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- EMDB-15061: Fibroblast nucleus sub-volume. -

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Basic information

Entry
Database: EMDB / ID: EMD-15061
TitleFibroblast nucleus sub-volume.
Map datasub-volume of EMD-14924. corresponds to Supplementary Movie S6.
Sample
  • Cell: WI-38 fibroblast cell
Keywordsnucleus / chromatin / STEM / DNA
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsSedat J / McDonald A / Elbaum M
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation1696/18 Israel
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence.
Authors: John Sedat / Angus McDonald / Hu Cang / Joseph Lucas / Muthuvel Arigovindan / Zvi Kam / Cornelis Murre / Michael Elbaum /
Abstract: Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome ...Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diameter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman , 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes.
History
DepositionMay 30, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15061.png

Downloads & links

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Map

FileDownload / File: emd_15061.map.gz / Format: CCP4 / Size: 63.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsub-volume of EMD-14924. corresponds to Supplementary Movie S6.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
33.5 Å/pix.
x 100 pix.
= 3350. Å		33.5 Å/pix.
x 470 pix.
= 15745. Å		33.5 Å/pix.
x 356 pix.
= 11926. 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: 33.5 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum1500.0 - 3073.685500000000047
Average (Standard dev.)1679.505000000000109 (±171.782000000000011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin18040187
Dimensions470356100
Spacing356470100
CellA: 11926.0 Å / B: 15745.0 Å / C: 3350.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : WI-38 fibroblast cell

EntireName: WI-38 fibroblast cell
Components
  • Cell: WI-38 fibroblast cell

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Supramolecule #1: WI-38 fibroblast cell

SupramoleculeName: WI-38 fibroblast cell / type: cell / ID: 1 / Parent: 0 / Details: cells cultured directly on gold EM grid
Source (natural)Organism: Homo sapiens (human) / Organ: lung / Tissue: cell culture

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Details: Minimal Essential Medium (Gibco) supplemented with 15% fetal calf serum, L-glutamine, and penicillin/streptomycin.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP
DetailsWI-38 embryonic lung fibroblast cells (obtained from Coriell Institute) were cultured directly on gold EM grids and imaged intact by cryo-STEM tomography (CSTET).
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: obtained from L Duchesne (https://doi.org/10.1021/la802876u )
Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TECNAI F20
Specialist opticsDetails: STEM data collection in BF mode.
DetailsNanoProbe STEM acquisition.
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 61 / Average exposure time: 12.6 sec. / Average electron dose: 3.8 e/Å2 / Details: Cryo-STEM tilt series
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsGatan STEM BF/ADF detector
Final reconstructionAlgorithm: BACK PROJECTION / Software: (Name: TOMO3D, PRIISM/IVE) / Number images used: 56

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