6WES

Crystal structure of the effector SnTox3 from Parastagonospora nodorum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors.

Outram, M.A.Sung, Y.C.Yu, D.Dagvadorj, B.Rima, S.A.Jones, D.A.Ericsson, D.J.Sperschneider, J.Solomon, P.S.Kobe, B.Williams, S.J.

(2021) New Phytol 231: 2282-2296

  • DOI: https://doi.org/10.1111/nph.17516
  • Primary Citation of Related Structures:  
    6WES

  • PubMed Abstract: 

    Plant pathogens cause disease through secreted effector proteins, which act to promote infection. Typically, the sequences of effectors provide little functional information and further targeted experimentation is required. Here, we utilized a structure/function approach to study SnTox3, an effector from the necrotrophic fungal pathogen Parastagonospora nodorum, which causes cell death in wheat-lines carrying the sensitivity gene Snn3. We developed a workflow for the production of SnTox3 in a heterologous host that enabled crystal structure determination and functional studies. We show this approach can be successfully applied to study effectors from other pathogenic fungi. The β-barrel fold of SnTox3 is a novel fold among fungal effectors. Structure-guided mutagenesis enabled the identification of residues required for Snn3 recognition. SnTox3 is a pre-pro-protein, and the pro-domain of SnTox3 can be cleaved in vitro by the protease Kex2. Complementing this, an in silico study uncovered the prevalence of a conserved motif (LxxR) in an expanded set of putative pro-domain-containing fungal effectors, some of which can be cleaved by Kex2 in vitro. Our in vitro and in silico study suggests that Kex2-processed pro-domain (designated here as K2PP) effectors are common in fungi and this may have broad implications for the approaches used to study their functions.


  • Organizational Affiliation

    Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tox3158Parastagonospora nodorum SN15Mutation(s): 0 
Gene Names: Tox3
UniProt
Find proteins for C5IAW5 (Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173))
Explore C5IAW5 
Go to UniProtKB:  C5IAW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5IAW5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.87α = 90
b = 29.91β = 102.12
c = 56.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE160100893
Australian Research Council (ARC)AustraliaDP160102244
Australian Research Council (ARC)AustraliaDP190102526
Australian Research Council (ARC)AustraliaDP180102355
Australian Research Council (ARC)AustraliaDP120103558
Australian Research Council (ARC)AustraliaFL180100109

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2021-06-16
    Changes: Database references
  • Version 1.3: 2021-09-01
    Changes: Database references