Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B4C2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.02 kDa 
• Atom Count: 3527 
• Modelled Residue Count: 425 
• Deposited Residue Count: 522 
• Unique protein chains: 2

4FXE

Crystal structure of the intact E. coli RelBE toxin-antitoxin complex

• PDB DOI: 10.2210/pdb4FXE/pdb

• Classification: TOXIN/TOXIN INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-07-03 Released: 2012-08-29 
• Deposition Author(s): Brodersen, D.E., Boggild, A., Sofos, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.285 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

Literature

The crystal structure of the intact E. coli RelBE toxin-antitoxin complex provides the structural basis for conditional cooperativity.

Boggild, A., Sofos, N., Andersen, K.R., Feddersen, A., Easter, A.D., Passmore, L.A., Brodersen, D.E.

(2012) Structure 20: 1641-1648

• PubMed: 22981948 
• DOI: 10.1016/j.str.2012.08.017
• Primary Citation of Related Structures:  
  4FXE, 4FXH, 4FXI


• PubMed Abstract: 
  

The bacterial relBE locus encodes a toxin-antitoxin complex in which the toxin, RelE, is capable of cleaving mRNA in the ribosomal A site cotranslationally. The antitoxin, RelB, both binds and inhibits RelE, and regulates transcription through operator binding and conditional cooperativity controlled by RelE. Here, we present the crystal structure of the intact Escherichia coli RelB2E2 complex at 2.8 Å resolution, comprising both the RelB-inhibited RelE and the RelB dimerization domain that binds DNA. RelE and RelB associate into a V-shaped heterotetrameric complex with the ribbon-helix-helix (RHH) dimerization domain at the apex. Our structure supports a model in which relO is optimally bound by two adjacent RelB2E heterotrimeric units, and is not compatible with concomitant binding of two RelB2E2 heterotetramers. The results thus provide a firm basis for understanding the model of conditional cooperativity at the molecular level.

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Organizational Affiliation: 

Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin RelB	A, B, C	79	Escherichia coli K-12	Mutation(s): 0  Gene Names: b1564, JW1556, relB
UniProt
Find proteins for P0C079 (Escherichia coli (strain K12)) Explore P0C079  Go to UniProtKB:  P0C079

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA interferase RelE	D, E, F	95	Escherichia coli K-12	Mutation(s): 1  Gene Names: b1563, JW1555, relE EC: 3.1
UniProt
Find proteins for P0C077 (Escherichia coli (strain K12)) Explore P0C077  Go to UniProtKB:  P0C077

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.285 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.23	α = 90
b = 77.23	β = 90
c = 362.82	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
SOLOMON	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-03 
• Released Date: 2012-08-29 
Deposition Author(s): Brodersen, D.E., Boggild, A., Sofos, N.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2012-12-26
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection