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- EMDB-29762: Cryo-Electron Tomography of Golgi Apparatus from a cryo-lamella o... -

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Basic information

Entry
Database: EMDB / ID: EMD-29762
TitleCryo-Electron Tomography of Golgi Apparatus from a cryo-lamella of a Zebra Fish Embryo
Map dataCryo-Electron Tomography of Golgi Apparatus from a Zebra Fish Embryo
Sample
  • Tissue: Zebra Fish Embryo
KeywordsGolgi apparatus / UNKNOWN FUNCTION
Biological speciesDanio rerio (zebrafish)
Methodelectron tomography
AuthorsTrepout S / Ramm G
Funding support Australia, United States, 3 items
OrganizationGrant numberCountry
Australian Research Council (ARC)LE150100132 Australia
Chan Zuckerberg Initiative2020-225399 United States
Australian Research Council (ARC)LE180100202 Australia
CitationJournal: To Be Published
Title: Cryo-Electron Tomography of a Cryo-Lamella Milled Inside a Zebra Fish Embryo Showing a Golgi Apparatus
Authors: Trepout S / Ramm G
History
DepositionFeb 14, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29762.png

Downloads & links

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Map

FileDownload / File: emd_29762.map.gz / Format: CCP4 / Size: 5.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-Electron Tomography of Golgi Apparatus from a Zebra Fish Embryo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.66 Å/pix.
x 400 pix.
= 5864. Å		14.66 Å/pix.
x 1854 pix.
= 27179.641 Å		14.66 Å/pix.
x 1918 pix.
= 28117.879 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: 14.66 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-398.761169999999993 - 510.950300000000027
Average (Standard dev.)4.619173 (±21.335481999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions18541918400
Spacing19181854400
CellA: 28117.879 Å / B: 27179.64 Å / C: 5864.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Zebra Fish Embryo

EntireName: Zebra Fish Embryo
Components
  • Tissue: Zebra Fish Embryo

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Supramolecule #1: Zebra Fish Embryo

SupramoleculeName: Zebra Fish Embryo / type: tissue / ID: 1 / Parent: 0
Details: Cryo-lamella cut inside the embryo using the bbq method.
Source (natural)Organism: Danio rerio (zebrafish) / Organ: tail / Tissue: skin

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Experimental details

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Structure determination

Processingelectron tomography
Aggregation statetissue

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Sample preparation

BufferpH: 6.9
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is HPF Wohlwend Compact 03. This is not in a list of allowed values {'LEICA EM HPM100', 'BAL-TEC HPM 010', 'EMS-002 RAPID IMMERSION ...Details: The value given for _em_high_pressure_freezing.instrument is HPF Wohlwend Compact 03. This is not in a list of allowed values {'LEICA EM HPM100', 'BAL-TEC HPM 010', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM PACT', 'LEICA EM PACT2'} 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: 1 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 100000 / Focused ion beam - Final thickness: 250
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Helios G4 UX. 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

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 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: Alignment performed with AreTomo 1.0.1 / Number images used: 47

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