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- EMDB-53275: Subtomogram average of nucleosome from NIH3T3 cells, class 1 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53275
TitleSubtomogram average of nucleosome from NIH3T3 cells, class 1
Map data
Sample
  • Cell: NIH3T3 cell
KeywordsNucleosome / Chromatin / DNA BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 12.6 Å
AuthorsZhou H / Hutchings J / Villa E / Rosen M
Funding support United States, 3 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
Howard Hughes Medical Institute (HHMI) United States
Welch FoundationI-1544 United States
CitationJournal: To Be Published
Title: Subtomogram average of nucleosome from NIH3T3 cells
Authors: Zhou H / Hutchings J / Villa E / Rosen M
History
DepositionMar 27, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53275.png

Downloads & links

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Map

FileDownload / File: emd_53275.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3 Å/pix.
x 80 pix.
= 240. Å		3 Å/pix.
x 80 pix.
= 240. Å		3 Å/pix.
x 80 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.44222486 - 1.3746263
Average (Standard dev.)0.011573929 (±0.118891574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53275_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53275_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 : NIH3T3 cell

EntireName: NIH3T3 cell
Components
  • Cell: NIH3T3 cell

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Supramolecule #1: NIH3T3 cell

SupramoleculeName: NIH3T3 cell / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2 / Details: DMEM
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 6470
ExtractionNumber tomograms: 4 / Number images used: 6470
CTF correctionSoftware - Name: Warp (ver. 1.10) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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