8BV0

Binary complex between the NB-ARC domain from the Tomato immune receptor NRC1 and the SPRY domain-containing effector SS15 from the potato cyst nematode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Resurrection of plant disease resistance proteins via helper NLR bioengineering.

Contreras, M.P.Pai, H.Selvaraj, M.Toghani, A.Lawson, D.M.Tumtas, Y.Duggan, C.Yuen, E.L.H.Stevenson, C.E.M.Harant, A.Maqbool, A.Wu, C.H.Bozkurt, T.O.Kamoun, S.Derevnina, L.

(2023) Sci Adv 9: eadg3861-eadg3861

  • DOI: https://doi.org/10.1126/sciadv.adg3861
  • Primary Citation of Related Structures:  
    8BV0

  • PubMed Abstract: 

    Parasites counteract host immunity by suppressing helper nucleotide binding and leucine-rich repeat (NLR) proteins that function as central nodes in immune receptor networks. Understanding the mechanisms of immunosuppression can lead to strategies for bioengineering disease resistance. Here, we show that a cyst nematode virulence effector binds and inhibits oligomerization of the helper NLR protein NRC2 by physically preventing intramolecular rearrangements required for activation. An amino acid polymorphism at the binding interface between NRC2 and the inhibitor is sufficient for this helper NLR to evade immune suppression, thereby restoring the activity of multiple disease resistance genes. This points to a potential strategy for resurrecting disease resistance in crop genomes.


  • Organizational Affiliation

    The Sainsbury Laboratory, University of East Anglia, Norwich, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NRC1
A, C
347Solanum lycopersicumMutation(s): 0 
UniProt
Find proteins for A1X877 (Solanum lycopersicum)
Explore A1X877 
Go to UniProtKB:  A1X877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1X877
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Truncated secreted SPRY domain-containing protein 15 (Fragment)
B, D
224Globodera rostochiensisMutation(s): 0 
UniProt
Find proteins for A0A024E1S8 (Globodera rostochiensis)
Explore A0A024E1S8 
Go to UniProtKB:  A0A024E1S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024E1S8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.56α = 90
b = 128.56β = 90
c = 170.68γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012574
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V002937/1
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUNDGermanyBoostR
The Gatsby Charitable FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection