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- EMDB-77709: Local refinement cryo-EM map of CXXC-NCP component of the mutant ... -

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Basic information

Entry
Database: EMDB / ID: EMD-77709
TitleLocal refinement cryo-EM map of CXXC-NCP component of the mutant MHKKKQ DNMT1-umNCP complex
Map dataSharpened
Sample
  • Complex: mutant MHKKKQ DNMT1-umNCP complex
KeywordsDNA C5 methyltransferase / Nucleosome complex / TRANSFERASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFang J / Lu J / Song J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2026
Title: The DNMT1 CXXC domain senses CpG islands for DNA methylation inhibition.
Authors: Jian Fang / Bo Pan / Wendan Ren / Jiuwei Lu / Ting Zhao / Yiran Guo / Ling Cai / Yinsheng Wang / Gang Greg Wang / Jikui Song /
Abstract: DNA methyltransferase DNMT1 plays an essential role in maintaining DNA methylation homeostasis. While DNMT1-mediated DNA methylation mainly occurs outside the active chromatin domains, such as CpG ...DNA methyltransferase DNMT1 plays an essential role in maintaining DNA methylation homeostasis. While DNMT1-mediated DNA methylation mainly occurs outside the active chromatin domains, such as CpG islands, how DNMT1 interplays with hypomethylated nucleosome environment to restrict CpG island methylation remains unclear. Here we report the structure of DNMT1 with a nucleosome containing unmodified CpG sites. The interaction of the DNMT1 CXXC domain with the unmodified CpG sites within the nucleosome core or the linker strengthens the DNMT1-nucleosome association, which contributes to the enrichment of DNMT1 in CpG islands. On the other hand, the CXXC domain is positioned in a manner that blocks the target recognition domain of DNMT1 from accessing potential DNA substrates. Consistently, disrupting the CXXC-CpG interaction leads to DNMT1 hyperactivity on nucleosomes with unmodified CpG sites, or those with spatially proximate unmodified and hemimethylated CpG sites. Furthermore, our whole-genome bisulfite-sequencing analysis reveals that introducing the CXXC-CpG interaction-defective DNMT1 mutation leads to substantial increase in CpG island methylation but not so much in overall genomic methylation, causing severe defects in transcriptional programming and stem cell differentiation. Together, this study establishes a role for the CXXC domain in safeguarding the CpG island hypomethylation, vital to DNA methylation homeostasis during development.
History
DepositionJun 22, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateNov 4, 2026-
Current statusNov 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77709.png

Downloads & links

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Map

FileDownload / File: emd_77709.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 256 pix.
= 380.877 Å		1.49 Å/pix.
x 256 pix.
= 380.877 Å		1.49 Å/pix.
x 256 pix.
= 380.877 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.0471225 - 2.00876
Average (Standard dev.)0.000051058116 (±0.03257321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 380.8768 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened

Fileemd_77709_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_77709_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_77709_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mutant MHKKKQ DNMT1-umNCP complex

EntireName: mutant MHKKKQ DNMT1-umNCP complex
Components
  • Complex: mutant MHKKKQ DNMT1-umNCP complex

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Supramolecule #1: mutant MHKKKQ DNMT1-umNCP complex

SupramoleculeName: mutant MHKKKQ DNMT1-umNCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.13 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
50.0 mMNaClSodium chloride
5.0 mMDTTDithiothreitol
5.0 %GlycerolGlycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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) / Number grids imaged: 2 / Number real images: 18114 / Average exposure time: 2.5 sec. / Average electron dose: 65.5 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: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7940000
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 287638
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7jzv

source_name: PDB, initial_model_type: experimental modelFor nucleosome

7xi9

chain_id: A, source_name: PDB, initial_model_type: experimental modelDNMT1

3pt6

chain_id: A, source_name: PDB, initial_model_type: experimental modelDNMT1
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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