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- EMDB-49924: Subtomogram averaging of nucleosomes in reconstituted chromatin c... -

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Basic information

Entry
Database: EMDB / ID: EMD-49924
TitleSubtomogram averaging of nucleosomes in reconstituted chromatin condensates
Map dataSubtomogram averaging of nucleosomes in the chromatin condensate
Sample
  • Complex: In vitro reconstituted nucleosome by using histone protein with 601 sequence
KeywordsNucleosome / chromatin / DNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 6.1 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 averaging of nucleosomes in chromatin condensates
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_49924.png

Downloads & links

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Map

FileDownload / File: emd_49924.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaging of nucleosomes in the chromatin condensate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.52 Å/pix.
x 150 pix.
= 227.4 Å		1.52 Å/pix.
x 150 pix.
= 227.4 Å		1.52 Å/pix.
x 150 pix.
= 227.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.516 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-3.3363724 - 4.845819
Average (Standard dev.)0.006741506 (±0.23478784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 227.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49924_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49924_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_49924_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 : In vitro reconstituted nucleosome by using histone protein with 6...

EntireName: In vitro reconstituted nucleosome by using histone protein with 601 sequence
Components
  • Complex: In vitro reconstituted nucleosome by using histone protein with 601 sequence

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Supramolecule #1: In vitro reconstituted nucleosome by using histone protein with 6...

SupramoleculeName: In vitro reconstituted nucleosome by using histone protein with 601 sequence
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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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: 7.5
Details: 20 mM Tris-OAc, 150 mM KOAc, 1 mM Mg(OAc)2, 5% glycerol, 0.1 mM EGTA
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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.10) / Number subtomograms used: 126125
ExtractionNumber tomograms: 10 / Number images used: 126125
CTF correctionSoftware - Name: Warp (ver. 1.10) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER / Software - Name: Warp (ver. 1.10)
FSC plot (resolution estimation)

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