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- EMDB-53990: Cryo-EM structure of the tomato NRC3 hexameric resistosome -

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Basic information

Entry
Database: EMDB / ID: EMD-53990
TitleCryo-EM structure of the tomato NRC3 hexameric resistosome
Map dataunsharpened consensus map
Sample
  • Complex: hexameric assembly of SlNRC3
    • Protein or peptide: SlNRC3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPlant Immunity / NLR / Resistosome / IMMUNE SYSTEM
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
Uncharacterized protein
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsSeager BA / Kamoun S / Madhuprakash J
Funding support United Kingdom, European Union, 4 items
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 BA / Kamoun S / Madhuprakash J
History
DepositionJun 11, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53990.png

Downloads & links

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Map

FileDownload / File: emd_53990.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened consensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 414. Å		0.83 Å/pix.
x 500 pix.
= 414. Å		0.83 Å/pix.
x 500 pix.
= 414. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.26278284 - 0.7050905
Average (Standard dev.)0.00020816403 (±0.012445518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened consensus map

Fileemd_53990_additional_1.map
Annotationsharpened consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_53990_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_53990_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : hexameric assembly of SlNRC3

EntireName: hexameric assembly of SlNRC3
Components
  • Complex: hexameric assembly of SlNRC3
    • Protein or peptide: SlNRC3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: hexameric assembly of SlNRC3

SupramoleculeName: hexameric assembly of SlNRC3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: hexameric resistosome formed by activation with Rx and CP
Source (natural)Organism: Solanum lycopersicum (tomato)

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Macromolecule #1: SlNRC3

MacromoleculeName: SlNRC3 / type: protein_or_peptide / ID: 1
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
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 104.763977 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MADVAVKFEL ENETQLEIDN ADLILGIQGE VENLLTDLNY FNAFLKEAAK SRRENEVLKE LVKKIRKVVN DAEDSIDKFV VEAKRHDDK NKFAQWFHIT HVARAKGVAD EIKSIRERVK EIRDNDAYGL QAITLDDNFN RGDEERKAPV VEEDDVVGFD D EAKTVIDR ...String:
MADVAVKFEL ENETQLEIDN ADLILGIQGE VENLLTDLNY FNAFLKEAAK SRRENEVLKE LVKKIRKVVN DAEDSIDKFV VEAKRHDDK NKFAQWFHIT HVARAKGVAD EIKSIRERVK EIRDNDAYGL QAITLDDNFN RGDEERKAPV VEEDDVVGFD D EAKTVIDR LIGGSDYVEV VPVVGMPGLG KTTLAYKIYK DPKVEYEFFT RVWVYVSQTF KRREIFLNII SKFTRNTKQY DD TPEDDLA NEVKELLGKG GKYLIVLDDV WTMEAWDRIK IAFPNNGKRN RVLMTTRQSN VAKRCNDKPH DLKFLTKDES WEL LEKKVF HKEKCPPELE LPGISIAEKC MGLPLAIVVI AGALIGKGKT TREWELVAAS VGEHLINRDP ENCKKLVQMS YDRL PYDLK ACFLYCGAFP GGSQIPAKKL IRLWIAEGFI QYQGPLALED VAEDHLNDLV NRNLVMVTQR SCSGQIKTCR VHDML HEFC RHEAMMEENL FQEIKQGQER SFPGKQELAT YRRLCIQSLI PEFLSMKPSG EHVRSFLCVG SKKIDMPPNE IPSIPK AFP LLRVLDAESI KFSRFSREFF KLFHLRYIAL STDKIKTIPA DFGNLWNIQT LIVETQQATL DIKADIWNMT RLRHVCT NA SATLPSTKRP KSSKDNLVNR CLQTLSTIAP ECCTAEVFTR TPNLKKLGVR GKIDALLESS KDGSGSGLFS NIGKLGCL E YLKLVNDTRL SSKPLHLPPA YIFPQKLKKL SLVDTWFEWK DMSILGLLPE LEVLKLKENA FKGQSWEQED GGFPRLQVL WIERTDLTSW KASSGNFPRL KHLALISCDK LEELPAELAD VKNLQLIELQ SSSESAARSA RAILKRNQEK EQDGDKGTGF KLSIFPHDL GLSDYKDHDG DYKDHDLDAA AADYKDDDDK

UniProtKB: Uncharacterized protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mM(HOCH2)3CNH2Tris
150.0 mMNaClSalt
5.0 mMMgCl2Salt
5.0 %C3H8O3Glycerol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6150 / Average electron dose: 50.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1660190
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 234243
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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