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- EMDB-53528: Tomogram of a PSD95-containing glutamatergic synapse from 'ultra ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53528
TitleTomogram of a PSD95-containing glutamatergic synapse from 'ultra fresh' prepared mouse.
Map dataTomogram of a PSD95-containing glutamatergic synapse from ultra fresh prepared mouse brains.
Sample
  • Tissue: Mouse forebrain (cortex and hippocampus) tissue
Keywordsglutamate receptor / Synapse / Neurotransmission / Ion channel / SIGNALING PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsPeukes J / Frank R / Briggs JAG
Funding supportEuropean Union, United Kingdom, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSIONEuropean Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
UK Research and Innovation (UKRI)MR/V022644/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011151/1 United Kingdom
Wellcome TrustSBF005/1046 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Wellcome Trust208395/Z/17/Z United Kingdom
CitationJournal: eLife / Year: 2024
Title: The molecular infrastructure of glutamatergic synapses in the mammalian forebrain
Authors: Peukes J / Lovatt C / Leistner C / Boulanger J / Morado DR / Fuller MJG / Kukulski W / Zhu F / Komiyama NH / Briggs JAG / Grant SGN / Frank RAW
History
DepositionApr 30, 2025-
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_53528.png

Downloads & links

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Map

FileDownload / File: emd_53528.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of a PSD95-containing glutamatergic synapse from ultra fresh prepared mouse brains.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.94 Å/pix.
x 315 pix.
= 3761.1 Å		11.94 Å/pix.
x 928 pix.
= 11080.319 Å		11.94 Å/pix.
x 960 pix.
= 11462.399 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: 11.94 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-54136.739999999997963 - 20590.895000000000437
Average (Standard dev.)1062.081899999999905 (±2431.993399999999838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1616158
Dimensions928960315
Spacing960928315
CellA: 11462.399 Å / B: 11080.319 Å / C: 3761.0999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse forebrain (cortex and hippocampus) tissue

EntireName: Mouse forebrain (cortex and hippocampus) tissue
Components
  • Tissue: Mouse forebrain (cortex and hippocampus) tissue

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Supramolecule #1: Mouse forebrain (cortex and hippocampus) tissue

SupramoleculeName: Mouse forebrain (cortex and hippocampus) tissue / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse) / Strain: PSD95-GFP knockin mouse / Organ: Brain / Tissue: 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: 125 mM NaCl, 25 mM KCl, 25 mM NHCO3, 25 mM glucose, 2.5 mM KCl, 2 mM CaCl2, 1.25 mM NaH2PO4, 1 mM MgCl2; Osmolality: 310 mOsM/L
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMouse forebrain homogeneized in artificial cerebrospinal fluid (ACSF) to generate suspension of Psd95-GFP containing synaptoneurosomes. Samples was applied to cryoEM grid and plunge frozen in liquid ethane. CryET dataset collection was guided by Psd95-GFP cryoCLEM.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.25 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61
CTF correctionType: NONE

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