5M41

Crystal structure of nigritoxine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report



Literature

Nigritoxin is a bacterial toxin for crustaceans and insects.

Labreuche, Y.Chenivesse, S.Jeudy, A.Le Panse, S.Boulo, V.Ansquer, D.Pages, S.Givaudan, A.Czjzek, M.Le Roux, F.

(2017) Nat Commun 8: 1248-1248

  • DOI: 10.1038/s41467-017-01445-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Tetraconata (Pancrustacea) concept proposes that insects are more closely related to aquatic crustaceans than to terrestrial centipedes or millipedes. The question therefore arises whether insects have kept crustacean-specific genetic traits that ...

    The Tetraconata (Pancrustacea) concept proposes that insects are more closely related to aquatic crustaceans than to terrestrial centipedes or millipedes. The question therefore arises whether insects have kept crustacean-specific genetic traits that could be targeted by specific toxins. Here we show that a toxin (nigritoxin), originally identified in a bacterial pathogen of shrimp, is lethal for organisms within the Tetraconata and non-toxic to other animals. X-ray crystallography reveals that nigritoxin possesses a new protein fold of the α/β type. The nigritoxin N-terminal domain is essential for cellular translocation and likely encodes specificity for Tetraconata. Once internalized by eukaryotic cells, nigritoxin induces apoptotic cell death through structural features that are localized in the C-terminal domain of the protein. We propose that nigritoxin will be an effective means to identify a Tetraconata evolutionarily conserved pathway and speculate that nigritoxin holds promise as an insecticidal protein.


    Organizational Affiliation

    Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France. frederique.le-roux@sb-roscoff.fr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NigritoxineA757Vibrio nigripulchritudoMutation(s): 0 
Gene Names: VIBNI_0175
Find proteins for F0V195 (Vibrio nigripulchritudo)
Explore F0V195 
Go to UniProtKB:  F0V195
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.16α = 90
b = 185.16β = 90
c = 185.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release