Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130.30 kDa 
• Atom Count: 8641 
• Modelled Residue Count: 492 
• Deposited Residue Count: 498 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3IYR

tmRNA-SmpB: a journey to the center of the bacterial ribosome

• PDB DOI: 10.2210/pdb3IYR/pdb
• EM Map EMD-5189: EMDB EMDataResource

• Classification: RIBOSOMAL PROTEIN/RNA
• Organism(s): Thermus thermophilus HB8
• Mutation(s): No 


• Deposited: 2010-04-16 Released: 2010-10-20 
• Deposition Author(s): Weis, F., Bron, P., Giudice, E., Rolland, J.P., Thomas, D., Felden, B., Gillet, R.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 13.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

tmRNA-SmpB: a journey to the centre of the bacterial ribosome.

Weis, F., Bron, P., Giudice, E., Rolland, J.P., Thomas, D., Felden, B., Gillet, R.

(2010) EMBO J 29: 3810-3818

• PubMed: 20953161 
• DOI: 10.1038/emboj.2010.252
• Primary Citation of Related Structures:  
  3IYQ, 3IYR


• PubMed Abstract: 
  

Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger RNA bound to small protein B (tmRNA-SmpB ribonucleoprotein complex). Trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. Here, we present the cryo-electron microscopy structures of tmRNA-SmpB accommodated or translocated into stalled ribosomes. Two atomic models for each state are proposed. This study reveals how tmRNA-SmpB crosses the ribosome and how, as the problematic mRNA is ejected, the tmRNA resume codon is placed onto the ribosomal decoding site by new contacts between SmpB and the nucleotides upstream of the tag-encoding sequence. This provides a structural basis for the transit of the large tmRNA-SmpB complex through the ribosome and for the means by which the tmRNA internal frame is set for translation to resume.

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Organizational Affiliation: 

Université de Rennes, UMR CNRS Equipe Structure et Dynamique des Macromolécules, Rennes, France.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SsrA-binding protein	B	149	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: smpB, TTHA0902
UniProt
Find proteins for Q8RR57 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q8RR57  Go to UniProtKB:  Q8RR57

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tmRNA	A	349	Thermus thermophilus HB8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 13.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-16 
• Released Date: 2010-10-20 
Deposition Author(s): Weis, F., Bron, P., Giudice, E., Rolland, J.P., Thomas, D., Felden, B., Gillet, R.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-07-18
  Changes: Data collection