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Open data
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Basic information
Entry | ![]() | ||||||||||||||||||||||||||||||
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Title | Subtomogram average of a yeast nucleosome from BY4741 cells | ||||||||||||||||||||||||||||||
![]() | Class 1 | ||||||||||||||||||||||||||||||
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![]() | Cell / yeast / nucleus / nucleosome / H2A / NUCLEAR PROTEIN / GFP | ||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 24.0 Å | ||||||||||||||||||||||||||||||
![]() | Tan ZY / Cai S / Noble AJ / Chen JK / Shi J / Gan L | ||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Heterogeneous non-canonical nucleosomespredominate in yeast cells in situ Authors: Tan ZY / Cai S / Noble AJ / Chen JK / Shi J / Gan L | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 140 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.8 KB 22.8 KB | Display Display | ![]() |
Images | ![]() | 32.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 141.8 KB 140.9 KB 141.6 KB 141.5 KB 141.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 574.6 KB | Display | ![]() |
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Full document | ![]() | 574.1 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Class 1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 6.8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Class 2, half map 1
File | emd_31086_additional_1.map | ||||||||||||
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Annotation | Class 2, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Class 2
File | emd_31086_additional_2.map | ||||||||||||
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Annotation | Class 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Class 2, half map 2
File | emd_31086_additional_3.map | ||||||||||||
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Annotation | Class 2, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Class 1, half map 1
File | emd_31086_half_map_1.map | ||||||||||||
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Annotation | Class 1, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Class 1, half map 2
File | emd_31086_half_map_2.map | ||||||||||||
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Annotation | Class 1, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nucleosome from budding yeast BY4741
Entire | Name: Nucleosome from budding yeast BY4741 |
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Components |
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-Supramolecule #1: Nucleosome from budding yeast BY4741
Supramolecule | Name: Nucleosome from budding yeast BY4741 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-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 |
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Grid | Model: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time: 1 second, blot force: 1. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 30369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.1 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 18000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 453 |
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Extraction | Number tomograms: 5 / Number images used: 129473 / Reference model: Featureless cylinder / Method: Template matching / Software - Name: PEET (ver. 1.15) |
Final 3D classification | Number classes: 2 / Software - Name: RELION (ver. 3.0.8) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8) |