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- EMDB-39541: Cryo-EM map of UHRF1 in complex with nucleosome containing hemime... -

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Basic information

Entry
Database: EMDB / ID: EMD-39541
TitleCryo-EM map of UHRF1 in complex with nucleosome containing hemimethylated CpG site at 5'linker DNA
Map data
Sample
  • Complex: UHRF1 in complex with nucleosome containing hemimethylated CpG site at 5'linker DNA
Keywordsnucleosome / UHRF1 / DNA methylation / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 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: J Biol Chem / Year: 2025
Title: Structural basis for E3 ubiquitin ligase UHRF1 binding to nucleosome core particle and histone H3 ubiquitination.
Authors: Reia Shikimachi / Shun Matsuzawa / Hiroki Onoda / Tsuyoshi Konuma / Atsushi Yamagata / Mikako Shirouzu / Kosuke Yamaguchi / Kyohei Arita /
Abstract: The maintenance of DNA methylation in differentiated cells is regulated by a ubiquitin signal generated by UHRF1 (ubiquitin-like with plant homeodomain and RING finger domain 1), which plays a ...The maintenance of DNA methylation in differentiated cells is regulated by a ubiquitin signal generated by UHRF1 (ubiquitin-like with plant homeodomain and RING finger domain 1), which plays a pivotal role in recruitment of DNA methyltransferase DNMT1 to hemimethylated CpG sites. UHRF1 catalyzes multiple monoubiquitinations on histone H3 within nucleosomes. However, the structural mechanisms underlying the binding of UHRF1 to nucleosomes and the subsequent formation of the ubiquitin signal remain incompletely understood. Here, we report cryo-EM structures of UHRF1 bound to nucleosome core particle (NCP) harboring H3K9me3 and a single hemimethylated CpG site. The structures of the UHRF1-NCP complexes reveal an unanticipated interaction between the UHRF1 tandem Tudor domain and the acidic patch of the NCP. This interaction enhances histone H3 ubiquitination and stabilizes UHRF1 binding to the NCP in a manner that is dependent on the position of the hemimethylated CpG site. These findings provide mechanistic insights into the binding of UHRF1 to the NCP and the multiple monoubiquitination of histone H3 within the NCP.
History
DepositionMar 21, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39541.png

Downloads & links

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Map

FileDownload / File: emd_39541.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.3788519 - 0.7476278
Average (Standard dev.)0.0016029462 (±0.02516153)
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_39541_msk_1.map
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Half map: #2

Fileemd_39541_half_map_1.map
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Half map: #1

Fileemd_39541_half_map_2.map
Projections & Slices
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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 5'linker DNA
Components
  • Complex: UHRF1 in complex with nucleosome containing hemimethylated CpG site at 5'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 5'linker DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 297019.4 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 (pH7.5) 150 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: 180 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / 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: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 452358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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