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- EMDB-15480: Subtomogram average of nucleosomes extracted from euchromatin and... -
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Open data
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Basic information
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Title | Subtomogram average of nucleosomes extracted from euchromatin and facultative heterochromatin nanodomains of Drosophila melanogaster embryos | |||||||||||||||
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![]() | nucleosome tomography chromatin / STRUCTURAL GENOMICS | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.5 Å | |||||||||||||||
![]() | Fatmaoui F / Eltsov M / Leforestier A | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cryo-electron tomography and deep learning-based denoising reveal native chromatin landscapes of interphase nuclei Authors: Fatmaoui F / Carrivain P / Grewe D / Jakob B / Victor JM / Leforestier A / Eltsov M | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1005.4 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.7 KB 12.7 KB | Display Display | ![]() |
Images | ![]() | 39 KB | ||
Others | ![]() ![]() | 1005.2 KB 1005.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 508.7 KB | Display | ![]() |
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Full document | ![]() | 508.3 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 4.25 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15480_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15480_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : nucleosome
Entire | Name: nucleosome |
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Components |
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-Supramolecule #1: nucleosome
Supramolecule | Name: nucleosome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 210 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: C-flat-2/2 / Material: COPPER/PALLADIUM / Mesh: 200 / Support film - Material: CARBON |
Vitrification | Cryogen name: OTHER / Details: high pressure freezer HPM010 (ABRA Fluid AG). |
Details | Drosophila melanogaster embryos were high-pressure frozen. Vitreous sections were cut with a nominal thickness of 75 nm and collected onto 200 mesh C-flat grids |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.25 µm / Nominal defocus min: 0.25 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 552 |
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Extraction | Number tomograms: 1 / Number images used: 552 |
Final angle assignment | Type: NOT APPLICABLE |