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Yorodumi- EMDB-0119: Cryo-electron tomogram of chromatin plates from metaphase chromosomes -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0119 | |||||||||
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Title | Cryo-electron tomogram of chromatin plates from metaphase chromosomes | |||||||||
Map data | Cryo-electron tomogram of chromatin plates from metaphase chromosomes | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Chicano A / Crosas E / Engel BD / Melero R / Oton J / Daban JR | |||||||||
Funding support | Spain, 1 items
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Citation | Journal: EMBO J / Year: 2019 Title: Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure. Authors: Andrea Chicano / Eva Crosas / Joaquín Otón / Roberto Melero / Benjamin D Engel / Joan-Ramon Daban / Abstract: Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated ...Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated chromatin emanated from chromosomes is planar and forms multilayered plates. The layer thickness was measured accounting for the contrast transfer function fringes at the plate edges, yielding a width of ~ 7.5 nm, which is compatible with the dimensions of a monolayer of nucleosomes slightly tilted with respect to the layer surface. Individual nucleosomes are visible decorating distorted plates, but typical plates are very dense and nucleosomes are not identifiable as individual units, indicating that they are tightly packed. Two layers in contact are ~ 13 nm thick, which is thinner than the sum of two independent layers, suggesting that nucleosomes in the layers interdigitate. X-ray scattering of whole chromosomes shows a main scattering peak at ~ 6 nm, which can be correlated with the distance between layers and between interdigitating nucleosomes interacting through their faces. These observations support a model where compact chromosomes are composed of many chromatin layers stacked along the chromosome axis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0119.map.gz | 425.2 MB | EMDB map data format | |
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Header (meta data) | emd-0119-v30.xml emd-0119.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_0119.png | 130.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0119 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0119 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0119.map.gz / Format: CCP4 / Size: 762.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-electron tomogram of chromatin plates from metaphase chromosomes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : chromatin plates from metaphase chromosomes
Entire | Name: chromatin plates from metaphase chromosomes |
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Components |
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-Supramolecule #1: chromatin plates from metaphase chromosomes
Supramolecule | Name: chromatin plates from metaphase chromosomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Nucleosome particles in the plates |
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Source (natural) | Organism: Homo sapiens (human) / Strain: HeLa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: 5 mM Pipes (pH 7.2), 5 mM NaCl, and 5 mM MgCl2 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK III |
Details | Chromatin emanated from soft-denatured metaphase chromosomes |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Aurion BSA / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF 2002 |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 1.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: INTEGRATING / #1 - Average electron dose: 1.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Number images used: 59 |
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Image recording ID | 1 |