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- EMDB-41921: Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modifie... -

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Basic information

Entry
Database: EMDB / ID: EMD-41921
TitleCryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
Map datamain map
Sample
  • Complex: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex
    • Complex: DNMT3A N-terminal domain/ubiquitin/nucleosome DNA
    • Complex: histone
KeywordsDNA cytosine methyltransferase / TRANSFERASE
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsChen X / Song J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction.
Authors: Xinyi Chen / Yiran Guo / Ting Zhao / Jiuwei Lu / Jian Fang / Yinsheng Wang / Gang Greg Wang / Jikui Song /
Abstract: Isoform 1 of DNA methyltransferase DNMT3A (DNMT3A1) specifically recognizes nucleosome monoubiquitylated at histone H2A lysine-119 (H2AK119ub1) for establishment of DNA methylation. Mis-regulation of ...Isoform 1 of DNA methyltransferase DNMT3A (DNMT3A1) specifically recognizes nucleosome monoubiquitylated at histone H2A lysine-119 (H2AK119ub1) for establishment of DNA methylation. Mis-regulation of this process may cause aberrant DNA methylation and pathogenesis. However, the molecular basis underlying DNMT3A1-nucleosome interaction remains elusive. Here we report the cryo-EM structure of DNMT3A1's ubiquitin-dependent recruitment (UDR) fragment complexed with H2AK119ub1-modified nucleosome. DNMT3A1 UDR occupies an extensive nucleosome surface, involving the H2A-H2B acidic patch, a surface groove formed by H2A and H3, nucleosomal DNA, and H2AK119ub1. The DNMT3A1 UDR's interaction with H2AK119ub1 affects the functionality of DNMT3A1 in cells in a context-dependent manner. Our structural and biochemical analysis also reveals competition between DNMT3A1 and JARID2, a cofactor of polycomb repression complex 2 (PRC2), for nucleosome binding, suggesting the interplay between different epigenetic pathways. Together, this study reports a molecular basis for H2AK119ub1-dependent DNMT3A1-nucleosome association, with important implications in DNMT3A1-mediated DNA methylation in development.
History
DepositionSep 12, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41921.png

Downloads & links

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Map

FileDownload / File: emd_41921.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 192 pix.
= 237.062 Å		1.23 Å/pix.
x 192 pix.
= 237.062 Å		1.23 Å/pix.
x 192 pix.
= 237.062 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2347 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.069
Minimum - Maximum-0.26567253 - 0.4934858
Average (Standard dev.)-0.0007764817 (±0.0048267036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 237.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_41921_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_41921_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNMT3A N-terminal domain and H2AK119Ub nucleosome complex

EntireName: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex
Components
  • Complex: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex
    • Complex: DNMT3A N-terminal domain/ubiquitin/nucleosome DNA
    • Complex: histone

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Supramolecule #1: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex

SupramoleculeName: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: DNMT3A N-terminal domain/ubiquitin/nucleosome DNA

SupramoleculeName: DNMT3A N-terminal domain/ubiquitin/nucleosome DNA / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: histone

SupramoleculeName: histone / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86685
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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