5M41 | pdb_00005m41

Crystal structure of nigritoxine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5M41

This is version 1.1 of the entry. See complete history

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: https://doi.org/10.1038/s41467-017-01445-z
  • Primary Citation Related Structures: 
    5M41

  • 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 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
    • Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.

Macromolecule Content 

  • Total Structure Weight: 83.03 kDa 
  • Atom Count: 5,764 
  • Modeled Residue Count: 712 
  • Deposited Residue Count: 757 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nigritoxine757Vibrio nigripulchritudoMutation(s): 0 
Gene Names: VIBNI_0175

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations