Biochimie Pharmaceutique, 2 Avenue du Professeur Léon Bernard, 35043 Rennes, France.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SsrA-binding proteinC [auth B],
D [auth C]
156Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for O66640 (Aquifex aeolicus (strain VF5))
Explore O66640 
Go to UniProtKB:  O66640
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66640
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
transfer-messenger RNA328Thermus thermophilus
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
16S ribosomal RNAB [auth D]86Thermus thermophilus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.6 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: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Refinement description