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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: To Be Published
Title: Structural Insights into DNMT3A-3L-Mediated de novo DNA Methylation on Chromatin
Authors: Yan Y / Zhou XE / Thomas TL / Liu M / O'Leary T / Griffin PR / Lai G / Worden E / Jones PA / Xu TH
History
DepositionDec 29, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 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
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_48493_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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