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Yorodumi- EMDB-6949: Subtomogram average of a nucleosome with short linker DNA from a ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6949 | |||||||||||||||
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Title | Subtomogram average of a nucleosome with short linker DNA from a Volta phase contrast cryotomogram of a cryo-FIB lamella of an interphase HeLa cell | |||||||||||||||
Map data | HeLa nucleosome, short linker | |||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 24.0 Å | |||||||||||||||
Authors | Cai S / Bock D / Pilhofer M / Gan L | |||||||||||||||
Funding support | Singapore, Switzerland, 4 items
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Citation | Journal: Mol Biol Cell / Year: 2018 Title: The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Authors: Shujun Cai / Désirée Böck / Martin Pilhofer / Lu Gan / Abstract: The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa ...The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level. | |||||||||||||||
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_6949.map.gz | 69.7 KB | EMDB map data format | |
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Header (meta data) | emd-6949-v30.xml emd-6949.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_6949.png | 57.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6949 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6949 | HTTPS FTP |
-Validation report
Summary document | emd_6949_validation.pdf.gz | 80.2 KB | Display | EMDB validaton report |
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Full document | emd_6949_full_validation.pdf.gz | 79.3 KB | Display | |
Data in XML | emd_6949_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6949 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6949 | HTTPS FTP |
-Related structure data
Related structure data | 6948C 6950C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10179 (Title: The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin Data size: 1.9 Data #1: Tilt series of a cryo-FIB lamella of an interphase HeLa cell [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6949.map.gz / Format: CCP4 / Size: 85.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HeLa nucleosome, short linker | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.9 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 cell, interphase
Entire | Name: HeLa cell, interphase |
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Components |
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-Supramolecule #1: HeLa cell, interphase
Supramolecule | Name: HeLa cell, interphase / type: cell / ID: 1 / Parent: 0 / Details: CCL2- |
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Source (natural) | Organism: Homo sapiens (human) / Organ: cervix |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: yeast-extract supplemented |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 61 / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 14493 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |