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- PDB-9ux9: local ATPase-NCP structure of the ncBAF-nucleosome complex in the... -

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Basic information

Entry
Database: PDB / ID: 9ux9
Titlelocal ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state
Components
  • (DNA (167-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
KeywordsGENE REGULATION/DNA / Chromatin remodeling / SWI/SNF / Epigenetics / GENE REGULATION-DNA complex
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / GBAF complex / regulation of G0 to G1 transition ...positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / GBAF complex / regulation of G0 to G1 transition / nucleosome array spacer activity / Tat protein binding / RNA polymerase I preinitiation complex assembly / RSC-type complex / host-mediated activation of viral transcription / ATP-dependent chromatin remodeler activity / regulation of nucleotide-excision repair / nucleosome disassembly / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of myoblast differentiation / positive regulation of signal transduction by p53 class mediator / ATP-dependent activity, acting on DNA / positive regulation of Wnt signaling pathway / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / helicase activity / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Formation of the beta-catenin:TCF transactivating complex / negative regulation of cell growth / positive regulation of miRNA transcription / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / fibrillar center / RMTs methylate histone arginines / p53 binding / structural constituent of chromatin / transcription corepressor activity / nervous system development / nucleosome / heterochromatin formation / nucleosome assembly / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / hydrolase activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / : / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain, conserved site / Bromodomain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
artificial sequences (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSun, F. / Zou, B. / Li, H. / Xu, C. / Luo, Q. / Wang, C. / Xu, P. / Pei, D. / Chen, J. / Qin, D. ...Sun, F. / Zou, B. / Li, H. / Xu, C. / Luo, Q. / Wang, C. / Xu, P. / Pei, D. / Chen, J. / Qin, D. / Zhang, Y. / He, J.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32361163669 China
Other government2023M743512 China
National Natural Science Foundation of China (NSFC)32170189 China
National Natural Science Foundation of China (NSFC)32241021 China
Other governmentGZC20232691 China
Other government2023A1515110923 China
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural basis for BCL7B-mediated ncBAF-nucleosome engagement.
Authors: Fahui Sun / Binqian Zou / He Li / Chongshen Xu / Qiaohong Luo / Chi Wang / Pengqi Xu / Duanqing Pei / Jiekai Chen / Dajiang Qin / Ying Zhang / Jun He /
Abstract: The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble ...The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble nucleosomes to regulate gene expression and chromatin structure dependent on ATP hydrolysis energy. While the chromatin engagement mechanisms of cBAF and PBAF have been structurally resolved, the molecular architecture governing ncBAF interaction with chromatin remains elusive. In this study, by integrating cryo-electron microscopy, biochemical assays, and cross-linking mass spectrometry, we resolved the conformational transition of ncBAF-nucleosome complexes from nucleotide-free to nucleotide-bound states. Our analyses establish BCL7 proteins as dynamic molecular tethers connecting the ARP module to the nucleosomal acidic patch and demonstrate that BCL7B promotes ncBAF-mediated nucleosome remodeling, with BRG1-catalyzed ATP hydrolysis triggering conformational changes that modulate BCL7-mediated histone association. Structurally and biochemically, we further demonstrate that β-actin within the BCL7-containing ARP module retains ATP hydrolysis activity, rendering its exposed pointed end structurally compatible with incorporation into the barbed end of nuclear actin filaments, which provides a potential molecular basis for coordinating nuclear actin networks with chromatin remodeling. Collectively, our findings unravel a dynamic role of BCL7 in regulating ncBAF-mediated chromatin remodeling and establish a distinct chromatin engagement mode of ncBAF from that of cBAF/PBAF.
History
DepositionMay 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (167-MER)
J: DNA (167-MER)
K: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,07614
Polymers396,55811
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 14163.421 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496
#7: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / ...SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / Transcription activator BRG1


Mass: 184934.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Mammalia (mammals)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (167-MER)


Mass: 51271.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial sequences (others) / Production host: synthetic construct (others)
#6: DNA chain DNA (167-MER)


Mass: 51840.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial sequences (others) / Production host: synthetic construct (others)

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Non-polymers , 3 types, 3 molecules

#8: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1ncBAF-nucleosome complexCOMPLEX#1-#70MULTIPLE SOURCES
2Xenopus nucleosomeCOMPLEX#1-#41RECOMBINANT
3The ARP module of ncBAF complexCOMPLEX#5-#7, #11MULTIPLE SOURCES
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.873 MDaNO
21NO
31NO
43
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Xenopus (frog)262014
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mammalia (mammals)40674
32Escherichia coli (E. coli)562
43Mammalia (mammals)40674
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72416 / Symmetry type: POINT
RefinementHighest resolution: 3.05 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215725
ELECTRON MICROSCOPYf_angle_d0.46522238
ELECTRON MICROSCOPYf_dihedral_angle_d26.8683771
ELECTRON MICROSCOPYf_chiral_restr0.0322524
ELECTRON MICROSCOPYf_plane_restr0.0031992

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