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- PDB-9ria: Cryo-EM structure of tomato NRC3-AVRcap1b complex -

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Basic information

Entry
Database: PDB / ID: 9ria
TitleCryo-EM structure of tomato NRC3-AVRcap1b complex
Components
  • NRC3
  • RxLR effector protein PITG_16705
KeywordsIMMUNE SYSTEM / Effector / NLR / Plant Immunity / Resistosome
Function / homology
Function and homology information


defense response to other organism / ADP binding / defense response to virus / host cell cytoplasm / extracellular region / ATP binding / plasma membrane
Similarity search - Function
: / Effector PexRD54, WY-domain / RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / : / Disease resistance protein Winged helix domain / Disease resistance protein, plants ...: / Effector PexRD54, WY-domain / RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / : / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / RxLR effector protein PITG_16705
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Phytophthora infestans (potato late blight agent)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSeager, B.A. / Kamoun, S. / Madhuprakash, J.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y002997/1 United Kingdom
European Research Council (ERC)EP/Y032187/1European Union
Citation
Journal: Sci Adv / Year: 2026
Title: A plant pathogen effector blocks stepwise assembly of a helper NLR resistosome.
Authors: Benjamin A Seager / Adeline Harant / Mauricio P Contreras / Liang-Yu Hou / Chih Hang Wu / Sophien Kamoun / Jogi Madhuprakash /
Abstract: Helper NLRs function as central nodes in plant immune networks. Upon activation, they oligomerize into inflammasome-like resistosomes to initiate immune signaling, yet the dynamics of resistosome ...Helper NLRs function as central nodes in plant immune networks. Upon activation, they oligomerize into inflammasome-like resistosomes to initiate immune signaling, yet the dynamics of resistosome assembly remain poorly understood. Here, we show that the virulence effector AVRcap1b from the Irish potato famine pathogen suppresses immune activation by directly engaging oligomerization intermediates of the tomato helper NLR SlNRC3. Cryo-EM structures of SlNRC3 in AVRcap1b-bound and unbound states reveal that AVRcap1b bridges multiple protomers, stabilizing a stalled intermediate and preventing formation of a functional resistosome. Leveraging AVRcap1b as a molecular tool, we also capture an additional SlNRC3 resistosome intermediate showing that assembly proceeds in a stepwise manner from dissociated monomers. These findings uncover a previously unrecognized vulnerability in NLR activation and reveal a pathogen strategy that disrupts immune complex assembly. This work advances mechanistic understanding of resistosome formation and uncovers a previously unrecognized facet of pathogen-plant coevolution.
#1: Journal: Biorxiv / Year: 2025
Title: A plant pathogen effector blocks stepwise assembly of a helper NLR resistosome
Authors: Seager, B.A. / Harant, A. / Contreras, M.P. / Hou, L.Y. / Wu, C.H. / Kamoun, S. / Madhuprakash, J.
History
DepositionJun 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2026Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NRC3
B: NRC3
C: NRC3
G: RxLR effector protein PITG_16705
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,9527
Polymers392,4304
Non-polymers1,5223
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NRC3 / Helper nucleotide-binding leucine-rich repeat (NLR) protein / SlNRC3


Mass: 104763.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: LOC101260638 / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A3Q7GDL1
#2: Protein RxLR effector protein PITG_16705


Mass: 78138.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans (potato late blight agent)
Gene: PITG_16705 / Production host: Nicotiana benthamiana (plant) / References: UniProt: D0NVF3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1NRC3-AVRcap1b complexCOMPLEX#1-#20MULTIPLE SOURCES
2NRC3COMPLEX#11RECOMBINANT
3AVRcap1bCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Solanum lycopersicum (tomato)4081
32Solanum lycopersicum (tomato)4081
43Phytophthora infestans (potato late blight agent)4787
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Nicotiana benthamiana (plant)4100
32Nicotiana benthamiana (plant)4100
43Nicotiana benthamiana (plant)4100
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2150 mMSaltNaCl1
35 mMSaltMgCl21
45 %Glycerol1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.13 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7555
EM imaging opticsEnergyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPU3.4image acquisition
4cryoSPARC4.6.2CTF correction
7Coot0.9.8.95model fitting
8UCSF ChimeraX1.8model fitting
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC4.6.23D reconstruction
14PHENIX1.21.2model refinement
15ISOLDE1.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3531889
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: OTHER / Num. of particles: 267047 / Details: composite map / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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