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- EMDB-41256: Cryotomogram of DIV 4 cultured hippocampal neuron -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-41256
TitleCryotomogram of DIV 4 cultured hippocampal neuron
Map dataDIV 4 Hippocampal Neuron (Weighted Backprojection)
Sample
  • Cell: DIV 4 Hippocampal Neuron
KeywordsNeuron / Tomogram / denoise / segmentation / CELL ADHESION
Biological speciesRattus norvegicus (Norway rat)
Methodelectron tomography / cryo EM
AuthorsSwulius MT
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To be Published
Title: Rapid Synthesis of Cryo-ET Data for Training Deep Learning Models.
Authors: Purnell C / Heebner J / Hylton RH / Kabonick S / Grillo M / Grigoryev S / Heberle F / Waxham NM / Swulius MT
History
DepositionJul 15, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41256.png

Downloads & links

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Map

FileDownload / File: emd_41256.map.gz / Format: CCP4 / Size: 107.3 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationDIV 4 Hippocampal Neuron (Weighted Backprojection)
Voxel sizeX=Y=Z: 13.6 Å
Density
Minimum - Maximum-78.0 - 55.0
Average (Standard dev.)0.683545 (±1.6098703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0059
Dimensions1173121479
Spacing1214117379
CellA: 16510.4 Å / B: 15952.801 Å / C: 1074.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DIV 4 Hippocampal Neuron (regression denoised)

Fileemd_41256_additional_1.map
AnnotationDIV 4 Hippocampal Neuron (regression denoised)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DIV 4 Hippocampal Neuron (Greyscale Segmentation)

Fileemd_41256_additional_2.map
AnnotationDIV 4 Hippocampal Neuron (Greyscale Segmentation)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DIV 4 Hippocampal Neuron

EntireName: DIV 4 Hippocampal Neuron
Components
  • Cell: DIV 4 Hippocampal Neuron

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Supramolecule #1: DIV 4 Hippocampal Neuron

SupramoleculeName: DIV 4 Hippocampal Neuron / type: cell / ID: 1 / Parent: 0
Details: Weighted Backprojection, Regression Denoised, and Greyscale Segmentation
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
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 60

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