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- EMDB-71608: Focus map of nucleosome 2 for Cryo-EM structure of DNMT3A2/3B3 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-71608
TitleFocus map of nucleosome 2 for Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Map data
Sample
  • Complex: DNMT3A/3B tetramer bound to H3K36me2 di-nucleosome
KeywordsDNMT3A2/DNMT3B3 / DNA methylation / H3K36me2 di-nucleosome / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsXie X / Zhou XE / Worden EJ / Jones PA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: Mol Cell / Year: 2026
Title: Nucleosome spacing regulates linker methylation by DNMT3A2/3B3.
Authors: Xiaoyan Xie / Minmin Liu / Gabriella N L Chua / X Edward Zhou / Michelle L Dykstra / Shixin Liu / Peter A Jones / Evan J Worden /
Abstract: De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get ...De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get targeted by DNMT3 enzymes are not understood. We show that nucleosome spacing controls linker DNA methylation and H3K36me2 recognition by human DNMT3A2/3B3, linking de novo methylation to chromatin architecture. We present structures of DNMT3A2/3B3 bound to dinucleosomes, revealing that short linkers promote dinucleosome bridging, blocking access to linker DNA and suppressing methylation, whereas long linkers allow DNMT3A2/3B3 to engage each nucleosome separately and methylate linker DNA. Finally, we show that DNMT3A2/3B3 positions proline-tryptophan-tryptophan-proline (PWWP) domains to scan for H3K36me2. However, H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges dinucleosomes with short linkers, imposing an additional structural constraint on DNMT3A2/3B3 function. Together, these findings uncover the mechanisms that govern de novo methylation in chromatin and explain how DNMT3 enzymes target linkers in cells.
History
DepositionJul 6, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71608.png

Downloads & links

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Map

FileDownload / File: emd_71608.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 370.944 Å		0.83 Å/pix.
x 448 pix.
= 370.944 Å		0.83 Å/pix.
x 448 pix.
= 370.944 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0288
Minimum - Maximum-0.16492236 - 0.32491723
Average (Standard dev.)-0.00027765575 (±0.0073662368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 370.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_71608_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_71608_half_map_1.map
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Histogram (log scale)

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Half map: #2

Fileemd_71608_half_map_2.map
Projections & Slices
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Sample components

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Entire : DNMT3A/3B tetramer bound to H3K36me2 di-nucleosome

EntireName: DNMT3A/3B tetramer bound to H3K36me2 di-nucleosome
Components
  • Complex: DNMT3A/3B tetramer bound to H3K36me2 di-nucleosome

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Supramolecule #1: DNMT3A/3B tetramer bound to H3K36me2 di-nucleosome

SupramoleculeName: DNMT3A/3B tetramer bound to H3K36me2 di-nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
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

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6p7a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123813
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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