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- EMDB-35654: cryo-electron tomogram from mouse islets lift-out sample(TOMO_003) -

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Basic information

Entry
Database: EMDB / ID: EMD-35654
Titlecryo-electron tomogram from mouse islets lift-out sample(TOMO_003)
Map data
Sample
  • Tissue: mouse islets lift-out sample
Keywordsislet / vesicle / insulin / EXOCYTOSIS
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsWu Y / Qin C / Du W / Chen L / Guo Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol / Year: 2023
Title: A practical multicellular sample preparation pipeline broadens the application of in situ cryo-electron tomography.
Authors: Yichun Wu / Changdong Qin / Wenjing Du / Zhenxi Guo / Liangyi Chen / Qiang Guo /
Abstract: The structural studies of macromolecules in their physiological context, particularly in tissue, is constrained by the bottleneck of sample preparation. In this study, we present a practical pipeline ...The structural studies of macromolecules in their physiological context, particularly in tissue, is constrained by the bottleneck of sample preparation. In this study, we present a practical pipeline for preparing multicellular samples for cryo-electron tomography. The pipeline comprises sample isolation, vitrification, and lift-out-based lamella preparation using commercially available instruments. We demonstrate the efficacy of our pipeline by visualizing pancreatic β cells from mouse islets at the molecular level. This pipeline enables the determination of the properties of insulin crystals in situ for the first time, using unperturbed samples.
History
DepositionMar 15, 2023-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35654.png

Downloads & links

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Map

FileDownload / File: emd_35654.map.gz / Format: CCP4 / Size: 1019.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
15.3 Å/pix.
x 300 pix.
= 4590. Å		15.3 Å/pix.
x 960 pix.
= 14688. Å		15.3 Å/pix.
x 928 pix.
= 14198.4 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: 15.3 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-7681.520000000000437 - 2795.280799999999999
Average (Standard dev.)0.00000008764524 (±251.617459999999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960928300
Spacing928960300
CellA: 14198.4 Å / B: 14688.0 Å / C: 4590.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : mouse islets lift-out sample

EntireName: mouse islets lift-out sample
Components
  • Tissue: mouse islets lift-out sample

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Supramolecule #1: mouse islets lift-out sample

SupramoleculeName: mouse islets lift-out sample / type: tissue / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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
VitrificationCryogen name: NITROGEN / Details: high pressure freezing.
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica EM HP100. This is not in a list of allowed values {'BAL-TEC HPM 010', 'LEICA EM HPM100', 'LEICA EM PACT', 'LEICA EM PACT2', ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EM HP100. This is not in a list of allowed values {'BAL-TEC HPM 010', 'LEICA EM HPM100', 'LEICA EM PACT', 'LEICA EM PACT2', 'OTHER', 'EMS-002 RAPID IMMERSION FREEZER'} so OTHER is written into the XML file.
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: 1800 / Focused ion beam - Temperature: 81 K / Focused ion beam - Initial thickness: 10000 / Focused ion beam - Final thickness: 440
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.89 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 38

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