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- EMDB-55442: mouse hippocampal CA1-sr synapse tomogram: CA1-sr dataset 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-55442
Titlemouse hippocampal CA1-sr synapse tomogram: CA1-sr dataset 2
Map datamouse hippocampal CA1-sr synapse from CA1-sr dataset 2. Isonet deconvolve only.
Sample
  • Tissue: mouse hippocampal CA1 stratum radiatum
Keywordssynapse / vesicles / cell adhesion molecules / CELL ADHESION
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsGlynn C / Smith JLR
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust225902/Z/22/Z United Kingdom
Wellcome Trust220526/Z/20/Z United Kingdom
Wellcome Trust226810/Z/22/Z United Kingdom
CitationJournal: Cell Rep Methods / Year: 2025
Title: A generalizable and targeted molecular biopsy approach for in situ cryogenic electron tomography of vitreous brain tissue.
Authors: Calina Glynn / Jake L R Smith / Matthew Case / Rebecca Csöndör / Ana Katsini / Maria E Sanita / Thomas S Glen / Avery Pennington / Michael Grange /
Abstract: Cellular cryogenic electron tomography (cryo-ET) enables the capture of detailed structural information within a biologically relevant environment. However, information in more complex samples, such ...Cellular cryogenic electron tomography (cryo-ET) enables the capture of detailed structural information within a biologically relevant environment. However, information in more complex samples, such as multicellular specimens and tissues, is lacking. Importantly, these observations need to be set in the context of populations. Currently, imaging on the molecular scale is limited to a few observations in situ that struggle to be generalized. This is due to limitations in throughput and versatility employed by current instrumentation. Here, we utilize plasma focused ion beam milling to examine the molecular landscape of mouse hippocampus by cryo-ET. We reveal the complex organization of macromolecules in targeted regions across CA1 stratum pyramidale (sp) to radiatum (sr), representing a molecular atlas of hippocampal architecture in adult mice. The combination of instrumentation and application of technical advancements provides a framework to explore specific structural questions within other tissues in a targeted manner.
History
DepositionOct 21, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55442.png

Downloads & links

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Map

FileDownload / File: emd_55442.map.gz / Format: CCP4 / Size: 200 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmouse hippocampal CA1-sr synapse from CA1-sr dataset 2. Isonet deconvolve only.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.84 Å/pix.
x 200 pix.
= 3168. Å		15.84 Å/pix.
x 512 pix.
= 8110.08 Å		15.84 Å/pix.
x 512 pix.
= 8110.08 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: 15.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.7438213 - 3.128836
Average (Standard dev.)0.8627833 (±0.21079305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512200
Spacing512512200
CellA: 8110.08 Å / B: 8110.08 Å / C: 3168.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : mouse hippocampal CA1 stratum radiatum

EntireName: mouse hippocampal CA1 stratum radiatum
Components
  • Tissue: mouse hippocampal CA1 stratum radiatum

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Supramolecule #1: mouse hippocampal CA1 stratum radiatum

SupramoleculeName: mouse hippocampal CA1 stratum radiatum / type: tissue / ID: 1 / Parent: 0
Details: synapse from hippocampal layer CA1-sr from the right hemisphere of a 172 day old female mouse
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6 / Organ: brain

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 7.4
Details: 92 mM NMDG, 2.5 mM KCl, 1.25 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na-ascorbate, 3 mM Na-pyruvate, 0.5 mM CaCl2 2H2O, and 10 mM MgSO4 7H2O
GridMaterial: COPPER
VitrificationCryogen name: NITROGEN / Details: Leica EM Ice HPF.
Detailssynapse from the right hemisphere of a 172 day old female mouse hippocampus CA1 stratum radiatum.
High pressure freezingInstrument: OTHER
Details: 3 mm x 0.5 mm gold plated copper high pressure freezing carriers with 0.1 mm recess. Carriers were coated with hexadecene > 45 minutes prior to use.. The value given for _em_high_pressure_ ...Details: 3 mm x 0.5 mm gold plated copper high pressure freezing carriers with 0.1 mm recess. Carriers were coated with hexadecene > 45 minutes prior to use.. The value given for _em_high_pressure_freezing.instrument is Leica EM Ice. This is not in a list of allowed values {'LEICA EM PACT2', 'LEICA EM PACT', 'OTHER', 'BAL-TEC HPM 010', 'LEICA EM HPM100', 'EMS-002 RAPID IMMERSION FREEZER'} so OTHER is written into the XML file.
Cryo protectant10% dextran 10% sucrose in NMDG buffer pH 7.4
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.001 / Focused ion beam - Duration: 3600 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 100000 / Focused ion beam - Final thickness: 177
Focused ion beam - Details: Lamella were prepared starting from 100 micron thick tissue sections in high pressure freezing carriers using the serial lift-out method on a Helios Hydra plasma FIB. ...Focused ion beam - Details: Lamella were prepared starting from 100 micron thick tissue sections in high pressure freezing carriers using the serial lift-out method on a Helios Hydra plasma FIB. Milling and serial sectioning was carried out using xenon gas and currents ranging from 1 nA to 60 nA depending on step. Thinning was then carried out on an Arctis pFIB starting with xenon gas and progressively lower currents from 4 nA to 100 pA. Once the lamella reached 400-600 nm thickness, argon was used for polishing with currents of 60 pA followed by 20 pA to the final thickness.. The value given for _em_focused_ion_beam.instrument is helios hydra and Arctis. 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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 130.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
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

Detailspreprocessing carried out in warp. reconstruction carried out in aretomo2 with SART reconstruction at bin8.
Final reconstructionAlgorithm: ALGEBRAIC (ARTS) / Software - Name: Warp / Software - details: aretomo2, not warp / Number images used: 41
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING ONLY

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