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- EMDB-0119: Cryo-electron tomogram of chromatin plates from metaphase chromosomes -

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Entry
Database: EMDB / ID: 0119
TitleCryo-electron tomogram of chromatin plates from metaphase chromosomes
Map dataCryo-electron tomogram of chromatin plates from metaphase chromosomes
Samplechromatin plates from metaphase chromosomes:
SourceHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsChicano A / Crosas E / Engel BD / Melero R / Oton J / Daban JR
CitationJournal: 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.
DateDeposition: Jul 10, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

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Map

Fileemd_0119.map.gz (map file in CCP4 format, 799179 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
464 pix
4.21 Å/pix.
= 1953.44 Å
928 pix
4.21 Å/pix.
= 3906.88 Å
928 pix
4.21 Å/pix.
= 3906.88 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.21 Å
Density
Minimum - Maximum-320.0 - 192.0
Average (Standard dev.)2.5221488 (27.551013999999999)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions928928464
Origin0.00.0232.0
Limit927.0927.0695.0
Spacing928928464
CellA: 3906.8801 Å / B: 3906.8801 Å / C: 1953.4401 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z4.214.214.21
M x/y/z928928464
origin x/y/z0.0000.0000.000
length x/y/z3906.8803906.8801953.440
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS00232
NC/NR/NS928928464
D min/max/mean-320.000192.0002.522

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Supplemental data

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Sample components

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Entire chromatin plates from metaphase chromosomes

EntireName: chromatin plates from metaphase chromosomes / Details: Nucleosome particles in the plates / Number of components: 1

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Component #1: protein, chromatin plates from metaphase chromosomes

ProteinName: chromatin plates from metaphase chromosomes / Details: Nucleosome particles in the plates / Recombinant expression: No
SourceSpecies: Homo sapiens (human) / Strain: HeLa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 5 mM Pipes (pH 7.2), 5 mM NaCl, and 5 mM MgCl2
pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD / Energy filter: GIF 2002
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 59
3D reconstructionAlgorithm: BACK PROJECTION

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