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- EMDB-39548: Cryo-EM map of UHRF1 in complex with nucleosome containing hemime... -

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Basic information

Entry
Database: EMDB / ID: EMD-39548
TitleCryo-EM map of UHRF1 in complex with nucleosome containing hemimethylated CpG site at 3'linker DNA
Map data
Sample
  • Complex: UHRF1 in complex with nucleosome containing hemimethylated CpG site at 3'linker DNA
Keywordsnucleosome / UHRF1 / DNA methylation / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsShikimachi R / Arita K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02392 Japan
Japan Society for the Promotion of Science (JSPS)19H05294 Japan
Japan Society for the Promotion of Science (JSPS)19H05741 Japan
CitationJournal: To Be Published
Title: Cryo-EM structures of UHRF1:nucleosome complex revealing the basis for UHRF1 binding to nucleosome and histone H3 ubiquitination
Authors: Shikimachi R / Matsuzawa S / Onoda H / YAmagata A / Konuma T / Shirouzu M / Arita K
History
DepositionMar 21, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39548.png

Downloads & links

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Map

FileDownload / File: emd_39548.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.968 Å		0.83 Å/pix.
x 256 pix.
= 211.968 Å		0.83 Å/pix.
x 256 pix.
= 211.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.379996 - 0.69070244
Average (Standard dev.)0.0015455429 (±0.023372032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39548_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39548_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39548_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 : UHRF1 in complex with nucleosome containing hemimethylated CpG si...

EntireName: UHRF1 in complex with nucleosome containing hemimethylated CpG site at 3'linker DNA
Components
  • Complex: UHRF1 in complex with nucleosome containing hemimethylated CpG site at 3'linker DNA

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Supramolecule #1: UHRF1 in complex with nucleosome containing hemimethylated CpG si...

SupramoleculeName: UHRF1 in complex with nucleosome containing hemimethylated CpG site at 3'linker DNA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 295.7 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 / Details: 20 mM Tris-HCl (pH 7.5) 150 mM NaCl 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.623 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347226
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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