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- EMDB-45161: Cryo-Electron Tomography of Cultured Neuronal Synapses -

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Basic information

Entry
Database: EMDB / ID: EMD-45161
TitleCryo-Electron Tomography of Cultured Neuronal Synapses
Map dataCryoCARE denoised tomogram of a cultured neuronal synapse.
Sample
  • Cell: Tomograms of Cultured Neuronal Synapses
KeywordsSynapse / Neuron / Vesicles / EXOCYTOSIS
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsHeld RG / Brunger AT / Liang J
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH063105 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2024
Title: Nanoscale Architecture of Synaptic Vesicles and Scaffolding Complexes Revealed by Cryo-Electron Tomography
Authors: Held RG / Liang J / Brunger AT
History
DepositionMay 31, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45161.png

Downloads & links

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Map

FileDownload / File: emd_45161.map.gz / Format: CCP4 / Size: 120.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.6 Å/pix.
x 86 pix.
= 1169.6 Å		13.6 Å/pix.
x 720 pix.
= 9792. Å		13.6 Å/pix.
x 512 pix.
= 6963.2 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: 13.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-133.228360000000009 - 127.245099999999994
Average (Standard dev.)36.529240000000001 (±5.163511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125104-70
Dimensions72051286
Spacing51272086
CellA: 6963.2 Å / B: 9792.0 Å / C: 1169.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_1.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_10.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_11.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_12.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_2.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_3.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_4.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_5.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_6.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_7.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_8.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: CryoCARE denoised tomogram of a cultured neuronal synapse.

Fileemd_45161_additional_9.map
AnnotationCryoCARE denoised tomogram of a cultured neuronal synapse.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tomograms of Cultured Neuronal Synapses

EntireName: Tomograms of Cultured Neuronal Synapses
Components
  • Cell: Tomograms of Cultured Neuronal Synapses

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Supramolecule #1: Tomograms of Cultured Neuronal Synapses

SupramoleculeName: Tomograms of Cultured Neuronal Synapses / type: cell / ID: 1 / Parent: 0
Details: Tomograms of cryo-FIB lamellae of from cultured neurons.
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6J / Organ: Brain / Tissue: Hippocampus

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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: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
Detailstomograms from FIB-milled lamellae of cultured mouse hippocampal neurons, targeting neuronal synapses.
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 175
Focused ion beam - Details: The milling sequence was the following (all at 30 keV): rough milling: 0.3 nA, 3 um pattern separation in Y; medium milling: 0.1 nA, 1 um pattern separation; fine milling: ...Focused ion beam - Details: The milling sequence was the following (all at 30 keV): rough milling: 0.3 nA, 3 um pattern separation in Y; medium milling: 0.1 nA, 1 um pattern separation; fine milling: 50 pA, 500 nm pattern separation; polishing: 30 pA, 175 nm pattern separation.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.
Fiducial markerDiameter: 2.5 nm

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 9.0 µm / Nominal defocus min: 3.0 µm
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 reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD
Details: IMOD was used for tilt-series alignment and weighted back-projection, followed by denoising using CryoCARE.
Number images used: 41

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