9RDC | pdb_00009rdc

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

• PDB DOI: https://doi.org/10.2210/pdb9RDC/pdb

• Classification: PROTEIN BINDING
• Organism(s): Phytophthora infestans, Nicotiana benthamiana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-02 Released: 2025-07-16 
• Deposition Author(s): Contreras, M.P., Madhuprakash, J., Lawson, D.M., Kamoun, S.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC)

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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

Literature

An effector from the potato late blight pathogen bridges ENTH-domain protein TOL9a to 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.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.07.06.663370

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RxLR effector protein PITG_16705	A, B	619	Phytophthora infestans	Mutation(s): 0  Gene Names: PITG_16705
UniProt
Find proteins for D0NVF3 (Phytophthora infestans (strain T30-4)) Explore D0NVF3  Go to UniProtKB:  D0NVF3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Target of myb protein 1	C, D	150	Nicotiana benthamiana	Mutation(s): 0  Gene Names: A4A49_18419
UniProt
Find proteins for A0A1U7W2Q6 (Nicotiana sylvestris) Explore A0A1U7W2Q6  Go to UniProtKB:  A0A1U7W2Q6

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 = 85.874	α = 90
b = 136.912	β = 90
c = 195.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Contreras, M.P., Madhuprakash, J., Lawson, D.M., Kamoun, S.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V002937/1
European Research Council (ERC)	European Union	743165

Revision History  

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