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- EMDB-53988: Consensus cryo-EM map of SlNRC3-AVRcap1b complex -

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Basic information

Entry
Database: EMDB / ID: EMD-53988
TitleConsensus cryo-EM map of SlNRC3-AVRcap1b complex
Map dataunsharpened consensus map
Sample
  • Complex: NRC3-AVRcap1b complex
    • Complex: NRC3
    • Complex: AVRcap1b
KeywordsEffector / NLR / Plant Immunity / Resistosome / IMMUNE SYSTEM
Biological speciesSolanum lycopersicum (tomato) / Phytophthora infestans (potato late blight agent)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsSeager BA / Kamoun S / Madhuprakash J
Funding support United Kingdom, European Union, 3 items
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 BA / Harant A / Contreras MP / Hou LY / Wu CH / Kamoun S / Madhuprakash J
History
DepositionJun 11, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53988.png

Downloads & links

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Map

FileDownload / File: emd_53988.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 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: 0.03
Minimum - Maximum-0.10052674 - 0.20189397
Average (Standard dev.)-0.00021681446 (±0.0045542326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_53988_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_53988_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 : NRC3-AVRcap1b complex

EntireName: NRC3-AVRcap1b complex
Components
  • Complex: NRC3-AVRcap1b complex
    • Complex: NRC3
    • Complex: AVRcap1b

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Supramolecule #1: NRC3-AVRcap1b complex

SupramoleculeName: NRC3-AVRcap1b complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Solanum lycopersicum (tomato)

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Supramolecule #2: NRC3

SupramoleculeName: NRC3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Solanum lycopersicum (tomato)

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Supramolecule #3: AVRcap1b

SupramoleculeName: AVRcap1b / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Phytophthora infestans (potato late blight agent)

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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:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSaltNaCl
5.0 mMSaltMgCl2
5.0 %Glycerol
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 - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7555 / Average electron dose: 50.13 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: 2.0 µm / Nominal defocus min: 0.6 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: 3531889
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 267047
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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