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- EMDB-53557: Architecture of the Drosophila nephrocyte slit diaphragm revealed... -

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Basic information

Entry
Database: EMDB / ID: EMD-53557
TitleArchitecture of the Drosophila nephrocyte slit diaphragm revealed by cryo-electron tomography
Map dataPrimary map of the nephrocyte slit diaphragm.
Sample
  • Complex: Slit diaphragm from Drosophila garland nephrocytes
KeywordsCell-cell junction / MEMBRANE PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsubtomogram averaging / cryo EM / Resolution: 38.0 Å
AuthorsMoser D / Scheffer MP / Frangakis AF
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)2566 Germany
CitationJournal: To Be Published
Title: The slit diaphragm in Drosophila exhibits a bilayered, fishnet architecture
Authors: Moser D / Lang K / Birtasu AN / Grahammer F / Scheffer MP / Helmstaedter M / Hermle T / Frangakis AF
History
DepositionMay 6, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53557.png

Downloads & links

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Map

FileDownload / File: emd_53557.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map of the nephrocyte slit diaphragm.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 384 pix.
= 1029.12 Å		2.68 Å/pix.
x 384 pix.
= 1029.12 Å		2.68 Å/pix.
x 384 pix.
= 1029.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-1.5554198 - 2.5294254
Average (Standard dev.)0.000000000005906 (±0.35511073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 1029.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53557_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw map.

Fileemd_53557_additional_1.map
AnnotationRaw map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1.

Fileemd_53557_half_map_1.map
AnnotationHalf-map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2.

Fileemd_53557_half_map_2.map
AnnotationHalf-map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Slit diaphragm from Drosophila garland nephrocytes

EntireName: Slit diaphragm from Drosophila garland nephrocytes
Components
  • Complex: Slit diaphragm from Drosophila garland nephrocytes

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Supramolecule #1: Slit diaphragm from Drosophila garland nephrocytes

SupramoleculeName: Slit diaphragm from Drosophila garland nephrocytes / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.65 / Details: Schneider's medium, 10% glycerol
GridMaterial: COPPER/PALLADIUM / Mesh: 100
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV
DetailsGarland nephrocytes dissected from Drosophila larvae (L3).

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum SE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.125 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: 7.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 595
ExtractionNumber tomograms: 16 / Number images used: 848 / Software - Name: RELION (ver. 5.0)
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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