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- EMDB-49923: Subtomogram average of nucleosome structure extracted from the He... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49923
TitleSubtomogram average of nucleosome structure extracted from the HeLa cell nuclei
Map data
Sample
  • Complex: Subtomogram average of nucleosome structure
KeywordsNucleosome / chromatin / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsZhou H / Hutchings J / Villa E / Rosen M
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
Welch FoundationI-1544 United States
CitationJournal: To Be Published
Title: Subtomogram average of nucleosome structure extracted from the HeLa cell nuclei
Authors: Zhou H / Hutchings J / Villa E / Rosen M
History
DepositionMar 26, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49923.png

Downloads & links

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Map

FileDownload / File: emd_49923.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 50 pix.
= 200. Å		4 Å/pix.
x 50 pix.
= 200. Å		4 Å/pix.
x 50 pix.
= 200. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.43154952 - 1.3978592
Average (Standard dev.)0.01554334 (±0.119836666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions505050
Spacing505050
CellA=B=C: 200.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49923_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_49923_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 : Subtomogram average of nucleosome structure

EntireName: Subtomogram average of nucleosome structure
Components
  • Complex: Subtomogram average of nucleosome structure

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Supramolecule #1: Subtomogram average of nucleosome structure

SupramoleculeName: Subtomogram average of nucleosome structure / 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
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.9
Details: 20 mM HEPES, pH 7.9, 100 mM KOAc, 1 mM Mg(OAc)2, 0.15 uM Spermine, 10 mM Sodium Butyrate, 10 mM Nicotinamide, 10 uM Pepstatin, 3 mM AEBSF, 10 uM E-64, 2 uM Antipain, 500 uM leupeptin, 2ug/ml ...Details: 20 mM HEPES, pH 7.9, 100 mM KOAc, 1 mM Mg(OAc)2, 0.15 uM Spermine, 10 mM Sodium Butyrate, 10 mM Nicotinamide, 10 uM Pepstatin, 3 mM AEBSF, 10 uM E-64, 2 uM Antipain, 500 uM leupeptin, 2ug/ml aprotinin, 4 uM TSA, 1 mM DTT
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 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: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 35503
ExtractionNumber tomograms: 13 / Number images used: 35503
CTF correctionSoftware - Name: Warp (ver. 1.10) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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