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- PDB-9ri9: Cryo-EM structure of the tomato NRC3 hexameric resistosome -

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Basic information

Entry
Database: PDB / ID: 9ri9
TitleCryo-EM structure of the tomato NRC3 hexameric resistosome
ComponentsNRC3
KeywordsIMMUNE SYSTEM / Plant Immunity / NLR / Resistosome
Function / homology
Function and homology information


defense response to other organism / ADP binding / defense response to virus / ATP binding / plasma membrane
Similarity search - Function
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 / : ...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
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsSeager, B.A. / Kamoun, S. / Madhuprakash, J.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y002997/1 United Kingdom
Gatsby Charitable Foundation United Kingdom
European Research Council (ERC)EP/Y032187/1European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: NRC3
D: NRC3
G: NRC3
I: NRC3
J: NRC3
L: NRC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)631,62712
Polymers628,5846
Non-polymers3,0436
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.: 6 / Mutation: L9E, L13E, L17E
Source method: isolated from a genetically manipulated source
Details: This is a fusion protein. The first 18 residues were not modelled. The protein contains a single amino acid linker followed by a 3x FLAG tag
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: LOC101260638 / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A3Q7GDL1
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / 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

ComponentName: Hexameric assembly of NRC3 / Type: COMPLEX
Details: hexameric resistosome formed by activation with Rx and CP
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Solanum lycopersicum (tomato)
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(HOCH2)3CNH21
2150 mMSaltNaCl1
35 mMSaltMgCl21
45 %GlycerolC3H8O31
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: 2700 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.84 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6150
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 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
21PHENIX1.21.2model refinement
22ISOLDE1.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1660190
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 234243 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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