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- EMDB-71301: Consensus map for Cryo-EM structure of DNMT3A2/3B3 tetramer in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-71301
TitleConsensus map for Cryo-EM structure of DNMT3A2/3B3 tetramer in complex with a 167H3K36me2 nucleosome
Map data
Sample
  • Complex: DNMT 3A2/3B3 in complex with a 167H3K36me2-nucleosome
KeywordsDNA methylation / DNMT3A2/3B3 / H3K36me2-nucleosome / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsXie X / Liu M / Zhou XE / Worden E / Jones P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147261 United States
CitationJournal: To Be Published
Title: The structural basis for de novo DNA methylation in chromatin
Authors: Xie X / Liu M / Zhou XE / Worden E / Jones P
History
DepositionJun 18, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71301.png

Downloads & links

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Map

FileDownload / File: emd_71301.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 208 pix.
= 344.448 Å		1.66 Å/pix.
x 208 pix.
= 344.448 Å		1.66 Å/pix.
x 208 pix.
= 344.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.107
Minimum - Maximum-0.27496505 - 0.7683047
Average (Standard dev.)0.0005002351 (±0.027675219)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 344.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71301_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71301_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 : DNMT 3A2/3B3 in complex with a 167H3K36me2-nucleosome

EntireName: DNMT 3A2/3B3 in complex with a 167H3K36me2-nucleosome
Components
  • Complex: DNMT 3A2/3B3 in complex with a 167H3K36me2-nucleosome

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Supramolecule #1: DNMT 3A2/3B3 in complex with a 167H3K36me2-nucleosome

SupramoleculeName: DNMT 3A2/3B3 in complex with a 167H3K36me2-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: 50.0 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

Particle selectionNumber selected: 7152655
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6pa7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111367
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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