9RDC | pdb_00009rdc

Crystal structure of Phytophthora infestans effector AVRcap1b in complex with the ENTH domain of Nicotiana benthamiana NbTOL9a protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 
    0.286 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A potato late blight pathogen effector interacts with ENTH-domain protein TOL9a and an activated helper NLR to suppress immunity.

Madhuprakash, J.Toghani, A.Pai, H.Harvey, M.Bentham, A.R.Seager, B.A.Yuen, E.L.H.De la Concepcion, J.C.Lawson, D.M.Stevenson, C.E.M.Vergara-Cruces, A.Derevnina, L.Bozkurt, T.O.Banfield, M.J.Kamoun, S.Contreras, M.P.

(2026) Sci Adv 12: eaea4500-eaea4500

  • DOI: https://doi.org/10.1126/sciadv.aea4500
  • Primary Citation Related Structures: 
    9RDC

  • PubMed Abstract: 

    Pathogens counteract central nodes of NLR immune receptor networks to suppress immunity. However, the mechanisms by which pathogens hijack helper NLR pathways are poorly understood. We show that an effector from the late blight pathogen Phytophthora infestans interacts with the host protein NbTOL9a and a helper NLR to suppress immunity. We solved the crystal structure of the RXLR-LWY effector AVRcap1b in complex with the ENTH domain of NbTOL9a. The structure revealed that, unlike other RXLR-LWY effectors, AVRcap1b has a previously unidentified L-shaped fold that defines a distinct structural family of effectors in the genus Phytophthora . We defined the AVRcap1b/NbTOL9a binding interface and designed effector mutants that do not bind NbTOL9a, impairing immune suppression. This suggests that ENTH binding is required for full virulence activity. Last, we show that AVRcap1b associates specifically with activated NbNRC2 independently of NbTOL9a binding. We propose a model in which the effector interconnects NbNRC2 with the NbTOL9a pathway. Our results illustrate a previously uncharacterized pathogen mechanism to hijack NLR pathways and suppress immunity.


  • Organizational Affiliation
    • The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.

Macromolecule Content 

  • Total Structure Weight: 174.91 kDa 
  • Atom Count: 11,839 
  • Modeled Residue Count: 1,470 
  • Deposited Residue Count: 1,538 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RxLR effector protein PITG_16705
A, B
619Phytophthora infestansMutation(s): 0 
Gene Names: PITG_16705
UniProt
Find proteins for D0NVF3 (Phytophthora infestans (strain T30-4))
Explore D0NVF3 
Go to UniProtKB:  D0NVF3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0NVF3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Target of myb protein 1
C, D
150Nicotiana benthamianaMutation(s): 0 
Gene Names: A4A49_18419
UniProt
Find proteins for A0A1U7W2Q6 (Nicotiana sylvestris)
Explore A0A1U7W2Q6 
Go to UniProtKB:  A0A1U7W2Q6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U7W2Q6
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free:  0.286 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.874α = 90
b = 136.912β = 90
c = 195.574γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V002937/1
European Research Council (ERC)European Union743165

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references
  • Version 1.2: 2026-06-17
    Changes: Database references