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Yorodumi- EMDB-13878: Cryo-electron tomogram from a cryo-FIB lift-out lamella of Drosop... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13878 | ||||||||||||
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Title | Cryo-electron tomogram from a cryo-FIB lift-out lamella of Drosophila melanogaster egg chambers | ||||||||||||
Map data | Tomogram from cryo-lift-out of D. melanogaster egg chambers | ||||||||||||
Sample |
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Keywords | cyro-FIB / cryo-electron tomography / D. melanogaster / Golgi apparatus / RIBOSOME | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Klumpe S / Fung HKH / Goetz SK / Plitzko JM / Mahamid J | ||||||||||||
Funding support | European Union, 3 items
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Citation | Journal: Elife / Year: 2021 Title: A modular platform for automated cryo-FIB workflows. Authors: Sven Klumpe / Herman Kh Fung / Sara K Goetz / Ievgeniia Zagoriy / Bernhard Hampoelz / Xiaojie Zhang / Philipp S Erdmann / Janina Baumbach / Christoph W Müller / Martin Beck / Jürgen M ...Authors: Sven Klumpe / Herman Kh Fung / Sara K Goetz / Ievgeniia Zagoriy / Bernhard Hampoelz / Xiaojie Zhang / Philipp S Erdmann / Janina Baumbach / Christoph W Müller / Martin Beck / Jürgen M Plitzko / Julia Mahamid / Abstract: Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ...Lamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga ion beam currents required to maintain the structural integrity of vitreous specimens, common preparation protocols are time-consuming and labor intensive. The improved stability of new-generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available Python packages, and interfaces with three-dimensional correlative light and electron microscopy (CLEM) tools. SerialFIB enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM-guided lamella preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13878.map.gz | 711.4 MB | EMDB map data format | |
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Header (meta data) | emd-13878-v30.xml emd-13878.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_13878.png | 259 KB | ||
Filedesc metadata | emd-13878.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13878 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13878 | HTTPS FTP |
-Validation report
Summary document | emd_13878_validation.pdf.gz | 569.1 KB | Display | EMDB validaton report |
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Full document | emd_13878_full_validation.pdf.gz | 568.6 KB | Display | |
Data in XML | emd_13878_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_13878_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13878 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13878 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13878.map.gz / Format: CCP4 / Size: 768.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tomogram from cryo-lift-out of D. melanogaster egg chambers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 14.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : D. melanogaster
Entire | Name: D. melanogaster |
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Components |
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-Supramolecule #1: D. melanogaster
Supramolecule | Name: D. melanogaster / type: tissue / ID: 1 / Parent: 0 Details: Tomogram from cryo-FIB lift-out lamella performed on a D. melanogaster egg chamber |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) Strain: w[*]; P{w[+mC]=sqh-mCherry.M}3 (Flybase ID: FBst0059024) Tissue: Egg Chamber |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: NITROGEN / Details: Leica EM Ice. |
High pressure freezing | Instrument: OTHER Details: 20% ficol in Schneider's medium. The value given for _em_high_pressure_freezing.instrument is EM Ice. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT', 'BAL-TEC ...Details: 20% ficol in Schneider's medium. The value given for _em_high_pressure_freezing.instrument is EM Ice. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT', 'BAL-TEC HPM 010', 'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER'} so OTHER is written into the XML file. |
Cryo protectant | Ficol |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 1 / Focused ion beam - Duration: 60 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 10000 / Focused ion beam - Final thickness: 200 Focused ion beam - Details: Cryo-FIB Lift-Out method Various milling steps. The value given for _em_focused_ion_beam.instrument is TFS Aquilos. This is not in a list of allowed values {'DB235', ...Focused ion beam - Details: Cryo-FIB Lift-Out method Various milling steps. The value given for _em_focused_ion_beam.instrument is TFS Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Software - Name: IMOD / Number images used: 59 |
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