6GY8

Crystal structure of XaxA from Xenorhabdus nematophila

• PDB DOI:  https://doi.org/10.2210/pdb6GY8/pdb

• Classification: TOXIN
• Organism(s): Xenorhabdus nematophila ATCC 19061
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2018-06-28 Released: 2018-07-25 
• Deposition Author(s): Schubert, E., Raunser, S.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.286 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 

Literature

Membrane insertion of alpha-xenorhabdolysin in near-atomic detail.

Schubert, E., Vetter, I.R., Prumbaum, D., Penczek, P.A., Raunser, S.

(2018) Elife 7

• PubMed: 30010541 
• DOI: https://doi.org/10.7554/eLife.38017
• Primary Citation of Related Structures:  
  6GY6, 6GY7, 6GY8


• PubMed Abstract: 
  

α-Xenorhabdolysins (Xax) are α-pore-forming toxins (α-PFT) that form 1-1.3 MDa large pore complexes to perforate the host cell membrane. PFTs are used by a variety of bacterial pathogens to attack host cells. Due to the lack of structural information, the molecular mechanism of action of Xax toxins is poorly understood. Here, we report the cryo-EM structure of the XaxAB pore complex from Xenorhabdus nematophila and the crystal structures of the soluble monomers of XaxA and XaxB. The structures reveal that XaxA and XaxB are built similarly and appear as heterodimers in the 12-15 subunits containing pore, classifying XaxAB as bi-component α-PFT. Major conformational changes in XaxB, including the swinging out of an amphipathic helix are responsible for membrane insertion. XaxA acts as an activator and stabilizer for XaxB that forms the actual transmembrane pore. Based on our results, we propose a novel structural model for the mechanism of Xax intoxication.

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Organizational Affiliation: 

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.19 kDa 
• Atom Count: 5,616 
• Modelled Residue Count: 677 
• Deposited Residue Count: 816 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XaxA	A, B	408	Xenorhabdus nematophila ATCC 19061	Mutation(s): 0  Gene Names: xaxA, XNC1_3766 Membrane Entity: Yes
UniProt
Find proteins for D3VB22 (Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / CCUG 14189 / LMG 1036 / NCIMB 9965 / AN6)) Explore D3VB22  Go to UniProtKB:  D3VB22

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.286 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.27	α = 90
b = 90.83	β = 90
c = 153.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
HKL2Map	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Schubert, E., Raunser, S.

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Funding Organization	Location	Grant Number
European Research Council	Germany	615984

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release