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- EMDB-62686: ATRX with the nucleosomal DNA (focus refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-62686
TitleATRX with the nucleosomal DNA (focus refinement)
Map dataATRX_Focus
Sample
  • Complex: ATRX C-terminal domains in complex with the nucleosome
Keywordschromatin remodeler / nucleosome / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou K / Duan S / Liu Y
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)27122123 Hong Kong
CitationJournal: To Be Published
Title: Mechanistic insights into chromatin modulation by the orphan remodeler ATRX
Authors: Zhou K / Liu Y
History
DepositionDec 11, 2024-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62686.png

Downloads & links

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Map

FileDownload / File: emd_62686.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATRX_Focus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 384 pix.
= 366.989 Å		0.96 Å/pix.
x 384 pix.
= 366.989 Å		0.96 Å/pix.
x 384 pix.
= 366.989 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.314635 - 1.7435415
Average (Standard dev.)0.0031395536 (±0.020912403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 366.9888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62686_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62686_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62686_half_map_2.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 : ATRX C-terminal domains in complex with the nucleosome

EntireName: ATRX C-terminal domains in complex with the nucleosome
Components
  • Complex: ATRX C-terminal domains in complex with the nucleosome

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Supramolecule #1: ATRX C-terminal domains in complex with the nucleosome

SupramoleculeName: ATRX C-terminal domains in complex with the nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 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

Concentration1.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 15000 / Average electron dose: 40.0 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 / Nominal magnification: 135000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2364881
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147422
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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