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- EMDB-39550: Cryo-EM map of UHRF1 in complex with nucleosome containing hemime... -

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Basic information

Entry
Database: EMDB / ID: EMD-39550
TitleCryo-EM map of UHRF1 in complex with nucleosome containing hemimethylated CpG site at widom601 sequence
Map data
Sample
  • Complex: UHRF1 in complex with nucleosome containing hemimethylated CpG site at widom601 sequence
Keywordsnucleosome / UHRF1 / DNA methylation / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsShikimachi R / Arita K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02392 Japan
Japan Science and Technology19H05294 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 / Konuma T / Yamagata A / 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_39550.png

Downloads & links

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Map

FileDownload / File: emd_39550.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-0.24282008 - 0.49983466
Average (Standard dev.)0.0014251779 (±0.018241225)
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_39550_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39550_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_39550_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 widom601 sequence
Components
  • Complex: UHRF1 in complex with nucleosome containing hemimethylated CpG site at widom601 sequence

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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 widom601 sequence
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 292 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) 50 mM NaCl 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 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: 58.582 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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229682
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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