2XDD | pdb_00002xdd

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 (Depositor) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2XDD

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 95.4 kDa 
  • Atom Count: 6,308 
  • Modeled Residue Count: 594 
  • Deposited Residue Count: 621 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TOXNA,
B,
C [auth E]
171Pectobacterium atrosepticumMutation(s): 0 
EC: 3.1.27.3 (PDB Primary Data), 3.1 (UniProt)
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
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
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 (Depositor) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
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

View Full Validation Report



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
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary