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- EMDB-62041: Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-62041
TitleCryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C1 symmetry)
Map datamap
Sample
  • Complex: Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA
Keywordsnucleosome / histone / H2A.Z / Arabidopsis / NUCLEAR PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsWang Y / Dong A
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930017 China
CitationJournal: Structure / Year: 2025
Title: Structural and functional interrelationships of histone H2A with its variants H2A.Z and H2A.W in Arabidopsis
Authors: Wang Y / Dong A
History
DepositionOct 21, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62041.png

Downloads & links

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Map

FileDownload / File: emd_62041.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.40219665 - 1.3056955
Average (Standard dev.)0.001965342 (±0.05199691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62041_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half A

Fileemd_62041_half_map_1.map
Annotationmap_half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half B

Fileemd_62041_half_map_2.map
Annotationmap_half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA

EntireName: Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA
Components
  • Complex: Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA

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Supramolecule #1: Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA

SupramoleculeName: Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.8 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 114381
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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