[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

TitleArchitecture and function of holocentric CENP-A-independent inner kinetochores.
Journal, issue, pagesSci Adv, Vol. 12, Page eaeb5817, Year 2026
Publish dateMay 10, 2025
AuthorsChristine Yu / Sundar Ram Sankaranarayanan / Gaetan Cornilleau / Anna C Howes / Caleigh M Azumaya / Eric S Day / Inna Zilberleyb / Bobby Brillantes / Tommy K Cheung / Leonie Dec / Damarys Loew / Phong Tran / Christopher M Rose / Ines Anna Drinnenberg / Claudio Ciferri / Stanislau Yatskevich /
PubMed AbstractKinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of ...Kinetochores are essential macromolecular complexes anchoring chromosomes to the mitotic spindle, ensuring faithful cell division. Despite their critical role, the structural organization of kinetochores across diverse species remains poorly understood. We present the inner kinetochore constitutive centromere-associated network (CCAN) structure of the silkmoth , an insect that lacks the canonical centromere-specifying histone variant CENP-A and exhibits chromosome-wide centromeric activity (holocentric). The CCAN incorporates four previously uncharacterized centromeric subunit proteins that are structurally related to the Dam1/DASH complex but function in scaffolding the inner kinetochore rather than in microtubule binding. Similar to the yeast and human systems, the CCAN also entraps DNA within its central closed chamber. However, unlike these systems, the CCAN can also assemble in vitro into a self-contained head-to-head dimer via atypical histone-fold protein dimerization. On the basis of our findings, we propose that the holocentric organization may emerge from the modular arrangement of discrete kinetochore units.
External linksSci Adv / PubMed:42319948 / PubMed Central
MethodsEM (single particle)
Resolution2.83 - 4.5 Å
Structure data

70558

9okb

EMDB-70558, PDB-9okb:
Structure of the dimeric Bombyx mori CCAN bound to DNA
Method: EM (single particle) / Resolution: 4.5 Å

70560

9okd

EMDB-70560, PDB-9okd:
Structure of the monomeric Bombyx mori CCAN bound to linear DNA
Method: EM (single particle) / Resolution: 2.83 Å

70561
EMDB Unreleased entry

9oke

EMDB-70561, PDB-9oke:
Structure of the Bombyx mori bmCENP-HIKM-LN-T-OP complex without the CS module
Method: EM (single particle) / Resolution: 3.24 Å

70567
EMDB Unreleased entry

9okk

EMDB-70567, PDB-9okk:
Bombyx mori bmCENP-LN-HIKM sub-complex structure
Method: EM (single particle) / Resolution: 3.23 Å

70568

9okl

EMDB-70568, PDB-9okl:
Structure of the Bombyx mori apo-bmCCAN
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • bombyx mori (domestic silkworm)
  • synthetic construct (others)
  • spodoptera frugiperda (fall armyworm)
KeywordsDNA BINDING PROTEIN/DNA / CCAN / complex / protein-DNA / segregation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / CELL CYCLE / DNA-protein / kinetochore

+
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