+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31086 | ||||||||||||||||||||||||||||||
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Title | Subtomogram average of a yeast nucleosome from BY4741 cells | ||||||||||||||||||||||||||||||
Map data | Class 1 | ||||||||||||||||||||||||||||||
Sample |
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Keywords | Cell / yeast / nucleus / nucleosome / H2A / NUCLEAR PROTEIN / GFP | ||||||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 24.0 Å | ||||||||||||||||||||||||||||||
Authors | Tan ZY / Cai S / Noble AJ / Chen JK / Shi J / Gan L | ||||||||||||||||||||||||||||||
Funding support | Singapore, United States, 9 items
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Citation | Journal: Elife / Year: 2023 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 | emd_31086.map.gz | 140 KB | EMDB map data format | |
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Header (meta data) | emd-31086-v30.xml emd-31086.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
Images | emd_31086.png | 32.9 KB | ||
Others | emd_31086_additional_1.map.gz emd_31086_additional_2.map.gz emd_31086_additional_3.map.gz emd_31086_half_map_1.map.gz emd_31086_half_map_2.map.gz | 141.8 KB 140.9 KB 141.6 KB 141.5 KB 141.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31086 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31086 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31086.map.gz / Format: CCP4 / Size: 182.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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 |
-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: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741 / Organelle: Nucleus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 30369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.1 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 18000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 5 / Number images used: 129473 / Reference model: Featureless cylinder / Method: Template matching / Software - Name: PEET (ver. 1.15) |
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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) |
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 |