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- EMDB-24918: Molecular Organization of the Early Stages of Nucleosome Phase Se... -

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Basic information

Entry
Database: EMDB / ID: EMD-24918
TitleMolecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography
Map dataLate stage of irregular tetranucleosome condensate (1)
Sample
  • Complex: Late stage of irregular tetranucleosome condensates
Biological speciesXenopus laevis (African clawed frog)
Methodelectron tomography / cryo EM
AuthorsZhang M / Diaz-Celis C / Onoa B / Canari-Chumpitaz C / Requejo KI / Liu J / Vien M / Nogales E / Ren G / Bustamante C
Funding support United States, 7 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL115153 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104427 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK042667 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127018 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032543 United States
CitationJournal: Mol Cell / Year: 2022
Title: Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography.
Authors: Meng Zhang / César Díaz-Celis / Bibiana Onoa / Cristhian Cañari-Chumpitaz / Katherinne I Requejo / Jianfang Liu / Michael Vien / Eva Nogales / Gang Ren / Carlos Bustamante /
Abstract: It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, ...It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.
History
DepositionSep 19, 2021-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24918.png

Downloads & links

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Map

FileDownload / File: emd_24918.map.gz / Format: CCP4 / Size: 200 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLate stage of irregular tetranucleosome condensate (1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.68 Å/pix.
x 200 pix.
= 2336. Å		11.68 Å/pix.
x 512 pix.
= 5980.16 Å		11.68 Å/pix.
x 512 pix.
= 5980.16 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1.1183197 - 3.6035326
Average (Standard dev.)0.0054521295 (±0.069244534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512200
Spacing512512200
CellA: 5980.16 Å / B: 5980.16 Å / C: 2336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Late stage of irregular tetranucleosome condensates

EntireName: Late stage of irregular tetranucleosome condensates
Components
  • Complex: Late stage of irregular tetranucleosome condensates

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Supramolecule #1: Late stage of irregular tetranucleosome condensates

SupramoleculeName: Late stage of irregular tetranucleosome condensates / type: complex / ID: 1 / Parent: 0
Details: Irregular condensates formed at physiological salt condition (20 mM HEPES-KOH pH 7.5; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT) after 10 min incubation.
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 40 / Average exposure time: 2.5 sec. / Average electron dose: 7.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 40

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