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Yorodumi- EMDB-21953: Downsampled and filtered tomogram of a region from a cryoFIB-SEM-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21953 | |||||||||||||||||||||
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Title | Downsampled and filtered tomogram of a region from a cryoFIB-SEM-generated lamellae of yeast cells under heat shock stress showing large protein aggregates | |||||||||||||||||||||
Map data | Binned-by-8 and filtered tomogram of a region from a cryoFIB-SEM-generated lamellae of yeast cells under heat shock stress showing large protein aggregates. | |||||||||||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||||||||
Authors | Wu GH / Mitchell PG / Galaz-Montoya JG / Hecksel CW / Sontag EM / Gangadharan V / Marshman J / Mankus D / Bisher ME / Lytton-Jean AKR ...Wu GH / Mitchell PG / Galaz-Montoya JG / Hecksel CW / Sontag EM / Gangadharan V / Marshman J / Mankus D / Bisher ME / Lytton-Jean AKR / Frydman J / Czymmek K / Chiu W | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Structure / Year: 2020 Title: Multi-scale 3D Cryo-Correlative Microscopy for Vitrified Cells. Authors: Gong-Her Wu / Patrick G Mitchell / Jesus G Galaz-Montoya / Corey W Hecksel / Emily M Sontag / Vimal Gangadharan / Jeffrey Marshman / David Mankus / Margaret E Bisher / Abigail K R Lytton- ...Authors: Gong-Her Wu / Patrick G Mitchell / Jesus G Galaz-Montoya / Corey W Hecksel / Emily M Sontag / Vimal Gangadharan / Jeffrey Marshman / David Mankus / Margaret E Bisher / Abigail K R Lytton-Jean / Judith Frydman / Kirk Czymmek / Wah Chiu / Abstract: Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging ...Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21953.map.gz | 161.2 MB | EMDB map data format | |
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Header (meta data) | emd-21953-v30.xml emd-21953.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_21953.png | 314.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21953 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21953 | HTTPS FTP |
-Validation report
Summary document | emd_21953_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_21953_full_validation.pdf.gz | 77.9 KB | Display | |
Data in XML | emd_21953_validation.xml.gz | 498 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21953 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21953 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21953.map.gz / Format: CCP4 / Size: 174.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Binned-by-8 and filtered tomogram of a region from a cryoFIB-SEM-generated lamellae of yeast cells under heat shock stress showing large protein aggregates. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 27.664 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 : Downsamples and filtered tomogram of a region from a cryoFIB-SEM-...
Entire | Name: Downsamples and filtered tomogram of a region from a cryoFIB-SEM-generated lamellae of yeast cells under heat shock stress showing large protein aggregates |
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Components |
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-Supramolecule #1: Downsamples and filtered tomogram of a region from a cryoFIB-SEM-...
Supramolecule | Name: Downsamples and filtered tomogram of a region from a cryoFIB-SEM-generated lamellae of yeast cells under heat shock stress showing large protein aggregates type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 20 nA / Focused ion beam - Duration: 60 sec. / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 520 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Zeiss Crossbeam 540 FIB-SEM. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is ...Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Zeiss Crossbeam 540 FIB-SEM. This is not in a list of allowed values set(['DB235', 'OTHER']) so OTHER is written into the XML file. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.8264 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD Details: The SIRT, downsampled, and filtered tomogram was computed for visualization only. The related EMDB entry showcasing a ribosome subtomogram average used similar tomograms but reconstructed ...Details: The SIRT, downsampled, and filtered tomogram was computed for visualization only. The related EMDB entry showcasing a ribosome subtomogram average used similar tomograms but reconstructed with weighted-back-projection, at full-size, and unfiltered. Number images used: 121 |
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CTF correction | Software - Name: IMOD / Details: 3D CTF correction |