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

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Basic information

Entry
Database: EMDB / ID: EMD-0119
TitleCryo-electron tomogram of chromatin plates from metaphase chromosomes
Map dataCryo-electron tomogram of chromatin plates from metaphase chromosomes
Sample
  • Complex: chromatin plates from metaphase chromosomes
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsChicano A / Crosas E / Engel BD / Melero R / Oton J / Daban JR
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2010-18939 Spain
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.
History
DepositionJul 10, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseJan 16, 2019-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

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

emd_0119.png

Downloads & links

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Map

FileDownload / File: emd_0119.map.gz / Format: CCP4 / Size: 762.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryo-electron tomogram of chromatin plates from metaphase chromosomes
Projections & slices

Image control

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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.21 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-320.0 - 192.0
Average (Standard dev.)2.5221488 (±27.551014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00232
Dimensions928928464
Spacing928928464
CellA: 3906.8801 Å / B: 3906.8801 Å / C: 1953.4401 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: chromatin plates from metaphase chromosomes

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Supramolecule #1: chromatin plates from metaphase chromosomes

SupramoleculeName: chromatin plates from metaphase chromosomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Nucleosome particles in the plates
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2 / Details: 5 mM Pipes (pH 7.2), 5 mM NaCl, and 5 mM MgCl2
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK III
DetailsChromatin emanated from soft-denatured metaphase chromosomes
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion BSA / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 59

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