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- PDB-9uxc: The ADP-bound structure of BCL7B-containing ARP module of the hum... -

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Basic information

Entry
Database: PDB / ID: 9uxc
TitleThe ADP-bound structure of BCL7B-containing ARP module of the human SWI/SNF complex
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Actin-like protein 6A
  • B-cell CLL/lymphoma 7 protein family member B
  • Transcription activator BRG1
KeywordsGENE REGULATION / chromatin remodeling / SWI/SNF / nuclear actin
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 / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / 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 / ADENOSINE-5'-TRIPHOSPHATE / Actin-like protein 6A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / B-cell CLL/lymphoma 7 protein family member B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 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

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Assembly

Deposited unit
A: Transcription activator BRG1
B: Actin, cytoplasmic 1, N-terminally processed
C: Actin-like protein 6A
D: B-cell CLL/lymphoma 7 protein family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4838
Polymers123,5004
Non-polymers9834
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 , 4 types, 4 molecules ABCD

#1: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 11774.223 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
#2: 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
#3: 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: 47580.891 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
#4: 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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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, 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

ComponentName: The BCL7B-containing ARP module of the human SWI/SNF complex
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental 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

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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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239509 / Symmetry type: POINT

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