+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8057 | |||||||||
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Title | In situ sub-tomogram average of HeLa cytosolic ribosomes | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 28.0 Å | |||||||||
Authors | Mahamid J / Pfeffer S / Schaffer M / Villa E / Danev R / Kuhn-Cuellar L / Foerster F / Hyman A / Plitzko J / Baumeister W | |||||||||
Citation | Journal: Science / Year: 2016 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8057.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-8057-v30.xml emd-8057.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd_8057.png | 55.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8057 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8057 | HTTPS FTP |
-Validation report
Summary document | emd_8057_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_8057_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_8057_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8057 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8057 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8057.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.21 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 : HeLa Cytosolic Ribosomes
Entire | Name: HeLa Cytosolic Ribosomes |
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Components |
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-Supramolecule #1: HeLa Cytosolic Ribosomes
Supramolecule | Name: HeLa Cytosolic Ribosomes / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) / Location in cell: Cytoplasm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Details: Fourier shell cross resolution / Number subtomograms used: 900 |
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Extraction | Number tomograms: 1 / Number images used: 900 |
Final angle assignment | Type: NOT APPLICABLE |