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- EMDB-52069: The molecular architecture of the murine kidney slit diaphragm re... -

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Basic information

Entry
Database: EMDB / ID: EMD-52069
TitleThe molecular architecture of the murine kidney slit diaphragm revealed by cryo-electron tomography
Map data
Sample
  • Tissue: Slit diaphragm from murine kidney tissue
Keywordscell-cell junction / slit diaphragm / murine glomerular filtration barrier / CELL ADHESION
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 36.0 Å
AuthorsFrangakis MP / Frangakis AS / Birtasu AN
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2566/1 Germany
CitationJournal: Kidney Int / Year: 2025
Title: The kidney slit diaphragm resembles a fishnet.
Authors: Alexandra N Birtasu / Konstantin Wieland / Utz H Ermel / Serena M Arghittu / Sina Manger / Maciej K Kocylowski / Bernd Fakler / Margot P Scheffer / Roberto Covino / Florian Grahammer / Achilleas S Frangakis /
Abstract: INTRODUCTION: An essential component of the kidney filtration barrier, the slit diaphragm, is a specialized cell-cell junction composed of the cell adhesion molecules Nephrin and Neph1.
METHODS: Here, we use cryo-electron tomography of vitreous lamellae from high pressure frozen wild-type C57BL/6J native mouse glomeruli.
RESULTS: The cryo-electron tomograms show that the slit diaphragm resembles a fishnet-like architecture. After sub-tomogram averaging and molecular dynamics flexible fitting of Nephrin and Neph1, the ...RESULTS: The cryo-electron tomograms show that the slit diaphragm resembles a fishnet-like architecture. After sub-tomogram averaging and molecular dynamics flexible fitting of Nephrin and Neph1, the resulting molecular model of the slit diaphragm reveals a criss-cross arrangement of these cell adhesion molecules with multiple homo- and hetero-philic interactions. This renders the slit diaphragm as a single- or a multi-layer fishnet, quasi-crystalline, sheet-like molecular polymer that can provide both stability and flexibility to compensate for mechanical forces.
CONCLUSIONS: The molecular architecture of the murine slit diaphragm provides a mechanistic framework for comprehending kidney cell-cell junctions with immediate implications in disease.
History
DepositionNov 12, 2024-
SupersessionNov 27, 2024ID: EMD-18876
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52069.png

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Map

FileDownload / File: emd_52069.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
5.36 Å/pix.
x 192 pix.
= 1028.736 Å		5.36 Å/pix.
x 192 pix.
= 1028.736 Å		5.36 Å/pix.
x 192 pix.
= 1028.736 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 5.358 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00645
Minimum - Maximum-0.054584645 - 0.08696505
Average (Standard dev.)-0.00024884052 (±0.009232026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 1028.736 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52069_msk_1.map
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Half map: #1

Fileemd_52069_half_map_1.map
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Half map: #2

Fileemd_52069_half_map_2.map
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Sample components

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Entire : Slit diaphragm from murine kidney tissue

EntireName: Slit diaphragm from murine kidney tissue
Components
  • Tissue: Slit diaphragm from murine kidney tissue

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Supramolecule #1: Slit diaphragm from murine kidney tissue

SupramoleculeName: Slit diaphragm from murine kidney tissue / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6J / Organ: Kidney

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7 / Details: HBSS
GridMaterial: COPPER/PALLADIUM / Mesh: 75
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.4 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 / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 944
ExtractionNumber tomograms: 28 / Number images used: 1445
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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