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- PDB-9uxa: local ARP-NCP structure of the ncBAF-nucleosome complex in the ap... -

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Entry
Database: PDB / ID: 9uxa
Titlelocal ARP-NCP structure of the ncBAF-nucleosome complex in the apo state
Components
  • (DNA (167-MER)) x 2
  • Actin, cytoplasmic 1, N-terminally processed
  • Actin-like protein 6A
  • B-cell CLL/lymphoma 7 protein family member B
  • 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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / Formation of the embryonic stem cell BAF (esBAF) complex / cellular response to cytochalasin B / neural retina development / npBAF complex ...positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / Formation of the embryonic stem cell BAF (esBAF) complex / cellular response to cytochalasin B / neural retina development / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / negative regulation of androgen receptor signaling pathway / regulation of transepithelial transport / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / morphogenesis of a polarized epithelium / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Gap junction degradation / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / protein localization to adherens junction / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / dense body / Folding of actin by CCT/TriC / Tat protein binding / nucleosome array spacer activity / RNA polymerase I preinitiation complex assembly / postsynaptic actin cytoskeleton / Ino80 complex / RSC-type complex / blastocyst formation / Regulation of CDH1 Function / host-mediated activation of viral transcription / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / nucleosome disassembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / ATP-dependent chromatin remodeler activity / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / nuclear androgen receptor binding / apical junction complex / positive regulation of double-strand break repair / spinal cord development / regulation of chromosome organization / maintenance of blood-brain barrier / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / establishment or maintenance of cell polarity / Recycling pathway of L1 / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of DNA replication / nitric-oxide synthase binding / regulation of embryonic development / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / positive regulation of signal transduction by p53 class mediator / kinesin binding / ATP-dependent activity, acting on DNA / regulation of DNA repair / positive regulation of Wnt signaling pathway / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / Chromatin modifying enzymes / DNA polymerase binding / EPHB-mediated forward signaling / cytoskeleton organization / axonogenesis / substantia nigra development / Interleukin-7 signaling / telomere maintenance / calyx of Held / transcription initiation-coupled chromatin remodeling / nitric-oxide synthase regulator activity / positive regulation of DNA repair
Similarity search - Function
BCL7 / BCL7, N-terminal conserver region / 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. ...BCL7 / BCL7, N-terminal conserver region / 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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / : / 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. / ATPase, nucleotide binding domain / 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
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / Actin-like protein 6A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / Histone H4 / Histone H2A / B-cell CLL/lymphoma 7 protein family member B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
artificial sequences (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 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 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Actin, cytoplasmic 1, N-terminally processed
J: Actin-like protein 6A
K: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
L: B-cell CLL/lymphoma 7 protein family member B
X: DNA (167-MER)
Y: DNA (167-MER)


Theoretical massNumber of molelcules
Total (without water)507,36714
Polymers507,36714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 8 types, 12 molecules AEBFCGDHIJKL

#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
#5: Protein Actin, cytoplasmic 1, N-terminally processed


Mass: 41853.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Mammalia (mammals) / References: UniProt: P60709
#6: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 46663.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A, BAF53, BAF53A, INO80K / Production host: Mammalia (mammals) / References: UniProt: O96019
#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
#8: Protein B-cell CLL/lymphoma 7 protein family member B


Mass: 22291.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL7B / Production host: Mammalia (mammals) / References: UniProt: Q9BQE9

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DNA chain , 2 types, 2 molecules XY

#9: 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)
#10: 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)

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Details

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

ComponentName: ncBAF-nucleosome complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.873 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalia (mammals)
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
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 253908 / Symmetry type: POINT

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