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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
ComponentsSlNRC3
KeywordsIMMUNE SYSTEM / Plant Immunity / NLR / Resistosome
Function / homology
Function and homology information


defense response to other organism / ADP binding / 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 / : / Leucine-rich repeat region ...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
CitationJournal: To Be Published
Title: Cryo-EM structure of the tomato NRC3 hexameric resistosome
Authors: Seager, B.A. / 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: SlNRC3
D: SlNRC3
G: SlNRC3
I: SlNRC3
J: SlNRC3
L: SlNRC3
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
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 SlNRC3 / 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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