Biological Assembly 1  

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

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.03 kDa 
• Atom Count: 2347 
• Modelled Residue Count: 202 
• Deposited Residue Count: 228 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4ATO

New insights into the mechanism of bacterial Type III toxin-antitoxin systems: selective toxin inhibition by a non-coding RNA pseudoknot

• PDB DOI: 10.2210/pdb4ATO/pdb
• NDB: NA2159

• Classification: TOXIN/ANTITOXIN
• Organism(s): Bacillus thuringiensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-09 Released: 2012-12-26 
• Deposition Author(s): Short, F.L., Pei, X.Y., Blower, T.R., Ong, S.L., Luisi, B.F., Salmond, G.P.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Selectivity and Self-Assembly in the Control of a Bacterial Toxin by an Antitoxic Noncoding RNA Pseudoknot.

Short, F.L., Pei, X.Y., Blower, T.R., Ong, S.L., Fineran, P.C., Luisi, B.F., Salmond, G.P.C.

(2013) Proc Natl Acad Sci U S A 110: E241

• PubMed: 23267117 
• DOI: 10.1073/pnas.1216039110
• Primary Citation of Related Structures:  
  4ATO


• PubMed Abstract: 
  

Bacterial small RNAs perform numerous regulatory roles, including acting as antitoxic components in toxin-antitoxin systems. In type III toxin-antitoxin systems, small processed RNAs directly antagonize their toxin protein partners, and in the systems characterized the toxin and antitoxin components together form a trimeric assembly. In the present study, we sought to define how the RNA antitoxin, ToxI, inhibits its potentially lethal protein partner, ToxN. We show through cross-inhibition experiments with the ToxIN systems from Pectobacterium atrosepticum (ToxIN(Pa)) and Bacillus thuringiensis (ToxIN(Bt)) that ToxI RNAs are highly selective enzyme inhibitors. Both systems have an "addictive" plasmid maintenance phenotype. We demonstrate that ToxI(Pa) can inhibit ToxN(Pa) in vitro both in its processed form and as a repetitive precursor RNA, and this inhibition is linked to the self-assembly of the trimeric complex. Inhibition and self-assembly are both mediated entirely by the ToxI(Pa) RNA, with no requirement for cellular factors or exogenous energy. Finally, we explain the origins of ToxI antitoxin selectivity through our crystal structure of the ToxIN(Bt) complex. Our results show how a processed RNA pseudoknot can inhibit a deleterious protein with exquisite molecular specificity and how these self-contained and addictive RNA-protein pairs can confer different adaptive benefits in their bacterial hosts.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOXN	A	194	Bacillus thuringiensis	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for Q3YN09 (Bacillus thuringiensis subsp. kurstaki) Explore Q3YN09  Go to UniProtKB:  Q3YN09

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TOXI	B [auth G]	34	Bacillus thuringiensis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.1	α = 90
b = 127.1	β = 90
c = 37.735	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-09 
• Released Date: 2012-12-26 
Deposition Author(s): Short, F.L., Pei, X.Y., Blower, T.R., Ong, S.L., Luisi, B.F., Salmond, G.P.C.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-01-09
  Changes: Database references
• Version 1.2: 2013-01-30
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other