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Yorodumi- EMDB-50110: Electron tomogram of ER-nuclear envelope junction of HeLa cell in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50110 | |||||||||
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Title | Electron tomogram of ER-nuclear envelope junction of HeLa cell in early telophase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Endoplasmic reticulum / Nuclear envelope / Organelle contact site / Membrane junction / CELL CYCLE | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM / negative staining | |||||||||
Authors | Bragulat-Teixidor H / Otsuka S | |||||||||
Funding support | Austria, 2 items
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Citation | Journal: Embo Rep. / Year: 2024 Title: The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis. Authors: Bragulat-Teixidor H / Ishihara K / Szucs GM / Otsuka S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50110.map.gz | 14.7 GB | EMDB map data format | |
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Header (meta data) | emd-50110-v30.xml emd-50110.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_50110.png | 232.8 KB | ||
Filedesc metadata | emd-50110.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50110 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50110 | HTTPS FTP |
-Validation report
Summary document | emd_50110_validation.pdf.gz | 503.2 KB | Display | EMDB validaton report |
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Full document | emd_50110_full_validation.pdf.gz | 502.8 KB | Display | |
Data in XML | emd_50110_validation.xml.gz | 4 KB | Display | |
Data in CIF | emd_50110_validation.cif.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50110 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50110 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50110.map.gz / Format: CCP4 / Size: 20.6 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.51 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : HeLa Kyoto cell
Entire | Name: HeLa Kyoto cell |
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Components |
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-Supramolecule #1: HeLa Kyoto cell
Supramolecule | Name: HeLa Kyoto cell / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: HeLa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Details: DMEM without Riboflavin and Phenol Red, containing 10% FBS, 1% Pen/Strep, and 50 nM SiR-DNA |
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Staining | Type: NEGATIVE / Material: Uranyl acetate and lead citrate |
Sugar embedding | Material: Agar 100 Epoxy resin Details: Frozen cells were substituted in 0.1% uranyl acetate (UA), 2% Osmium tetroxide and 5% H2O in acetone following this temperature ramp: -90 C to -80 C for 10 hours, -80 C to -30 C for 10 ...Details: Frozen cells were substituted in 0.1% uranyl acetate (UA), 2% Osmium tetroxide and 5% H2O in acetone following this temperature ramp: -90 C to -80 C for 10 hours, -80 C to -30 C for 10 hours, -30 C for 4 hours, -30 C to 0 C for 6 ours, 0 C to 20 C for 4 hours, 20 C for 5-6 hours. |
Vitrification | Cryogen name: NITROGEN |
High pressure freezing | Instrument: OTHER Details: High pressure freezing chamber was 1 mm thick, 6.0 mm diameter, with central cavities 5.0 mm x 5.0 mm x 25 um deep. The chamber had been in contact with 1-hexadecene.. The value given for _ ...Details: High pressure freezing chamber was 1 mm thick, 6.0 mm diameter, with central cavities 5.0 mm x 5.0 mm x 25 um deep. The chamber had been in contact with 1-hexadecene.. The value given for _em_high_pressure_freezing.instrument is Leica EM ICE. This is not in a list of allowed values {'LEICA EM PACT', 'LEICA EM PACT2', 'BAL-TEC HPM 010', 'OTHER', 'LEICA EM HPM100', 'EMS-002 RAPID IMMERSION FREEZER'} so OTHER is written into the XML file. |
Cryo protectant | 20% Ficoll-PM400 |
Sectioning | Ultramicrotomy - Instrument: Leica Ultracut UCT / Ultramicrotomy - Temperature: 298 K / Ultramicrotomy - Final thickness: 250 |
Fiducial marker | Manufacturer: Cytodiagnostics / Diameter: 15 nm |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Number images used: 110 |
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