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- EMDB-71693: Focused map of mouse KDM6B+cis-linker DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-71693
TitleFocused map of mouse KDM6B+cis-linker DNA
Map datafocused map of mouse KDM6B cis-linker DNA
Sample
  • Complex: KDM6B-nucleosome complex stabilized by H3K27C-UNC8015 covalent conjugate
    • Complex: histones of nucleosome
    • Complex: Widom601 sequence with 20 bp linker DNA at both ends.
    • Complex: Mouse KDM6B C-terminal domain
Keywordshistone H3K27 demethylation / GENE REGULATION / histone / chromatin / epigenetics
Biological speciesHomo sapiens (human) / synthetic construct (others) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsLin C-C / McGinty RK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133498 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35GM139514 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA010305 United States
CitationJournal: Mol Cell / Year: 2025
Title: Structural mechanism of H3K27 demethylation and crosstalk with heterochromatin markers.
Authors: Chien-Chu Lin / Yani Zhao / Caroline A Foley / Aspen T Hawkins / Lindsey I James / Stephen V Frye / Robert K McGinty /
Abstract: Histone H3 lysine 27 trimethylation (H3K27me3) is a repressive histone modification that is a hallmark of facultative heterochromatin. H3K27me3 is installed by the polycomb repressive complex 2 (PRC2) ...Histone H3 lysine 27 trimethylation (H3K27me3) is a repressive histone modification that is a hallmark of facultative heterochromatin. H3K27me3 is installed by the polycomb repressive complex 2 (PRC2) and removed by KDM6 family Jumonji C (JmjC) domain demethylases. Structural studies have elucidated how PRC2 functions on nucleosomes and its regulation by local histone modification signatures. However, the molecular mechanisms governing H3K27 demethylation to reactivate silenced chromatin remain poorly understood. Here, we report the cryoelectron microscopy (cryo-EM) structure of mouse KDM6B bound to the nucleosome. Our structure shows how KDM6B engages wrapped nucleosomal DNA together with both extranucleosomal DNA linkers to position its catalytic JmjC domain for H3K27 demethylation. KDM6B induces an overlapped linker DNA conformation consistent with function in a compact chromatin environment. We further show that linker histones and H2AK119ub1, both enriched in heterochromatin, antagonize KDM6B function, suggesting that linker histone eviction and H2A deubiquitylation precede H3K27 demethylation during heterochromatin activation.
History
DepositionJul 14, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71693.png

Downloads & links

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Map

FileDownload / File: emd_71693.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused map of mouse KDM6B cis-linker DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 336 pix.
= 294.336 Å		0.88 Å/pix.
x 336 pix.
= 294.336 Å		0.88 Å/pix.
x 336 pix.
= 294.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.876 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00441
Minimum - Maximum-0.011909535 - 0.023707084
Average (Standard dev.)0.000017504557 (±0.0003707093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 294.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half2-map

Fileemd_71693_half_map_1.map
Annotationhalf2-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1-map

Fileemd_71693_half_map_2.map
Annotationhalf1-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 : KDM6B-nucleosome complex stabilized by H3K27C-UNC8015 covalent co...

EntireName: KDM6B-nucleosome complex stabilized by H3K27C-UNC8015 covalent conjugate
Components
  • Complex: KDM6B-nucleosome complex stabilized by H3K27C-UNC8015 covalent conjugate
    • Complex: histones of nucleosome
    • Complex: Widom601 sequence with 20 bp linker DNA at both ends.
    • Complex: Mouse KDM6B C-terminal domain

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Supramolecule #1: KDM6B-nucleosome complex stabilized by H3K27C-UNC8015 covalent co...

SupramoleculeName: KDM6B-nucleosome complex stabilized by H3K27C-UNC8015 covalent conjugate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: histones of nucleosome

SupramoleculeName: histones of nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Widom601 sequence with 20 bp linker DNA at both ends.

SupramoleculeName: Widom601 sequence with 20 bp linker DNA at both ends. / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: Mouse KDM6B C-terminal domain

SupramoleculeName: Mouse KDM6B C-terminal domain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Mus musculus (house mouse)

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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

Concentration0.75 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2417051
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6esf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 43458
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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