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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11992 | |||||||||
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Title | the molecular sociology at the HeLa cell nuclear periphery | |||||||||
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Biological species | ![]() | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | Mahamid J / Pfeffer S / Schaffer M / Villa E / Danev R / Kuhn-Cuellar L / Foerster F / Hyman A / Plitzko J / Baumeister W | |||||||||
![]() | ![]() Title: Visualizing the molecular sociology at the HeLa cell nuclear periphery. Authors: Julia Mahamid / Stefan Pfeffer / Miroslava Schaffer / Elizabeth Villa / Radostin Danev / Luis Kuhn Cuellar / Friedrich Förster / Anthony A Hyman / Jürgen M Plitzko / Wolfgang Baumeister / ![]() ![]() Abstract: The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots ...The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots of the HeLa cell nuclear periphery. Subtomogram averaging and classification of ribosomes revealed the native structure and organization of the cytoplasmic translation machinery. Analysis of a large dynamic structure-the nuclear pore complex-revealed variations detectable at the level of individual complexes. Cryo-ET was used to visualize previously elusive structures, such as nucleosome chains and the filaments of the nuclear lamina, in situ. Elucidation of the lamina structure provides insight into its contribution to metazoan nuclear stiffness. | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 1.3 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.4 KB 10.4 KB | Display Display | ![]() |
Images | ![]() | 327.1 KB | ||
Masks | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 1.6 GB 1.6 GB 1.6 GB 821.3 MB 1.6 GB 1.6 GB 1.6 GB | ![]() | |
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 204.9 KB | Display | ![]() |
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Full document | ![]() | 204 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 16.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Interphase HeLa cell
Entire | Name: Interphase HeLa cell |
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Components |
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-Supramolecule #1: Interphase HeLa cell
Supramolecule | Name: Interphase HeLa cell / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
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: 1800 sec. / Focused ion beam - Temperature: 94 K / Focused ion beam - Initial thickness: 10000 nm / Focused ion beam - Final thickness: 190 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Quanta 3D FEG, FEI. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Software - Name: ![]() |
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