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- EMDB-28364: Cryo-ET 3D reconstruction of an individual di-nucleosome particle... -

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Basic information

Entry
Database: EMDB / ID: EMD-28364
TitleCryo-ET 3D reconstruction of an individual di-nucleosome particle in 5 mM NaCl and 20 mM HEPES buffer --- Particle #078
Map dataCryo-ET 3D reconstruction of an individual di-nucleosome particle in 5 mM NaCl and 20 mM HEPES buffer --- Particle #078
Sample
  • Complex: Dinucleosome array
KeywordsNucleosome Array / DNA BINDING PROTEIN
Biological speciesXenopus laevis (African clawed frog)
Methodelectron tomography / cryo EM
AuthorsZhang M / Celis CD / Liu JF / Bustamante C / Ren G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) United States
CitationJournal: Nat Commun / Year: 2024
Title: Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography.
Authors: Meng Zhang / César Díaz-Celis / Jianfang Liu / Jinhui Tao / Paul D Ashby / Carlos Bustamante / Gang Ren /
Abstract: The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo- ...The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.
History
DepositionOct 3, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28364.png

Downloads & links

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Map

FileDownload / File: emd_28364.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET 3D reconstruction of an individual di-nucleosome particle in 5 mM NaCl and 20 mM HEPES buffer --- Particle #078
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.4 Å/pix.
x 200 pix.
= 1480. Å		7.4 Å/pix.
x 200 pix.
= 1480. Å		7.4 Å/pix.
x 200 pix.
= 1480. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.4 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.27082214 - 1.0872593
Average (Standard dev.)0.00056840753 (±0.014510515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 1480.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dinucleosome array

EntireName: Dinucleosome array
Components
  • Complex: Dinucleosome array

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Supramolecule #1: Dinucleosome array

SupramoleculeName: Dinucleosome array / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 5 mM NaCl 20 mM HEPES 1 mM DTT 1 mM EDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 5.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: SPIDER / Number images used: 35

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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