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- EMDB-33496: Tomographic reconstruction of FIB-milled cryo-lamella of HepG2 ce... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-33496
TitleTomographic reconstruction of FIB-milled cryo-lamella of HepG2 cells containing a LD-mitochondria contact sites.
Map data
Sample
  • Cell: HepG2 cells with fluorescent reporter of LD-mitochondria contact
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsXiao K / Li W / Li Z / Guo Q / Tao X / Ji W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The functional universe of membrane contact sites.
Authors: Prinz WA / Toulmay A / Balla T
History
DepositionMay 26, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJan 4, 2023-
Current statusJan 4, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33496.png

Downloads & links

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Map

FileDownload / File: emd_33496.map.gz / Format: CCP4 / Size: 679.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
21.68 Å/pix.
x 200 pix.
= 4336. Å		21.68 Å/pix.
x 928 pix.
= 20119.041 Å		21.68 Å/pix.
x 960 pix.
= 20812.801 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: 21.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4615.074 - 3609.8938
Average (Standard dev.)8.1723066e-08 (±456.00635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928960200
Spacing960928200
CellA: 20812.8 Å / B: 20119.041 Å / C: 4336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HepG2 cells with fluorescent reporter of LD-mitochondria contact

EntireName: HepG2 cells with fluorescent reporter of LD-mitochondria contact
Components
  • Cell: HepG2 cells with fluorescent reporter of LD-mitochondria contact

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Supramolecule #1: HepG2 cells with fluorescent reporter of LD-mitochondria contact

SupramoleculeName: HepG2 cells with fluorescent reporter of LD-mitochondria contact
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 310 K
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.5 nA / Focused ion beam - Duration: 300 sec. / Focused ion beam - Temperature: 303 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 150 nm
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Tescan S8000G. 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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 35

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