[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

TitleAutoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.
Journal, issue, pagesScience, Vol. 389, Issue 6757, Page eadr3831, Year 2025
Publish dateJul 17, 2025
AuthorsUpneet Kaur / Hao Wu / Yifan Cheng / Geeta J Narlikar /
PubMed AbstractIncreasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like ...Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.
External linksScience / PubMed:40674492 / PubMed Central
MethodsEM (single particle)
Resolution2.55 - 4.18 Å
Structure data

45361

9c9g

EMDB-45361, PDB-9c9g:
S.c INO80 in complex with S.c 0/80 nucleosome
Method: EM (single particle) / Resolution: 2.91 Å

45369

9c9s

EMDB-45369, PDB-9c9s:
S.c INO80 in complex with S.c 0/40 nucleosome, Class 1
Method: EM (single particle) / Resolution: 3.09 Å

45370

9c9t

EMDB-45370, PDB-9c9t:
S.c INO80 in complex with S.c 0/40 nucleosome, Class 2
Method: EM (single particle) / Resolution: 3.16 Å

45375

9c9x

EMDB-45375, PDB-9c9x:
S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome
Method: EM (single particle) / Resolution: 2.83 Å

45377

9c9z

EMDB-45377, PDB-9c9z:
S.c INO80 in complex with Xenopus 0/80 nucleosome, INO80 Core
Method: EM (single particle) / Resolution: 2.55 Å

45397

9can

EMDB-45397, PDB-9can:
S.c INO80 in complex with Xenopus 0/40 nucleosome
Method: EM (single particle) / Resolution: 3.3 Å

45403

9cat

EMDB-45403, PDB-9cat:
DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module
Method: EM (single particle) / Resolution: 2.9 Å

45404

9cau

EMDB-45404, PDB-9cau:
DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome
Method: EM (single particle) / Resolution: 4.18 Å

45418

9cb7

EMDB-45418, PDB-9cb7:
DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome
Method: EM (single particle) / Resolution: 4.04 Å

45441

9ccd

EMDB-45441, PDB-9ccd:
DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module
Method: EM (single particle) / Resolution: 3.01 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN/DNA / Chromatin Remodeler / nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

+
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