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- EMDB-38445: 193 bp Widom601L nucleosome (open) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-38445
Title193 bp Widom601L nucleosome (open)
Map data
Sample
  • Complex: 193 bp Widom601L nucleosome (open)
KeywordsNucleosome / Chromatin / DNA / DEK / Complex / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKujirai T / Echigoya K / Takizawa Y / Kurumizaka H
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15033 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP22KJ0871 Japan
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin.
Authors: Tomoya Kujirai / Kenta Echigoya / Yusuke Kishi / Mai Saeki / Tomoko Ito / Junko Kato / Lumi Negishi / Hiroshi Kimura / Hiroshi Masumoto / Yoshimasa Takizawa / Yukiko Gotoh / Hitoshi Kurumizaka /
Abstract: Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In ...Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK-nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK-nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK.
History
DepositionDec 25, 2023-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38445.png

Downloads & links

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Map

FileDownload / File: emd_38445.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å

Surface

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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: 0.0124
Minimum - Maximum-0.016525222 - 0.055051055
Average (Standard dev.)0.00036904105 (±0.002419515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38445_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_38445_half_map_2.map
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Sample components

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Entire : 193 bp Widom601L nucleosome (open)

EntireName: 193 bp Widom601L nucleosome (open)
Components
  • Complex: 193 bp Widom601L nucleosome (open)

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Supramolecule #1: 193 bp Widom601L nucleosome (open)

SupramoleculeName: 193 bp Widom601L nucleosome (open) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: nucleosome reconstituted in vitro using histone H2A, H2B, H3.1, H4, and 193 base-pairs Widom601L DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14 kDa/nm

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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
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
1.0 mMDTTDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 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: 57.0 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242120
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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