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Yorodumi- EMDB-15437: In situ cryo-electron tomogram of an intact human induced pluripo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15437 | |||||||||
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Title | In situ cryo-electron tomogram of an intact human induced pluripotent stem cell derived neuronal process | |||||||||
Map data | In situ cryo-electron tomogram of a human induced pluripotent stem cell derived neuronal process | |||||||||
Sample |
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Keywords | Microtubules / Scaffold / protein transport | |||||||||
Biological species | Homo sapiens (human) | |||||||||
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: To Be Published Title: In situ cryo-electron tomogram of an intact human induced pluripotent stem cell derived neuronal process Authors: Chakraborty S / Martinez-Sanchez A / Baumeister W / Mahamid J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15437.map.gz | 196.6 MB | EMDB map data format | |
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Header (meta data) | emd-15437-v30.xml emd-15437.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_15437.png | 237.1 KB | ||
Filedesc metadata | emd-15437.cif.gz | 3.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15437 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15437 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15437.map.gz / Format: CCP4 / Size: 212.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Annotation | In situ cryo-electron tomogram of a human induced pluripotent stem cell derived neuronal process | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 17.033 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human induced pluripotent stem cell derived neurons
Entire | Name: Human induced pluripotent stem cell derived neurons |
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Components |
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-Supramolecule #1: Human induced pluripotent stem cell derived neurons
Supramolecule | Name: Human induced pluripotent stem cell derived neurons / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: blood |
-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 / Material: GOLD / Mesh: 200 / Support film - Film thickness: 1.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 310 K / Instrument: LEICA EM GP / Details: Blotting time 1.5 seconds. |
Details | grown on laminin coated micropatterned SiO2 R1/4 EM grid |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus min: 3.75 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 195.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.8 e/Å2 / Details: Dose symmetric acquisition scheme |
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: 60 |
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