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- PDB-9wc1: The structure of ARP module in ncBAF complex -

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Basic information

Entry
Database: PDB / ID: 9wc1
TitleThe structure of ARP module in ncBAF complex
Components
  • Actin, cytoplasmic 1
  • Actin-like protein 6A
  • B-cell CLL/lymphoma 7 protein family member A
  • Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
KeywordsGENE REGULATION / Chromatin remodeling 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 / bBAF complex / GBAF complex / brahma complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cellular response to cytochalasin B / neural retina development ...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 / bBAF complex / GBAF complex / brahma complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cellular response to cytochalasin B / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nBAF complex / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Formation of the polybromo-BAF (pBAF) complex / Gap junction degradation / protein localization to adherens junction / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / dense body / RSC-type complex / Folding of actin by CCT/TriC / nucleosome array spacer activity / Tat protein binding / RNA polymerase I preinitiation complex assembly / Ino80 complex / postsynaptic actin cytoskeleton / Regulation of CDH1 Function / host-mediated activation of viral transcription / apical protein localization / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / adherens junction assembly / RHOF GTPase cycle / regulation of nucleotide-excision repair / ATP-dependent chromatin remodeler activity / Sensory processing of sound by outer hair cells of the cochlea / tight junction / nucleosome disassembly / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / nuclear androgen receptor binding / positive regulation of T cell differentiation / apical junction complex / maintenance of blood-brain barrier / spinal cord development / positive regulation of stem cell population maintenance / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of double-strand break repair / Recycling pathway of L1 / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / establishment or maintenance of cell polarity / regulation of DNA replication / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / nitric-oxide synthase binding / brush border / EPH-ephrin mediated repulsion of cells / regulation of embryonic development / regulation of synaptic vesicle endocytosis / negative regulation of cell differentiation / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / kinesin binding / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / positive regulation of signal transduction by p53 class mediator / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / axonogenesis / cytoskeleton organization / Chromatin modifying enzymes / DNA polymerase binding / EPHB-mediated forward signaling / substantia nigra development / Interleukin-7 signaling / telomere maintenance / calyx of Held / transcription initiation-coupled chromatin remodeling / nitric-oxide synthase regulator activity / helicase activity / transcription coregulator binding / FCGR3A-mediated phagocytosis
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
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 A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen, K.J. / Chen, Z.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130016 China
CitationJournal: Cell Discov / Year: 2025
Title: ncBAF recognizes the nucleosome through BCL7A in chromatin remodeling.
Authors: Kangjing Chen / Liwen Du / Yumin Liu / Mo Chen / Zhucheng Chen /
History
DepositionAug 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 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: Actin, cytoplasmic 1
B: Actin-like protein 6A
C: B-cell CLL/lymphoma 7 protein family member A
D: Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Theoretical massNumber of molelcules
Total (without water)293,7584
Polymers293,7584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Homo sapiens (human)
References: UniProt: P60709, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: 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: 47509.812 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: Homo sapiens (human) / References: UniProt: O96019
#3: Protein B-cell CLL/lymphoma 7 protein family member A


Mass: 22842.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL7A / Production host: Homo sapiens (human) / References: UniProt: Q4VC05
#4: Protein Isoform 2 of 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: 181622.281 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: Homo sapiens (human)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
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: ARP module of ncBAF / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.19.2_4158:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55992 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037183
ELECTRON MICROSCOPYf_angle_d0.4289715
ELECTRON MICROSCOPYf_dihedral_angle_d3.67971
ELECTRON MICROSCOPYf_chiral_restr0.0411065
ELECTRON MICROSCOPYf_plane_restr0.0031257

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