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- EMDB-56821: C.t. INO80 chromatin remodeler bound to nucleosome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56821
TitleC.t. INO80 chromatin remodeler bound to nucleosome
Map data
Sample
  • Complex: Ct INO80 bound to nucleosome
Keywordschromatin remodeler / epigenetic / DNA BINDING PROTEIN
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.93 Å
AuthorsLecomte L / Grozavu DM / Kolesnikova O / Eustermann S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)101094131European Union
CitationJournal: To Be Published
Title: EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control
Authors: Lecomte L / Papp G
History
DepositionFeb 19, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56821.png

Downloads & links

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Map

FileDownload / File: emd_56821.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.06915623 - 0.49490875
Average (Standard dev.)0.0026036892 (±0.024999915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56821_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56821_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ct INO80 bound to nucleosome

EntireName: Ct INO80 bound to nucleosome
Components
  • Complex: Ct INO80 bound to nucleosome

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Supramolecule #1: Ct INO80 bound to nucleosome

SupramoleculeName: Ct INO80 bound to 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

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
30.0 mMHepesKOHHepesKOH
50.0 mMNaClsodium chloride
0.25 mMDTTDithiothreitol
1.0 mMATPAdenosine triphosphate
5.0 mMMgCl2Magnesium chloride
0.05 %OctylglucosideOctyglucoside
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CELLULOSE ACETATE / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 285.15 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2060 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 559056
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71058
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC

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