[English] 日本語
Yorodumi
- EMDB-24915: Molecular Organization of the Early Stages of Nucleosome Phase Se... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24915
TitleMolecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography
Map dataIntermediate stage of irregular tetranucleosome condensate (2)
Sample
  • Complex: Intermediate 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

-
Structure visualization

Supplemental images

emd_24915.png

Downloads & links

-
Map

FileDownload / File: emd_24915.map.gz / Format: CCP4 / Size: 200 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIntermediate stage of irregular tetranucleosome condensate (2)
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-1.2760932 - 4.0031466
Average (Standard dev.)0.008501816 (±0.088446155)
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 °

-
Supplemental data

-
Sample components

-
Entire : Intermediate stage of irregular tetranucleosome condensates

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

-
Supramolecule #1: Intermediate stage of irregular tetranucleosome condensates

SupramoleculeName: Intermediate 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 2 min incubation.
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %
SectioningOther: NO SECTIONING

-
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

-
Image processing

Final reconstructionNumber images used: 40

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more