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- EMDB-64579: The apo density map of BCL7B-containing ARP module of the human S... -

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Basic information

Entry
Database: EMDB / ID: EMD-64579
TitleThe apo density map of BCL7B-containing ARP module of the human SWI/SNF complex
Map data
Sample
  • Complex: The BCL7B-containing ARP module of the human SWI/SNF complex
    • Protein or peptide: Transcription activator BRG1
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: B-cell CLL/lymphoma 7 protein family member B
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordschromatin remodeling / SWI/SNF / nuclear actin / GENE REGULATION
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / brahma complex / positive regulation of norepinephrine uptake / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / perichromatin fibrils / negative regulation of androgen receptor signaling pathway ...positive regulation of glucose mediated signaling pathway / bBAF complex / nBAF complex / npBAF complex / brahma complex / positive regulation of norepinephrine uptake / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF 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 / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / RSC-type complex / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBP-mediated host defense / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / dense body / Tat protein binding / RNA polymerase I preinitiation complex assembly / Folding of actin by CCT/TriC / Regulation of CDH1 Function / Ino80 complex / postsynaptic actin cytoskeleton / host-mediated activation of viral transcription / apical protein localization / Adherens junctions interactions / Prefoldin mediated transfer of substrate to CCT/TriC / microtubule nucleation / RHOF GTPase cycle / adherens junction assembly / regulation of double-strand break repair / SWI/SNF complex / Sensory processing of sound by outer hair cells of the cochlea / ATP-dependent chromatin remodeler activity / spinal cord development / tight junction / positive regulation of T cell differentiation / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / nuclear androgen receptor binding / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / apical junction complex / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / Wnt signaling pathway / regulation of chromosome organization / regulation of norepinephrine uptake / Recycling pathway of L1 / lncRNA binding / transporter regulator activity / positive regulation of double-strand break repair / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / establishment or maintenance of cell polarity / negative regulation of cell differentiation / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / brush border / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / kinesin binding / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / positive regulation of Wnt signaling pathway / 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 / helicase activity / substantia nigra development / regulation of embryonic development / Interleukin-7 signaling / telomere maintenance / cell motility
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 / QLQ / Glutamine-Leucine-Glutamine, 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 / QLQ / Glutamine-Leucine-Glutamine, 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 B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 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, 6 items
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, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64579.png

Downloads & links

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Map

FileDownload / File: emd_64579.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.9421104 - 1.7534003
Average (Standard dev.)0.0001476538 (±0.025015382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64579_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64579_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64579_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The BCL7B-containing ARP module of the human SWI/SNF complex

EntireName: The BCL7B-containing ARP module of the human SWI/SNF complex
Components
  • Complex: The BCL7B-containing ARP module of the human SWI/SNF complex
    • Protein or peptide: Transcription activator BRG1
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: B-cell CLL/lymphoma 7 protein family member B
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: The BCL7B-containing ARP module of the human SWI/SNF complex

SupramoleculeName: The BCL7B-containing ARP module of the human SWI/SNF complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transcription activator BRG1

MacromoleculeName: Transcription activator BRG1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.774223 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString:
MSLREARITE KLEKQQKIEQ ERKRRQKHQE YLNSILQHAK DFKEYHRSVT GKIQKLTKAV ATYHANTERE QKKWSHPQFE KGGGSGGGS GGGSWSHPQF EK

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4

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Macromolecule #2: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.853738 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MADDDIAALV VDNGSGMCKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIEHGIVTNW DDMEKIWHH TFYNELRVAP EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT TGIVMDSGDG V THTVPIYE ...String:
MADDDIAALV VDNGSGMCKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIEHGIVTNW DDMEKIWHH TFYNELRVAP EEHPVLLTEA PLNPKANREK MTQIMFETFN TPAMYVAIQA VLSLYASGRT TGIVMDSGDG V THTVPIYE GYALPHAILR LDLAGRDLTD YLMKILTERG YSFTTTAERE IVRDIKEKLC YVALDFEQEM ATAASSSSLE KS YELPDGQ VITIGNERFR CPEALFQPSF LGMESCGIHE TTFNSIMKCD VDIRKDLYAN TVLSGGTTMY PGIADRMQKE ITA LAPSTM KIKIIAPPER KYSVWIGGSI LASLSTFQQM WISKQEYDES GPSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #3: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.580891 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MASGGVYGGD EVGALVFDIG SYTVRAGYAG EDCPKVDFPT AIGMVVERDD GSTLMEIDGD KGKQGGPTYY IDTNALRVPR ENMEAISPL KNGMVEDWDS FQAILDHTYK MHVKSEASLH PVLMSEAPWN TRAKREKLTE LMFEHYNIPA FFLCKTAVLT A FANGRSTG ...String:
MASGGVYGGD EVGALVFDIG SYTVRAGYAG EDCPKVDFPT AIGMVVERDD GSTLMEIDGD KGKQGGPTYY IDTNALRVPR ENMEAISPL KNGMVEDWDS FQAILDHTYK MHVKSEASLH PVLMSEAPWN TRAKREKLTE LMFEHYNIPA FFLCKTAVLT A FANGRSTG LILDSGATHT TAIPVHDGYV LQQGIVKSPL AGDFITMQCR ELFQEMNIEL VPPYMIASKE AVREGSPANW KR KEKLPQV TRSWHNYMCN CVIQDFQASV LQVSDSTYDE QVAAQMPTVH YEFPNGYNCD FGAERLKIPE GLFDPSNVKG LSG NTMLGV SHVVTTSVGM CDIDIRPGLY GSVIVAGGNT LIQSFTDRLN RELSQKTPPS MRLKLIANNT TVERRFSSWI GGSI LASLG TFQQMWISKQ EYEEGGKQCV ERKCP

UniProtKB: Actin-like protein 6A

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Macromolecule #4: B-cell CLL/lymphoma 7 protein family member B

MacromoleculeName: B-cell CLL/lymphoma 7 protein family member B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.291344 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MASGRSVRAE TRSRAKDDIK KVMAAIEKVR KWEKKWVTVG DTSLRIFKWV PVTDSKEKEK SKSNSSAARE PNGFPSDASA NSSLLLEFQ DENSNQSSVS DVYQLKVDSS TNSSPSPQQS ESLSPAHTSD FRTDDSQPPT LGQEILEEPS LPSSEVADEP P TLTKEEPV ...String:
MASGRSVRAE TRSRAKDDIK KVMAAIEKVR KWEKKWVTVG DTSLRIFKWV PVTDSKEKEK SKSNSSAARE PNGFPSDASA NSSLLLEFQ DENSNQSSVS DVYQLKVDSS TNSSPSPQQS ESLSPAHTSD FRTDDSQPPT LGQEILEEPS LPSSEVADEP P TLTKEEPV PLETQVVEEE EDSGAPPLKR FCVDQPTVPQ TASES

UniProtKB: B-cell CLL/lymphoma 7 protein family member B

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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: 7.5
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: 2.4 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 201998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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