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- EMDB-62350: G1 mononucleosome, no cryoprotectant -

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Basic information

Entry
Database: EMDB / ID: EMD-62350
TitleG1 mononucleosome, no cryoprotectant
Map dataG1 mononucleosome 1; no cryoprotectant
Sample
  • Complex: Nucleosome from RPE-1
KeywordsCell / RPE-1 / nucleus / nucleosome / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 30.6 Å
AuthorsChen JK / Cai S / Liu T / Ruan W / Ng CT / Shi J / Surana U / Gan L
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2019-T2-1-140 Singapore
Citation
Journal: EMBO J / Year: 2025
Title: Nanoscale analysis of human G1 and metaphase chromatin in situ.
Authors: Jon Ken Chen / Tingsheng Liu / Shujun Cai / Weimei Ruan / Cai Tong Ng / Jian Shi / Uttam Surana / Lu Gan /
Abstract: The structure of chromatin at the nucleosome level inside cells is still incompletely understood. Here we present in situ electron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 ...The structure of chromatin at the nucleosome level inside cells is still incompletely understood. Here we present in situ electron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 cells. G1 nucleosomes are concentrated in globular chromatin domains, and metaphase nucleosomes are concentrated in the chromatids. Classification analysis reveals that canonical mononucleosomes, and in some conditions ordered stacked dinucleosomes and mononucleosomes with a disordered gyre-proximal density, are abundant in both cell-cycle states. We do not detect class averages that have more than two stacked nucleosomes or side-by-side dinucleosomes, suggesting that groups of more than two nucleosomes are heterogeneous. Large multi-megadalton structures are abundant in G1 nucleoplasm, but not found in G1 chromatin domains and metaphase chromatin. The macromolecular phenotypes studied here represent a starting point for the comparative analysis of compaction in normal vs. unhealthy human cells, in other cell-cycle states, other organisms, and in vitro chromatin assemblies.
#1: Journal: Biorxiv / Year: 2023
Title: Nanoscale analysis of human G1 and metaphase chromatin in situ
Authors: Chen JK / Liu T / Cai S / Ruan W / Ng CT / Shi J / Surana U / Gan L
History
DepositionNov 11, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62350.png

Downloads & links

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Map

FileDownload / File: emd_62350.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationG1 mononucleosome 1; no cryoprotectant
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.8 Å/pix.
x 64 pix.
= 435.2 Å		6.8 Å/pix.
x 64 pix.
= 435.2 Å		6.8 Å/pix.
x 64 pix.
= 435.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 6.8 Å
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Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.53281033 - 1.2396387
Average (Standard dev.)0.00024254629 (±0.07326215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: G1 mononucleosome 2; no cryoprotectant

Fileemd_62350_additional_1.map
AnnotationG1 mononucleosome 2; no cryoprotectant
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Additional map: G1 mononucleosome 5; no cryoprotectant

Fileemd_62350_additional_10.map
AnnotationG1 mononucleosome 5; no cryoprotectant
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Additional map: G1 mononucleosome 5; no cryoprotectant. Half map 1.

Fileemd_62350_additional_11.map
AnnotationG1 mononucleosome 5; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 5; no cryoprotectant. Half map 2.

Fileemd_62350_additional_12.map
AnnotationG1 mononucleosome 5; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 6; no cryoprotectant

Fileemd_62350_additional_13.map
AnnotationG1 mononucleosome 6; no cryoprotectant
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Additional map: G1 mononucleosome 6; no cryoprotectant. Half map 1.

Fileemd_62350_additional_14.map
AnnotationG1 mononucleosome 6; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 6; no cryoprotectant. Half map 2.

Fileemd_62350_additional_15.map
AnnotationG1 mononucleosome 6; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 7; no cryoprotectant

Fileemd_62350_additional_16.map
AnnotationG1 mononucleosome 7; no cryoprotectant
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Additional map: G1 mononucleosome 7; no cryoprotectant. Half map 1.

Fileemd_62350_additional_17.map
AnnotationG1 mononucleosome 7; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 7; no cryoprotectant. Half map 2.

Fileemd_62350_additional_18.map
AnnotationG1 mononucleosome 7; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 8; no cryoprotectant

Fileemd_62350_additional_19.map
AnnotationG1 mononucleosome 8; no cryoprotectant
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Additional map: G1 mononucleosome 2; no cryoprotectant. Half map 1.

Fileemd_62350_additional_2.map
AnnotationG1 mononucleosome 2; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 8; no cryoprotectant. Half map 1.

Fileemd_62350_additional_20.map
AnnotationG1 mononucleosome 8; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 8; no cryoprotectant. Half map 2.

Fileemd_62350_additional_21.map
AnnotationG1 mononucleosome 8; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 9; no cryoprotectant

Fileemd_62350_additional_22.map
AnnotationG1 mononucleosome 9; no cryoprotectant
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Additional map: G1 mononucleosome 9; no cryoprotectant. Half map 1.

Fileemd_62350_additional_23.map
AnnotationG1 mononucleosome 9; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 9; no cryoprotectant. Half map 2.

Fileemd_62350_additional_24.map
AnnotationG1 mononucleosome 9; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 2; no cryoprotectant. Half map 2.

Fileemd_62350_additional_3.map
AnnotationG1 mononucleosome 2; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 3; no cryoprotectant

Fileemd_62350_additional_4.map
AnnotationG1 mononucleosome 3; no cryoprotectant
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Additional map: G1 mononucleosome 3; no cryoprotectant. Half map 1.

Fileemd_62350_additional_5.map
AnnotationG1 mononucleosome 3; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 3; no cryoprotectant. Half map 2.

Fileemd_62350_additional_6.map
AnnotationG1 mononucleosome 3; no cryoprotectant. Half map 2.
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Additional map: G1 mononucleosome 4; no cryoprotectant

Fileemd_62350_additional_7.map
AnnotationG1 mononucleosome 4; no cryoprotectant
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Additional map: G1 mononucleosome 4; no cryoprotectant. Half map 1.

Fileemd_62350_additional_8.map
AnnotationG1 mononucleosome 4; no cryoprotectant. Half map 1.
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Additional map: G1 mononucleosome 4; no cryoprotectant. Half map 2.

Fileemd_62350_additional_9.map
AnnotationG1 mononucleosome 4; no cryoprotectant. Half map 2.
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Half map: G1 mononucleosome 1; no cryoprotectant. Half map 1.

Fileemd_62350_half_map_1.map
AnnotationG1 mononucleosome 1; no cryoprotectant. Half map 1.
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Half map: G1 mononucleosome 1; no cryoprotectant. Half map 2.

Fileemd_62350_half_map_2.map
AnnotationG1 mononucleosome 1; no cryoprotectant. Half map 2.
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Sample components

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Entire : Nucleosome from RPE-1

EntireName: Nucleosome from RPE-1
Components
  • Complex: Nucleosome from RPE-1

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Supramolecule #1: Nucleosome from RPE-1

SupramoleculeName: Nucleosome from RPE-1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Organelle: Nucleus

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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
GridModel: C-flat / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 18000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 17312
ExtractionNumber tomograms: 5 / Number images used: 175229 / Reference model: Featureless cylinder / Method: Template matching
CTF correctionSoftware - Name: IMOD (ver. 4.11)
Details: The data is from the Volta phase plate, imaged close to focus.
Type: NONE
Final 3D classificationNumber classes: 9 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)

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