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- EMDB-42597: MagIC-cryo-EM of the H1.8-GFP nucleosome formed in the Xenopus eg... -

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Basic information

Entry
Database: EMDB / ID: EMD-42597
TitleMagIC-cryo-EM of the H1.8-GFP nucleosome formed in the Xenopus egg extract metaphase chromosomes
Map data
Sample
  • Complex: Nucleosome complexed with H1.8-GFP
Keywordsnucleosome / H1 / Xenopus egg extract / MagIC-cryo-EM / DNA BINDING PROTEIN-DNA complex
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsArimura Y / Funabiki H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132111 United States
CitationJournal: To Be Published
Title: MagIC-cryo-EM: a method for single particle cryo-EM analysis on magnetic beads
Authors: Arimura Y / Funabiki H
History
DepositionNov 2, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42597.png

Downloads & links

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Map

FileDownload / File: emd_42597.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.38752115 - 0.8934032
Average (Standard dev.)0.00064725784 (±0.0334073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42597_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_42597_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 : Nucleosome complexed with H1.8-GFP

EntireName: Nucleosome complexed with H1.8-GFP
Components
  • Complex: Nucleosome complexed with H1.8-GFP

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Supramolecule #1: Nucleosome complexed with H1.8-GFP

SupramoleculeName: Nucleosome complexed with H1.8-GFP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 200000 MDa

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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

Concentration0.0001 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE
Details: MagIC-cryo-EM beads capturing H1.8-GFP-nucleosomes were applied to the grid. The grid was then incubated on neodymium magnets for 5 minutes within a high-humidity chamber to facilitate magnetic bead capture..
DetailsH1.8-GFP nucleosomes formed in interphase and metaphase were isolated by MagIC-cryo-EM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22051
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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