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Yorodumi- EMDB-30364: Cryo-electron tomography of an excitatory synapse in cultured rat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30364 | |||||||||
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Title | Cryo-electron tomography of an excitatory synapse in cultured rat hippocampal neurons | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Rattus sp. (rats) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Tao C-L / Liu Y-T / Sun R / Zhang B / Qi L / Shivakoti S / Tian C-L / Zhang P / Lau P-M / Zhou ZH / Bi G-Q | |||||||||
Citation | ||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30364.map.gz | 84.7 MB | EMDB map data format | |
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Header (meta data) | emd-30364-v30.xml emd-30364.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_30364.png | 251.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30364 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30364 | HTTPS FTP |
-Validation report
Summary document | emd_30364_validation.pdf.gz | 302.3 KB | Display | EMDB validaton report |
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Full document | emd_30364_full_validation.pdf.gz | 301.8 KB | Display | |
Data in XML | emd_30364_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | emd_30364_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30364 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30364 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30364.map.gz / Format: CCP4 / Size: 143.8 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 26.1 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 : hippocampal neuronal synapse
Entire | Name: hippocampal neuronal synapse |
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Components |
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-Supramolecule #1: hippocampal neuronal synapse
Supramolecule | Name: hippocampal neuronal synapse / type: cell / ID: 1 / Parent: 0 Details: excitatory synapse in cultured rat hippocampal neurons |
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Source (natural) | Organism: Rattus sp. (rats) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Center for Molecular Medicine | University Medical Center Utrecht Diameter: 15 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm |
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: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD / Number images used: 64 |
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