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- EMDB-17767: Cryo electron tomography of human choriocarcinoma cells -

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Basic information

Entry
Database: EMDB / ID: EMD-17767
TitleCryo electron tomography of human choriocarcinoma cells
Map dataIMOD weighted back-projection reconstruction of tilt series from Position 09 using Ot2Rec.
Sample
  • Cell: JEG-3 human choriocarcinoma cell line
Keywordshuman / choriocarcinoma / cell / trophoblast / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsTun WM / Yee NB-Y / Ho EML / Darrow MC / Basham M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust212980/Z/18/Z United Kingdom
CitationJournal: Biol Imaging / Year: 2023
Title: Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow.
Authors: Neville B-Y Yee / Elaine M L Ho / Win Tun / Jake L R Smith / Maud Dumoux / Michael Grange / Michele C Darrow / Mark Basham /
Abstract: Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex ...Electron cryo-tomography is an imaging technique for probing 3D structures with at the nanometer scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With the advancement in technology, microscopes are currently capable of producing images amounting to terabytes of data per day, posing great challenges for scientists as the speed of processing of the images cannot keep up with the ever-higher throughput of the microscopes. Therefore, automation is an essential and natural pathway on which image processing-from individual micrographs to full tomograms-is developing. In this paper, we present Ot2Rec, an open-source pipelining tool which aims to enable scientists to build their own processing workflows in a flexible and automatic manner. The basic building blocks of Ot2Rec are plugins which follow a unified application programming interface structure, making it simple for scientists to contribute to Ot2Rec by adding features which are not already available. In this paper, we also present three case studies of image processing using Ot2Rec, through which we demonstrate the speedup of using a semi-automatic workflow over a manual one, the possibility of writing and using custom (prototype) plugins, and the flexibility of Ot2Rec which enables the mix-and-match of plugins. We also demonstrate, in the Supplementary Material, a built-in reporting feature in Ot2Rec which aggregates the metadata from all process being run, and output them in the Jupyter Notebook and/or HTML formats for quick review of image processing quality. Ot2Rec can be found at https://github.com/rosalindfranklininstitute/ot2rec.
History
DepositionJun 29, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17767.png

Downloads & links

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Map

FileDownload / File: emd_17767.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIMOD weighted back-projection reconstruction of tilt series from Position 09 using Ot2Rec.
Voxel sizeX=Y=Z: 14.96 Å
Density
Minimum - Maximum-493.020230000000026 - 491.525539999999978
Average (Standard dev.)11.63147 (±63.113579999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-256
Dimensions512512512
Spacing512512512
CellA=B=C: 7659.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : JEG-3 human choriocarcinoma cell line

EntireName: JEG-3 human choriocarcinoma cell line
Components
  • Cell: JEG-3 human choriocarcinoma cell line

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Supramolecule #1: JEG-3 human choriocarcinoma cell line

SupramoleculeName: JEG-3 human choriocarcinoma cell line / 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
GridModel: Quantifoil R2/2 / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.3 / Focused ion beam - Duration: 1.0E-14 / Focused ion beam - Temperature: 105 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: Note: initial thickness and duration of FIB milling was not recorded.. The value given for _em_focused_ion_beam.instrument is ThermoFisher Scios. This is not in a list of ...Focused ion beam - Details: Note: initial thickness and duration of FIB milling was not recorded.. The value given for _em_focused_ion_beam.instrument is ThermoFisher Scios. 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 64000
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 1.48 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11.1) / Software - details: Weighted back-projection / Details: Bin factor 8 applied. / Number images used: 41
DetailsImages were motion-corrected with MotionCor2 1.4.0 using Ot2Rec.

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