[English] 日本語
Yorodumi
- EMDB-55730: in situ nucleosome, open state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55730
Titlein situ nucleosome, open state
Map datarelion refine map
Sample
  • Complex: nucleosome
Keywordssubtomo averaging / nucleosome / cryoET / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 7.4 Å
AuthorsXu P / Wang Y / Sun YJ
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Cell Rep / Year: 2026
Title: NuMA promotes constitutive heterochromatin compaction by stabilizing linker histone H1 on chromatin.
Authors: Yao Wang / Wenxue Zhao / Jiahao Niu / Cuifang Liu / Xiaotian Wang / Weihong Yuan / Shanshan Ai / Wolfgang Baumeister / Guohong Li / Aibin He / Peng Xu / Cheng Li / Yujie Sun /
Abstract: Heterochromatin exerts pivotal functions of silencing specific genes and maintenance of genome stability. However, its formation and maintenance mechanisms remain unclear. Here, we discover that the ...Heterochromatin exerts pivotal functions of silencing specific genes and maintenance of genome stability. However, its formation and maintenance mechanisms remain unclear. Here, we discover that the mitotic regulator NuMA, as a nucleoskeleton protein, is required for constitutive heterochromatin organization at the nucleosome level in interphase. NuMA depletion results in shortened nucleosome repeat length, dispersed nucleosome clutches, increased chromatin accessibility, and disrupted transcription repression of long terminal repeats in heterochromatin regions. Such functions of NuMA rely on its interaction with linker histone H1, which stabilizes H1's binding to chromatin and facilitates nucleosome stacking, as directly visualized by in situ cryo-ET. Notably, NuMA oligomerizes into quasi-meshwork in the nucleoplasm, providing its organization basis as a nucleoskeleton protein. Collectively, our findings illuminate the concerted effect of nucleoskeleton and linker histone on chromatin compaction at the nucleosome level, unveiling a previously unexplored mechanism by which nucleoskeleton regulates heterochromatin formation and maintenance.
History
DepositionNov 17, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55730.png

Downloads & links

-
Map

FileDownload / File: emd_55730.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrelion refine map
Voxel sizeX=Y=Z: 1.89 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.31852195 - 1.6798304
Average (Standard dev.)0.0005466661 (±0.09798336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55730_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: relion postprocess masked map

Fileemd_55730_additional_1.map
Annotationrelion postprocess masked map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_55730_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_55730_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : nucleosome

EntireName: nucleosome
Components
  • Complex: nucleosome

-
Supramolecule #1: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: U2OS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1/4 / Material: GOLD
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.42 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 62000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number subtomograms used: 23652
ExtractionNumber tomograms: 98 / Number images used: 140000 / Software - Name: Warp (ver. 1.0.9)
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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