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)

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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

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:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0NVF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1U7W2Q6
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 = 85.874	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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Contreras, M.P.

Madhuprakash, J.

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 (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.