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- EMDB-54157: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL... -

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Basic information

Entry
Database: EMDB / ID: EMD-54157
TitleStructure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 (Consensus map)
Map data
Sample
  • Complex: BAF in complex with a OCT4/SOX2-bound nucleosome
    • Complex: Nucleosome core particle
    • Complex: BAF complex
    • Complex: OCT4/SOX2 heterodimer
KeywordsChromatin / remodeler / GENE REGULATION
Biological speciesHomo spaiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.52 Å
AuthorsVecchia L / Weiss J / Cavadini S / Kempf G / Kater L / Pathare GR / Thoma NH
Funding supportEuropean Union, Switzerland, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
European Molecular Biology Organization (EMBO)European Union
Other private
Other private
CitationJournal: To be published
Title: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2
Authors: Vecchia L
History
DepositionJun 24, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54157.png

Downloads & links

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Map

FileDownload / File: emd_54157.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 405.6 Å		0.85 Å/pix.
x 480 pix.
= 405.6 Å		0.85 Å/pix.
x 480 pix.
= 405.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0981
Minimum - Maximum-0.19718817 - 0.7354372
Average (Standard dev.)-0.0006914023 (±0.024644397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 405.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54157_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54157_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 : BAF in complex with a OCT4/SOX2-bound nucleosome

EntireName: BAF in complex with a OCT4/SOX2-bound nucleosome
Components
  • Complex: BAF in complex with a OCT4/SOX2-bound nucleosome
    • Complex: Nucleosome core particle
    • Complex: BAF complex
    • Complex: OCT4/SOX2 heterodimer

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Supramolecule #1: BAF in complex with a OCT4/SOX2-bound nucleosome

SupramoleculeName: BAF in complex with a OCT4/SOX2-bound nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17

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Supramolecule #2: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6

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Supramolecule #3: BAF complex

SupramoleculeName: BAF complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#16
Source (natural)Organism: Homo spaiens (human)

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Supramolecule #4: OCT4/SOX2 heterodimer

SupramoleculeName: OCT4/SOX2 heterodimer / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #17-#18

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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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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