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- EMDB-58100: In situ chromatosome structure from primary human T cells (C1 sym... -

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Basic information

Entry
Database: EMDB / ID: EMD-58100
TitleIn situ chromatosome structure from primary human T cells (C1 symmetry applied)
Map datasharpened, masked map of human chromatosome (C1 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: 7.4 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: Nat Commun / Year: 2026
Title: Molecular architecture of heterochromatin at the nuclear periphery of primary human cells.
Authors: Jan Philipp Kreysing / Sergio Cruz-León / Johannes Betz / Carlotta Penzo / Tomáš Majtner / Markus Schreiber / Beata Turoňová / Marina Lusic / Gerhard Hummer / Martin Beck /
Abstract: In eukaryotes, meters of DNA are packaged into micrometer scale nuclei. Nucleosomes, as the major organizational unit, have been extensively studied in vitro, yet the elaborate 3D structure of ...In eukaryotes, meters of DNA are packaged into micrometer scale nuclei. Nucleosomes, as the major organizational unit, have been extensively studied in vitro, yet the elaborate 3D structure of chromatin inside cells and its distinct oligo-nucleosome arrangements remain poorly resolved. Here, we combine cryo-electron tomography with template matching, subtomogram averaging and molecular simulations to visualize nucleosomes and chromatin structure inside human cells. We confidently assign individual nucleosomes and report their in-situ structure at secondary structure resolution. By predicting the paths of linker DNA, we identify oligo-nucleosome arrangements and uncover higher-order chromatin structures in situ, including a 37-nm wide, elongated but non-fibrous arrangement. In situ structural biology thus reveals the molecular chromatin organization inside cells and sets the stage for 3D genomics.
History
DepositionMay 14, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58100.png

Downloads & links

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Map

FileDownload / File: emd_58100.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened, masked map of human chromatosome (C1 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: 0.54
Minimum - Maximum-0.70754755 - 2.1339538
Average (Standard dev.)0.012530656 (±0.093812674)
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: sharpened, masked halfmap2 of human chromatosome (C1 symmetry...

Fileemd_58100_half_map_1.map
Annotationsharpened, masked halfmap2 of human chromatosome (C1 symmetry applied)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: sharpened, masked halfmap1 of human chromatosome (C1 symmetry...

Fileemd_58100_half_map_2.map
Annotationsharpened, masked halfmap1 of human chromatosome (C1 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.4 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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