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- EMDB-48406: Gamma-H2AX containing nucleosome bound to MCPH1 BRCT -

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Basic information

Entry
Database: EMDB / ID: EMD-48406
TitleGamma-H2AX containing nucleosome bound to MCPH1 BRCT
Map data
Sample
  • Complex: gamma-H2AX containing nucleosome bound to MCPH1 BRCT
Keywordsphosphorylation / nucleosome / nucleosome stacking / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsPanigrahi R / Edwards R / Glover JNM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural insights into γH2Ax containing nucleosomes.
Authors: Rashmi Panigrahi / Ross Edwards / Md Touhidul Islam / Jun Lu / Ayodeji Kulepa / Tae Hwan Kim / J N Mark Glover /
Abstract: The phosphorylation of the histone variant H2AX on the nucleosome, yielding γH2AX, acts as a 'master control switch', signaling the recruitment of DNA repair factors at DNA double-stranded break ...The phosphorylation of the histone variant H2AX on the nucleosome, yielding γH2AX, acts as a 'master control switch', signaling the recruitment of DNA repair factors at DNA double-stranded break sites. This phosphorylation is recognized by BRCA1 carboxy-terminal (BRCT) domains of specific repair proteins. Using cryogenic electron microscopy (cryo-EM), we provide structural insights into diverse mononucleosome architectures and inter-nucleosomal interactions in the presence of H2AX, mimicking nucleosomes during DNA repair. We resolved three distinct stacked structures where the nucleosomal dyad axes and disk planes align parallel. The inter-nucleosomal interactions involve unique contacts mediated by the H4 N-terminal tail, exposed H2B elements, and DNA. Geometric analysis of stacking constraints, including published structures, reveals a tight distribution of rotational parameters around 0o, with the greatest variability in the translational parameter 'slide'. Our studies indicate that phosphorylation-dependent binding of BRCT domains with γH2AX nucleosomes disrupts stacking. However, no clear densities for BRCT proteins were observed, indicative of dynamic interactions. Molecular simulations replicate the stability of BRCT binding to γH2AX but do not indicate stable docked conformations of BRCT to nucleosome. We propose that BRCT recognition of γH2AX nucleosomes could contribute to chromatin decondensation during DNA damage signaling, exposing the nucleosomal acidic patch for repair factor recognition.
History
DepositionDec 20, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48406.png

Downloads & links

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Map

FileDownload / File: emd_48406.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 280 pix.
= 274.4 Å		0.98 Å/pix.
x 280 pix.
= 274.4 Å		0.98 Å/pix.
x 280 pix.
= 274.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.3959735 - 0.90005976
Average (Standard dev.)-0.00013775195 (±0.03258971)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 274.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48406_msk_1.map
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Additional map: sharpened

Fileemd_48406_additional_1.map
Annotationsharpened
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Half map: #1

Fileemd_48406_half_map_1.map
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Half map: #2

Fileemd_48406_half_map_2.map
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Sample components

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Entire : gamma-H2AX containing nucleosome bound to MCPH1 BRCT

EntireName: gamma-H2AX containing nucleosome bound to MCPH1 BRCT
Components
  • Complex: gamma-H2AX containing nucleosome bound to MCPH1 BRCT

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Supramolecule #1: gamma-H2AX containing nucleosome bound to MCPH1 BRCT

SupramoleculeName: gamma-H2AX containing nucleosome bound to MCPH1 BRCT / type: complex / ID: 1 / Parent: 0
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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43533
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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