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- EMDB-54155: Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in AD... -

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Basic information

Entry
Database: EMDB / ID: EMD-54155
TitleStructure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 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
Keywordsremodeller / chromatin / transcription / GENE REGULATION
Biological speciesHomo spaiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.63 Å
AuthorsDomjan D / Weiss J / Cavadini S / Vecchia L / Kempf G / Kater L / Pathare GR / Thoma NH
Funding support Switzerland, European Union, 5 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research Council (ERC)European Union
European Molecular Biology Organization (EMBO)European Union
Other private
Other private
CitationJournal: Mol Cell / Year: 2026
Title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4-SOX2.
Authors: Joscha Weiss / Luca Vecchia / David Domjan / Simone Cavadini / Anton Sabantsev / Georg Kempf / Ganesh R Pathare / Klaus Brackmann / Alicia K Michael / Lukas Kater / Eric Hietter-Pfeiffer / ...Authors: Joscha Weiss / Luca Vecchia / David Domjan / Simone Cavadini / Anton Sabantsev / Georg Kempf / Ganesh R Pathare / Klaus Brackmann / Alicia K Michael / Lukas Kater / Eric Hietter-Pfeiffer / Mina Haddawi / Urja P Kuber / Sandra Mühlhäusser / Ralph S Grand / Michael B Stadler / Sebastian Deindl / Nicolas H Thomä /
Abstract: Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we ...Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4-SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4-SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4-SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes.
History
DepositionJun 24, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54155.png

Downloads & links

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Map

FileDownload / File: emd_54155.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 576 pix.
= 486.72 Å		0.85 Å/pix.
x 576 pix.
= 486.72 Å		0.85 Å/pix.
x 576 pix.
= 486.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0758
Minimum - Maximum-0.14303654 - 0.66768926
Average (Standard dev.)-0.0006718207 (±0.017949855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 486.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54155_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_54155_half_map_2.map
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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-#4, #16-#17

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Supramolecule #3: BAF complex

SupramoleculeName: BAF complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#13
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: #14-#15

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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: 5.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 33367
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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