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- EMDB-16978: Architecture of native chromatin fibres revealed by cryo-ET in situ -

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Basic information

Entry
Database: EMDB / ID: EMD-16978
TitleArchitecture of native chromatin fibres revealed by cryo-ET in situ
Map dataMain map
Sample
  • Cell: T-Lymphoblast CEM
Keywordsnucleosome / nucleus / histone / DNA / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsHou Z / Zhu Y / Zhang P
Funding support United Kingdom, European Union, United States, 3 items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
European Research Council (ERC)101021133European Union
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150481 United States
Citation
Journal: Nat Commun / Year: 2023
Title: Structure of native chromatin fibres revealed by Cryo-ET in situ.
Authors: Zhen Hou / Frank Nightingale / Yanan Zhu / Craig MacGregor-Chatwin / Peijun Zhang /
Abstract: The structure of chromatin plays pivotal roles in regulating gene transcription, DNA replication and repair, and chromosome segregation. This structure, however, remains elusive. Here, using cryo-FIB ...The structure of chromatin plays pivotal roles in regulating gene transcription, DNA replication and repair, and chromosome segregation. This structure, however, remains elusive. Here, using cryo-FIB and cryo-ET, we delineate the 3D architecture of native chromatin fibres in intact interphase human T-lymphoblasts and determine the in situ structures of nucleosomes in different conformations. These chromatin fibres are not structured as uniform 30 nm one-start or two-start filaments but are composed of relaxed, variable zigzag organizations of nucleosomes connected by straight linker DNA. Nucleosomes with little H1 and linker DNA density are distributed randomly without any spatial preference. This work will inspire future high-resolution investigations on native chromatin structures in situ at both a single-nucleosome level and a population level under many different cellular conditions in health and disease.
#1: Journal: Biorxiv / Year: 2023
Title: Structure of Native Chromatin Fibres Revealed by Cryo-ET in situ
Authors: Hou Z / Nightingale F / Zhu Y / MacGregor-Chatwin C / Zhang P
History
DepositionMar 31, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16978.png

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Map

FileDownload / File: emd_16978.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 96 pix.
= 418.56 Å		4.36 Å/pix.
x 96 pix.
= 418.56 Å		4.36 Å/pix.
x 96 pix.
= 418.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.09056714 - 0.6690163
Average (Standard dev.)0.001749569 (±0.022665832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 418.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1

Fileemd_16978_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_16978_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T-Lymphoblast CEM

EntireName: T-Lymphoblast CEM
Components
  • Cell: T-Lymphoblast CEM

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Supramolecule #1: T-Lymphoblast CEM

SupramoleculeName: T-Lymphoblast CEM / type: cell / 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 statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 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: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6790
ExtractionNumber tomograms: 5 / Number images used: 10000
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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