PaxB from Photorhabdus luminescens

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

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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: https://doi.org/10.1038/s41467-018-04139-2
  • Primary Citation of Related Structures:  
    6EK4, 6EK7, 6EK8, 6EL1

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
353Photorhabdus luminescensMutation(s): 0 
Gene Names: Phpb_01513
Find proteins for A0A1B8YJW8 (Photorhabdus namnaonensis)
Explore A0A1B8YJW8 
Go to UniProtKB:  A0A1B8YJW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B8YJW8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.59α = 90
b = 70.18β = 108.41
c = 136.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description