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- EMDB-54421: In situ cryo-electron tomogram of rat hippocampal synapse -

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Basic information

Entry
Database: EMDB / ID: EMD-54421
TitleIn situ cryo-electron tomogram of rat hippocampal synapse
Map data
Sample
  • Cell: primary hippocampal neurons
Keywordssynapse / synaptic vesicle / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodelectron tomography / cryo EM
AuthorsPetrovic A / Do TT / Siegert A / Fernandez-Busnadiego R
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)1286 Germany
CitationJournal: To Be Published
Title: A correlative workflow streamlines synaptic imaging by cryo-electron tomography
Authors: Do TT / Siegert A / Domart F / Hahn F / Zeising C / Muth S / Pape C / Kusch K / Dresbach T / Rizzoli SO / Petrovic A / Fernandez-Busnadiego R
History
DepositionJul 17, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54421.png

Downloads & links

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Map

FileDownload / File: emd_54421.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.6 Å/pix.
x 320 pix.
= 4672. Å		14.6 Å/pix.
x 1024 pix.
= 14950.4 Å		14.6 Å/pix.
x 1024 pix.
= 14950.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1156.704099999999926 - 522.779599999999959
Average (Standard dev.)6.5643125 (±33.825369999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024320
Spacing10241024320
CellA: 14950.4 Å / B: 14950.4 Å / C: 4672.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : primary hippocampal neurons

EntireName: primary hippocampal neurons
Components
  • Cell: primary hippocampal neurons

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Supramolecule #1: primary hippocampal neurons

SupramoleculeName: primary hippocampal neurons / type: cell / ID: 1 / Parent: 0 / Details: synapse
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsFIB-milled lamella of rat primary hippocampal neurons
Cryo protectant5% glycerol
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 500 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Acquilos2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 3.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 33000
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

Final reconstructionSoftware - Name: IMOD (ver. 4.12) / Number images used: 37
CTF correctionType: NONE

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