6EK4

PaxB from Photorhabdus luminescens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and mechanism of the two-component alpha-helical pore-forming toxin YaxAB.

Brauning, B.Bertosin, E.Praetorius, F.Ihling, C.Schatt, A.Adler, A.Richter, K.Sinz, A.Dietz, H.Groll, M.

(2018) Nat Commun 9: 1806-1806

  • DOI: 10.1038/s41467-018-04139-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxA ...

    Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA-YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures.


    Organizational Affiliation

    Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Chair of Biochemistry, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany. bastian.braeuning@tum.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PaxB
A, B, C, D
353Photorhabdus namnaonensisMutation(s): 0 
Find proteins for A0A1B8YJW8 (Photorhabdus namnaonensis)
Go to UniProtKB:  A0A1B8YJW8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.590α = 90.00
b = 70.180β = 108.41
c = 136.890γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release