[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleNanoscale analysis of human G1 and metaphase chromatin in situ.
Journal, issue, pagesEMBO J, Vol. 44, Issue 9, Page 2658-2694, Year 2025
Publish dateMar 17, 2025
AuthorsJon Ken Chen / Tingsheng Liu / Shujun Cai / Weimei Ruan / Cai Tong Ng / Jian Shi / Uttam Surana / Lu Gan /
PubMed AbstractThe structure of chromatin at the nucleosome level inside cells is still incompletely understood. Here we present in situ electron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 ...The structure of chromatin at the nucleosome level inside cells is still incompletely understood. Here we present in situ electron cryotomography analyses of chromatin in both G1 and metaphase RPE-1 cells. G1 nucleosomes are concentrated in globular chromatin domains, and metaphase nucleosomes are concentrated in the chromatids. Classification analysis reveals that canonical mononucleosomes, and in some conditions ordered stacked dinucleosomes and mononucleosomes with a disordered gyre-proximal density, are abundant in both cell-cycle states. We do not detect class averages that have more than two stacked nucleosomes or side-by-side dinucleosomes, suggesting that groups of more than two nucleosomes are heterogeneous. Large multi-megadalton structures are abundant in G1 nucleoplasm, but not found in G1 chromatin domains and metaphase chromatin. The macromolecular phenotypes studied here represent a starting point for the comparative analysis of compaction in normal vs. unhealthy human cells, in other cell-cycle states, other organisms, and in vitro chromatin assemblies.
External linksEMBO J / PubMed:40097852 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution24.0 - 36.8 Å
Structure data

EMDB-36992: G1 dinucleosome
Method: EM (subtomogram averaging) / Resolution: 26.8 Å

EMDB-36993: G1 mononucleosome
Method: EM (subtomogram averaging) / Resolution: 33.7 Å

EMDB-36994: G1 nucleosome gyre proximal
Method: EM (subtomogram averaging) / Resolution: 30.6 Å

EMDB-36998: Metaphase dinucleosome
Method: EM (subtomogram averaging) / Resolution: 26.3 Å

EMDB-36999: Metaphase mononucleosome
Method: EM (subtomogram averaging) / Resolution: 34.3 Å

EMDB-37000: Metaphase nucleosome proximal
Method: EM (subtomogram averaging) / Resolution: 32.5 Å

EMDB-37001: G1 preribosome
Method: EM (subtomogram averaging) / Resolution: 33.3 Å

EMDB-37002: G1 ribosome cytoplasmic
Method: EM (subtomogram averaging) / Resolution: 31.7 Å

EMDB-37003: Metaphase ribosome
Method: EM (subtomogram averaging) / Resolution: 36.8 Å

EMDB-37004: Oligonucleosome 0 DMSO
Method: EM (subtomogram averaging) / Resolution: 24.2 Å

EMDB-37005: Oligonucleosome 9% DMSO
Method: EM (subtomogram averaging) / Resolution: 24.0 Å

EMDB-62350: G1 mononucleosome, no cryoprotectant
Method: EM (subtomogram averaging) / Resolution: 30.6 Å

EMDB-62351: G1 mononucleosome, with glycerol cryoprotectant
Method: EM (subtomogram averaging) / Resolution: 29.3 Å

EMDB-62352: G1 nucleosome with gyre proximal density, with glycerol cryoprotectant
Method: EM (subtomogram averaging) / Resolution: 31.4 Å

Source
  • Homo sapiens (human)

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more