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- EMDB-63081: Cryo-EM structure of the native HeLa nucleosome in poly-nucleosom... -

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Basic information

Entry
Database: EMDB / ID: EMD-63081
TitleCryo-EM structure of the native HeLa nucleosome in poly-nucleosomes (class 3)
Map data
Sample
  • Complex: Nucleosome containing histone octamer and genomic DNA
KeywordsComplex / Nucleosome / Chromatin / Epigenetics / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsHatazawa S / Takizawa Y / Kurumizaka H
Funding support Japan, 9 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K14134 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02319 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
Japan Agency for Medical Research and Development (AMED)JP24ama121002 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Science and TechnologyJPMJCR24T3 Japan
CitationJournal: Genes Cells / Year: 2025
Title: Cryo-EM Structures of Native Chromatin Units From Human Cells.
Authors: Suguru Hatazawa / Yoshiyuki Fukuda / Yuki Kobayashi / Lumi Negishi / Masahide Kikkawa / Yoshimasa Takizawa / Hitoshi Kurumizaka /
Abstract: In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin ...In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin folding, by which genomic DNA is regulated in the nucleus. To study the structures of chromatin units in cells, we have established a method for the structural analysis of native mono- and poly-nucleosomes prepared from HeLa cells. In this method, the chromatin in isolated nuclei was crosslinked to preserve the proximity information between nucleosomes, followed by chromatin fragmentation by micrococcal nuclease treatment. The mono- and poly-nucleosomes were then fractionated by sucrose gradient ultracentrifugation, and their structures were analyzed by cryo-electron microscopy. Cryo-electron microscopy single particle analysis and cryo-electron tomography visualized a native nucleosome structure and secondary nucleosome arrangements in cellular chromatin. This method provides a complementary strategy to fill the gap between in vitro and in situ analyses of chromatin structure.
History
DepositionJan 10, 2025-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63081.png

Downloads & links

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Map

FileDownload / File: emd_63081.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å		1.06 Å/pix.
x 220 pix.
= 233.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.074646175 - 0.13443194
Average (Standard dev.)0.0003546409 (±0.00414296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63081_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63081_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome containing histone octamer and genomic DNA

EntireName: Nucleosome containing histone octamer and genomic DNA
Components
  • Complex: Nucleosome containing histone octamer and genomic DNA

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Supramolecule #1: Nucleosome containing histone octamer and genomic DNA

SupramoleculeName: Nucleosome containing histone octamer and genomic DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3tris (hydroxymethyl) aminomethane
30.0 mMNaClsodium chloride
1.0 mMC4H10O2S2dithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.094 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3afa

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 286265
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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