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

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Open data


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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: SlNRC3-AVRcap1b complex
    • Complex: SlNRC3
    • 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
CitationJournal: To Be Published
Title: Cryo-EM structure of tomato NRC3-AVRcap1b complex
Authors: Seager BA / Kamoun S / Madhuprakash J
History
DepositionJun 11, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing 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 : SlNRC3-AVRcap1b complex

EntireName: SlNRC3-AVRcap1b complex
Components
  • Complex: SlNRC3-AVRcap1b complex
    • Complex: SlNRC3
    • Complex: AVRcap1b

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Supramolecule #1: SlNRC3-AVRcap1b complex

SupramoleculeName: SlNRC3-AVRcap1b complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Solanum lycopersicum (tomato)

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Supramolecule #2: SlNRC3

SupramoleculeName: SlNRC3 / 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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