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- EMDB-48493: The nucleosome-focused cryo-EM map of nucleosome-bound DNA methyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-48493
TitleThe nucleosome-focused cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Map dataThe nucleosome-focused cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Sample
  • Complex: Nucleosome
Keywordsmethyltransferase / DNMT-nucleosome complex / TRANSFERASE / TRANSFERASE-DNA complex / DNA BINDING PROTEIN
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsYan Y / Zhou XE / Xu TH
Funding support United States, 2 items
OrganizationGrant numberCountry
Other privateStartup Funds
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mechanisms of DNMT3A-3L-mediated de novo DNA methylation on chromatin.
Authors: Yan Yan / X Edward Zhou / Stacey L Thomas / Minmin Liu / Gan-Qiang Lai / Evan J Worden / Peter A Jones / Ting-Hai Xu /
Abstract: De novo DNA methylation is mediated by DNA methyltransferases DNMT3A and DNMT3B, in cooperation with the catalytically inactive paralogs DNMT3L and DNMT3B3. DNMT3L is predominantly expressed in ...De novo DNA methylation is mediated by DNA methyltransferases DNMT3A and DNMT3B, in cooperation with the catalytically inactive paralogs DNMT3L and DNMT3B3. DNMT3L is predominantly expressed in embryonic stem cells to establish methylation patterns and is silenced upon differentiation, with DNMT3B3 substituting in somatic cells. Here we present high-resolution cryo-electron microscopy structures of nucleosome-bound, full-length DNMT3A2-3L and its oligomeric assemblies in the nucleosome-free state. We identified the critical role of DNMT3L as a histone modification sensor, guiding chromatin engagement through a mechanism distinct from DNMT3B3. The structures show a 180° rotated 'switching helix' in DNMT3L that prevents direct interaction with the nucleosome acidic patch. Instead, nucleosome binding is mediated by the DNMT3L ADD domain, while the DNMT3A PWWP domain exhibits reduced engagement in the absence of H3K36 methylation. The oligomeric arrangement of DNMT3A2-3L in nucleosome-free states highlights its dynamic assembly and potential allosteric regulation. We further capture dynamic structural movements of DNMT3A2-3L on nucleosomes. These findings uncover a previously unknown mechanism by which DNMT3A-3L mediates de novo DNA methylation on chromatin through complex assembly, histone tail sensing, dynamic DNA search and regulated nucleosome engagement, providing insights into epigenetic regulation.
History
DepositionDec 29, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48493.png

Downloads & links

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Map

FileDownload / File: emd_48493.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe nucleosome-focused cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0018018015 - 1.8835579
Average (Standard dev.)0.00079833 (±0.020430181)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48493_msk_1.map
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Mask #2

Fileemd_48493_msk_2.map
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Additional map: The nucleosome-focused cryo-EM unsharpened map of nucleosome-bound DNA...

Fileemd_48493_additional_1.map
AnnotationThe nucleosome-focused cryo-EM unsharpened map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The nucleosome-focused cryo-EM half map of nucleosome-bound DNA...

Fileemd_48493_half_map_1.map
AnnotationThe nucleosome-focused cryo-EM half map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The nucleosome-focused cryo-EM half map of nucleosome-bound DNA...

Fileemd_48493_half_map_2.map
AnnotationThe nucleosome-focused cryo-EM half map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleosome

EntireName: Nucleosome
Components
  • Complex: Nucleosome

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Supramolecule #1: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 211 KDa

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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

Concentration0.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
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 (6k x 4k) / Number grids imaged: 3 / Number real images: 31987 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10464848
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 627284
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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