2XDD

A processed non-coding RNA regulates a bacterial antiviral system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Phage Abortive Infection System, Toxin, Functions as a Protein-RNA Toxin-Antitoxin Pair.

Fineran, P.C.Blower, T.R.Foulds, I.J.Humphreys, D.P.Lilley, K.S.Salmond, G.P.C.

(2009) Proc Natl Acad Sci U S A 106: 894

  • DOI: https://doi.org/10.1073/pnas.0808832106
  • Primary Citation of Related Structures:  
    2XDD

  • PubMed Abstract: 

    Various mechanisms exist that enable bacteria to resist bacteriophage infection. Resistance strategies include the abortive infection (Abi) systems, which promote cell death and limit phage replication within a bacterial population. A highly effective 2-gene Abi system from the phytopathogen Erwinia carotovora subspecies atroseptica, designated ToxIN, is described. The ToxIN Abi system also functions as a toxin-antitoxin (TA) pair, with ToxN inhibiting bacterial growth and the tandemly repeated ToxI RNA antitoxin counteracting the toxicity. TA modules are currently divided into 2 classes, protein and RNA antisense. We provide evidence that ToxIN defines an entirely new TA class that functions via a novel protein-RNA mechanism, with analogous systems present in diverse bacteria. Despite the debated role of TA systems, we demonstrate that ToxIN provides viral resistance in a range of bacterial genera against multiple phages. This is the first demonstration of a novel mechanistic class of TA systems and of an Abi system functioning in different bacterial genera, both with implications for the dynamics of phage-bacterial interactions.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TOXNA,
B,
C [auth E]
171Pectobacterium atrosepticumMutation(s): 0 
EC: 3.1.27.3
UniProt
Find proteins for B8X8Z0 (Pectobacterium atrosepticum)
Explore B8X8Z0 
Go to UniProtKB:  B8X8Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8X8Z0
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
TOXID [auth F],
E [auth G],
F [auth H]
36Pectobacterium atrosepticum
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth E]
K [auth F]
G [auth A],
H [auth A],
I [auth B],
J [auth E],
K [auth F],
L [auth G],
M [auth G],
N [auth G],
O [auth H],
P [auth H],
Q [auth H],
R [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B,
C [auth E]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.85α = 90
b = 118.13β = 92.78
c = 41.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Version format compliance