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- EMDB-58101: In situ chromatosome structure from primary human T cells (C2 sym... -

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Basic information

Entry
Database: EMDB / ID: EMD-58101
TitleIn situ chromatosome structure from primary human T cells (C2 symmetry applied)
Map datasharpened, masked map of human chromatosome (C2 symmetry applied)
Sample
  • Cell: In situ chromatosome structure from FIB-milled primary human T cells
Keywordsnucleosome / chromatosome / histones / DNA / chromatin / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 6.8 Å
AuthorsKreysing JP / Majtner T / Turonova B / Beck M
Funding support Germany, United States, 3 items
OrganizationGrant numberCountry
Max Planck Society Germany
Chan Zuckerberg Initiative2021-234666 United States
German Research Foundation (DFG)240245660 Germany
CitationJournal: To Be Published
Title: Molecular architecture of heterochromatin at the nuclear periphery of primary human cells
Authors: Kreysing JP / Cruz-Leon S / Betz J / Penzo C / Majtner T / Schreiber M / Turonova B / Lusic M / Hummer G / Beck M
History
DepositionMay 14, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58101.png

Downloads & links

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Map

FileDownload / File: emd_58101.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened, masked map of human chromatosome (C2 symmetry applied)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.9 Å/pix.
x 140 pix.
= 265.3 Å		1.9 Å/pix.
x 140 pix.
= 265.3 Å		1.9 Å/pix.
x 140 pix.
= 265.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.895 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.52
Minimum - Maximum-0.8837148 - 2.2473462
Average (Standard dev.)0.012352461 (±0.09896645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 265.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap1 of human chromatosome (C2 symmetry applied)

Fileemd_58101_half_map_1.map
Annotationhalfmap1 of human chromatosome (C2 symmetry applied)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2 of human chromatosome (C2 symmetry applied)

Fileemd_58101_half_map_2.map
Annotationhalfmap2 of human chromatosome (C2 symmetry applied)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ chromatosome structure from FIB-milled primary human T cells

EntireName: In situ chromatosome structure from FIB-milled primary human T cells
Components
  • Cell: In situ chromatosome structure from FIB-milled primary human T cells

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Supramolecule #1: In situ chromatosome structure from FIB-milled primary human T cells

SupramoleculeName: In situ chromatosome structure from FIB-milled primary human T cells
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.25 µm / Nominal defocus min: 1.75 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 33560
ExtractionNumber tomograms: 14 / Number images used: 33560 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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