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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: Lin C-C / McGinty RK
History
DepositionJul 14, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 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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