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- EMDB-52220: Chaetomium thermophilum INO80 M2 nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52220
TitleChaetomium thermophilum INO80 M2 nucleosome complex
Map data
Sample
  • Complex: Chaetomium thermophilum Ino80 bound to M2 nucleosome
Keywordschromatin remodeling / TRANSLOCASE
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsKunert F / Lammens K / Hopfner KP
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Mol Cell / Year: 2025
Title: DNA bendability inside the nucleosome regulates INO80's nucleosome positioning.
Authors: Shagun Shukla / Mzwanele Ngubo / Somnath Paul / Franziska Kunert / Jim Persinger / Junwoo Lee / Karl-Peter Hopfner / Blaine Bartholomew /
Abstract: While some ATP-dependent chromatin remodelers are negatively regulated by short tracts of DNA sequences (i.e., poly d(A) or GC-rich), the INO80 chromatin remodeler is regulated by DNA not readily ...While some ATP-dependent chromatin remodelers are negatively regulated by short tracts of DNA sequences (i.e., poly d(A) or GC-rich), the INO80 chromatin remodeler is regulated by DNA not readily identified by its sequence but rather by its physical properties. The underlying reason for these differences appears to be the unique mechanism by which INO80 mobilizes nucleosomes. We find that the INO80 chromatin remodeler mobilizes nucleosomes by displacing DNA from the histone octamer and creating DNA "bulges" that translocate around the octamer in a wave-like manner. Nucleosome movement is blocked by inflexible nucleosomal DNA that interferes with the initial formation of DNA bulges and is linked to INO80's accurate positioning of nucleosomes at the +1 position of yeast gene promoters. Some of the interactions of the Arp5 subunit are lost when bound to inflexible DNA and may act as sensors to regulate INO80 remodeling in a DNA-shape-dependent manner.
History
DepositionNov 29, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52220.png

Downloads & links

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Map

FileDownload / File: emd_52220.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.38152117 - 0.90608394
Average (Standard dev.)0.0005060771 (±0.029984618)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 372.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_52220_additional_1.map
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Half map: #1

Fileemd_52220_half_map_1.map
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Half map: #2

Fileemd_52220_half_map_2.map
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Sample components

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Entire : Chaetomium thermophilum Ino80 bound to M2 nucleosome

EntireName: Chaetomium thermophilum Ino80 bound to M2 nucleosome
Components
  • Complex: Chaetomium thermophilum Ino80 bound to M2 nucleosome

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Supramolecule #1: Chaetomium thermophilum Ino80 bound to M2 nucleosome

SupramoleculeName: Chaetomium thermophilum Ino80 bound to M2 nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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