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- EMDB-65715: Cryo-EM map of the nucleosome reconstituted in E. coli cells -

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Basic information

Entry
Database: EMDB / ID: EMD-65715
TitleCryo-EM map of the nucleosome reconstituted in E. coli cells
Map dataMain map
Sample
  • Complex: Xenopus nucleosome in complex with the PL2-6 scFv
    • Complex: Xenopus nucleosome
    • Complex: PL2-6 scFv
KeywordsChromatin / Nucleosome / Histone / DNA / GENE REGULATION
Biological speciesXenopus laevis (African clawed frog) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsHo C-H / Takizawa Y / Kurumizaka H
Funding support Japan, 8 items
OrganizationGrant numberCountry
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 Science and TechnologyJPMJER1901 Japan
Japan Science and TechnologyJPMJCR24T3 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121009 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121002 Japan
Japan Society for the Promotion of Science (JSPS)JP25K18403 Japan
CitationJournal: Iscience / Year: 2026
Title: A method for cryo-EM analysis of eukaryotic nucleosomes reconstituted in bacterial cells
Authors: Ho CH / Kobayashi Y / Ogasawara M / Takizawa Y / Kurumizaka H
History
DepositionAug 5, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65715.png

Downloads & links

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Map

FileDownload / File: emd_65715.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.068
Minimum - Maximum-0.12066996 - 0.27431613
Average (Standard dev.)0.0011272782 (±0.012231818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer sharpened map

Fileemd_65715_additional_1.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65715_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65715_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Xenopus nucleosome in complex with the PL2-6 scFv

EntireName: Xenopus nucleosome in complex with the PL2-6 scFv
Components
  • Complex: Xenopus nucleosome in complex with the PL2-6 scFv
    • Complex: Xenopus nucleosome
    • Complex: PL2-6 scFv

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Supramolecule #1: Xenopus nucleosome in complex with the PL2-6 scFv

SupramoleculeName: Xenopus nucleosome in complex with the PL2-6 scFv / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #2: Xenopus nucleosome

SupramoleculeName: Xenopus nucleosome / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: PL2-6 scFv

SupramoleculeName: PL2-6 scFv / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
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: 60.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.25 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Software - details: Non-uniform Refinement / Number images used: 1450013
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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