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: 135.74 kDa 
• Atom Count: 9018 
• Modelled Residue Count: 495 
• Deposited Residue Count: 499 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3IZ4

Modified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpB

• PDB DOI: 10.2210/pdb3IZ4/pdb
• EM Map EMD-5234: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-21 Released: 2010-10-20 
• Deposition Author(s): Hashem, Y., Fu, J., Frank, J.

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Experimental Data Snapshot

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

Literature

Visualizing the transfer-messenger RNA as the ribosome resumes translation.

Fu, J., Hashem, Y., Wower, I., Lei, J., Liao, H.Y., Zwieb, C., Wower, J., Frank, J.

(2010) EMBO J 29: 3819-3825

• PubMed: 20940705 
• DOI: 10.1038/emboj.2010.255
• Primary Citation of Related Structures:  
  3IZ4


• PubMed Abstract: 
  

Bacterial ribosomes stalled by truncated mRNAs are rescued by transfer-messenger RNA (tmRNA), a dual-function molecule that contains a tRNA-like domain (TLD) and an internal open reading frame (ORF). Occupying the empty A site with its TLD, the tmRNA enters the ribosome with the help of elongation factor Tu and a protein factor called small protein B (SmpB), and switches the translation to its own ORF. In this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-formed complex containing ribosome and the tmRNA at the point where the TLD is accommodated into the ribosomal P site. We show that tmRNA maintains a stable 'arc and fork' structure on the ribosome when its TLD moves to the ribosomal P site and translation resumes on its ORF. Based on the density map, we built an atomic model, which suggests that SmpB interacts with the five nucleotides immediately upstream of the resume codon, thereby determining the correct selection of the reading frame on the ORF of tmRNA.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SsrA-binding protein	B	122	Escherichia coli	Mutation(s): 0
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
Modified E. coli transfer-messenger RNA	A	377	Escherichia coli

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-21 
• Released Date: 2010-10-20 
Deposition Author(s): Hashem, Y., Fu, J., Frank, J.

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