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- EMDB-51505: AvrSr35-focussed cryo-EM map of pentameric Sr35 assembly in 5:5 c... -

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Basic information

Entry
Database: EMDB / ID: EMD-51505
TitleAvrSr35-focussed cryo-EM map of pentameric Sr35 assembly in 5:5 complex with AvrSr35
Map dataFocussed cryo-EM map of pentameric Sr35 assembly in 5:5 complex with AvrSr35
Sample
  • Complex: Cryo-EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
    • Complex: CNL9
    • Complex: Avirulence factor
KeywordsComplex / Apoptosis / Immune receptor / Mildew / ANTIFUNGAL PROTEIN
Biological speciesTriticum monococcum (einkorn wheat) / Puccinia graminis f. sp. tritici (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMacha A / Gunkel M / Lawson AW / Behrmann E / Schulze-Lefert P
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
CitationJournal: To Be Published
Title: A versatile protocol for purifying recombinant proteins from Nicotiana benthamiana
Authors: Lawson AW / Macha A / Neumann U / Gunkel M / Chai JJ / Behrmann E / Schulze-Lefert P
History
DepositionSep 9, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51505.png

Downloads & links

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Map

FileDownload / File: emd_51505.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocussed cryo-EM map of pentameric Sr35 assembly in 5:5 complex with AvrSr35
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 310.32 Å		0.86 Å/pix.
x 360 pix.
= 310.32 Å		0.86 Å/pix.
x 360 pix.
= 310.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.71590257 - 1.3878357
Average (Standard dev.)0.0009036932 (±0.013841638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 310.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51505_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer-sharpened focussed cryo-EM map of pentameric Sr35 assembly...

Fileemd_51505_additional_1.map
AnnotationDeepEMhancer-sharpened focussed cryo-EM map of pentameric Sr35 assembly in 5:5 complex with AvrSr35
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focussed cryo-EM map of pentameric Sr35 assembly in...

Fileemd_51505_half_map_1.map
AnnotationFocussed cryo-EM map of pentameric Sr35 assembly in 5:5 complex with AvrSr35 - even half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focussed cryo-EM map of pentameric Sr35 assembly in...

Fileemd_51505_half_map_2.map
AnnotationFocussed cryo-EM map of pentameric Sr35 assembly in 5:5 complex with AvrSr35 - odd half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of oligomeric complex formed by wheat CNL Sr35 ...

EntireName: Cryo-EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
Components
  • Complex: Cryo-EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
    • Complex: CNL9
    • Complex: Avirulence factor

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Supramolecule #1: Cryo-EM structure of oligomeric complex formed by wheat CNL Sr35 ...

SupramoleculeName: Cryo-EM structure of oligomeric complex formed by wheat CNL Sr35 and the effector AvrSr35 of the wheat stem rust pathogen
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1 / Details: using Nicotiana benthamiana expression system
Source (natural)Organism: Triticum monococcum (einkorn wheat)
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: CNL9

SupramoleculeName: CNL9 / type: complex / ID: 2 / Parent: 1 / Details: 5 copies in complex
Source (natural)Organism: Triticum monococcum (einkorn wheat)

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Supramolecule #3: Avirulence factor

SupramoleculeName: Avirulence factor / type: complex / ID: 3 / Parent: 1 / Details: 5 copies in complex
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)

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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

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU (ver. 2.12.1.2782REL)
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1272 / Average exposure time: 43.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
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: 1226
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Software - details: patchCTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: local refinement / Number images used: 68164
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Software - details: non-uniform
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4) / Software - details: local refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7xc2


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.8)
RefinementProtocol: RIGID BODY FIT

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