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Yorodumi- EMDB-15442: In situ cryo-electron tomogram of an intact pluripotent P19 cellu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15442 | |||||||||
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Title | In situ cryo-electron tomogram of an intact pluripotent P19 cellular process after nocodazole treatment and washout. | |||||||||
Map data | In situ cryo-electron tomogram of an intact pluripotent P19 cellular process after nocodazole treatment and washout. | |||||||||
Sample |
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Keywords | Microtubules / Scaffold / protein transport | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Chakraborty S / Martinez-Sanchez A / Baumeister W / Mahamid J | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Biorxiv / Year: 2024 Title: Cryo-electron tomography suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules Authors: Chakraborty S / Martinez-Sanchez A / Beck F / Toro-Nahuelpan M / Hwang IY / Noh KM / Baumeister W / Mahamid J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15442.map.gz | 190.3 MB | EMDB map data format | |
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Header (meta data) | emd-15442-v30.xml emd-15442.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_15442.png | 251.7 KB | ||
Filedesc metadata | emd-15442.cif.gz | 3.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15442 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15442 | HTTPS FTP |
-Validation report
Summary document | emd_15442_validation.pdf.gz | 649.7 KB | Display | EMDB validaton report |
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Full document | emd_15442_full_validation.pdf.gz | 649.2 KB | Display | |
Data in XML | emd_15442_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_15442_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15442 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15442 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15442.map.gz / Format: CCP4 / Size: 205.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | In situ cryo-electron tomogram of an intact pluripotent P19 cellular process after nocodazole treatment and washout. | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 27.36 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : In situ cryo-electron tomogram of an intact pluripotent P19 cellu...
Entire | Name: In situ cryo-electron tomogram of an intact pluripotent P19 cellular process after nocodazole treatment and washout. |
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Components |
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-Supramolecule #1: In situ cryo-electron tomogram of an intact pluripotent P19 cellu...
Supramolecule | Name: In situ cryo-electron tomogram of an intact pluripotent P19 cellular process after nocodazole treatment and washout. type: cell / ID: 1 / Parent: 0 Details: The cells were treated with nocodazole for 30 minutes followed by washing out the drug. |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV Details: Blotted from backside for 10 seconds with blot force 10. |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | TFS KRIOS |
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Temperature | Min: 77.0 K |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9.0) / Number images used: 61 |
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