[English] 日本語
Yorodumi- EMDB-33495: Tomographic reconstruction of FIB-milled cryo-lamella of HeLa cel... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33495 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tomographic reconstruction of FIB-milled cryo-lamella of HeLa cells containing a centroile and subcellular structures. | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Xiao K / Li W / Li Z / Guo Q / Tao X / Ji W | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: To Be Published Title: The PACT domain, a conserved centrosomal targeting motif in the coiled-coil proteins AKAP450 and pericentrin Authors: Gillingham AK / Munro S | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_33495.map.gz | 628 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-33495-v30.xml emd-33495.xml | 7.5 KB 7.5 KB | Display Display | EMDB header |
Images | emd_33495.png | 248.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33495 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33495 | HTTPS FTP |
-Validation report
Summary document | emd_33495_validation.pdf.gz | 423.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_33495_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | emd_33495_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | emd_33495_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33495 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33495 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_33495.map.gz / Format: CCP4 / Size: 679.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 17.2 Å | ||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : HeLa cells that expressed mCherry fluorescent protein labeled per...
Entire | Name: HeLa cells that expressed mCherry fluorescent protein labeled pericentrin |
---|---|
Components |
|
-Supramolecule #1: HeLa cells that expressed mCherry fluorescent protein labeled per...
Supramolecule | Name: HeLa cells that expressed mCherry fluorescent protein labeled pericentrin type: cell / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 310 K / Instrument: LEICA EM GP |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.5 nA / Focused ion beam - Duration: 300 sec. / Focused ion beam - Temperature: 303 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 150 nm Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Tescan S8000G. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 5.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 39 |
---|