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- EMDB-65854: The structure of ARP module in ncBAF complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65854
TitleThe structure of ARP module in ncBAF complex
Map dataThe structure of ARP module
Sample
  • Complex: ARP module of ncBAF
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: B-cell CLL/lymphoma 7 protein family member A
    • Protein or peptide: Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
KeywordsChromatin remodeling complex / GENE REGULATION
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 / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / 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 / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / neural retina development / npBAF complex / brahma complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / neuron projection arborization / 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 / nucleosome array spacer activity / Tat protein binding / RNA polymerase I preinitiation complex assembly / postsynaptic actin cytoskeleton / Ino80 complex / RSC-type complex / blastocyst formation / Regulation of CDH1 Function / regulation of double-strand break repair / host-mediated activation of viral transcription / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / adherens junction assembly / nucleosome disassembly / RHOF GTPase cycle / apical protein localization / ATP-dependent chromatin remodeler activity / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / Interaction between L1 and Ankyrins / 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 / positive regulation of stem cell population maintenance / transporter regulator activity / NuA4 histone acetyltransferase complex / motor behavior / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / cortical cytoskeleton / establishment or maintenance of cell polarity / regulation of DNA replication / nitric-oxide synthase binding / brush border / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / kinesin binding / positive regulation of signal transduction by p53 class mediator / ATP-dependent activity, acting on DNA / regulation of DNA repair / positive regulation of Wnt signaling pathway / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen KJ / Chen ZC
Funding support China, 1 items
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, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65854.png

Downloads & links

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Map

FileDownload / File: emd_65854.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of ARP module
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å		1.08 Å/pix.
x 360 pix.
= 389.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.79291 - 3.0710838
Average (Standard dev.)0.000026261405 (±0.055287644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 389.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65854_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65854_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 : ARP module of ncBAF

EntireName: ARP module of ncBAF
Components
  • Complex: ARP module of ncBAF
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: B-cell CLL/lymphoma 7 protein family member A
    • Protein or peptide: Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4

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Supramolecule #1: ARP module of ncBAF

SupramoleculeName: ARP module of ncBAF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / 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: 41.78266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: Actin-like protein 6A

MacromoleculeName: Actin-like protein 6A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.509812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ...String:
MSGGVYGGDE VGALVFDIGS YTVRAGYAGE DCPKVDFPTA IGMVVERDDG STLMEIDGDK GKQGGPTYYI DTNALRVPRE NMEAISPLK NGMVEDWDSF QAILDHTYKM HVKSEASLHP VLMSEAPWNT RAKREKLTEL MFEHYNIPAF FLCKTAVLTA F ANGRSTGL ILDSGATHTT AIPVHDGYVL QQGIVKSPLA GDFITMQCRE LFQEMNIELV PPYMIASKEA VREGSPANWK RK EKLPQVT RSWHNYMCNC VIQDFQASVL QVSDSTYDEQ VAAQMPTVHY EFPNGYNCDF GAERLKIPEG LFDPSNVKGL SGN TMLGVS HVVTTSVGMC DIDIRPGLYG SVIVAGGNTL IQSFTDRLNR ELSQKTPPSM RLKLIANNTT VERRFSSWIG GSIL ASLGT FQQMWISKQE YEEGGKQCVE RKCP

UniProtKB: Actin-like protein 6A

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Macromolecule #3: B-cell CLL/lymphoma 7 protein family member A

MacromoleculeName: B-cell CLL/lymphoma 7 protein family member A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.842938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP NSAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME H SMNSSEKV ...String:
MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP NSAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME H SMNSSEKV DRQPSGDSGL AAETSAISQD LEGVPPSKKM KLEASQQNSE EM

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

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Macromolecule #4: Isoform 2 of SWI/SNF-related matrix-associated actin-dependent re...

MacromoleculeName: Isoform 2 of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
type: protein_or_peptide / ID: 4 / 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: 181.622281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTPDPPLGG TPRPGPSPGP GPSPGAMLGP SPGPSPGSAH SMMGPSPGPP SAGHPIPTQG PGGYPQDNMH QMHKPMESMH EKGMSDDPR YNQMKGMGMR SGGHAGMGPP PSPMDQHSQG YPSPLGGSEH ASSPVPASGP SSGPQMSSGP GGAPLDGADP Q ALGQQNRG ...String:
MSTPDPPLGG TPRPGPSPGP GPSPGAMLGP SPGPSPGSAH SMMGPSPGPP SAGHPIPTQG PGGYPQDNMH QMHKPMESMH EKGMSDDPR YNQMKGMGMR SGGHAGMGPP PSPMDQHSQG YPSPLGGSEH ASSPVPASGP SSGPQMSSGP GGAPLDGADP Q ALGQQNRG PTPFNQNQLH QLRAQIMAYK MLARGQPLPD HLQMAVQGKR PMPGMQQQMP TLPPPSVSAT GPGPGPGPGP GP GPGPAPP NYSRPHGMGG PNMPPPGPSG VPPGMPGQPP GGPPKPWPEG PMANAAAPTS TPQKLIPPQP TGRPSPAPPA VPP AASPVM PPQTQSPGQP AQPAPMVPLH QKQSRITPIQ KPRGLDPVEI LQEREYRLQA RIAHRIQELE NLPGSLAGDL RTKA TIELK ALRLLNFQRQ LRQEVVVCMR RDTALETALN AKAYKRSKRQ SLREARITEK LEKQQKIEQE RKRRQKHQEY LNSIL QHAK DFKEYHRSVT GKIQKLTKAV ATYHANTERE QKKENERIEK ERMRRLMAED EEGYRKLIDQ KKDKRLAYLL QQTDEY VAN LTELVRQHKA AQVAKEKKKK KKKKKAENAE GQTPAIGPDG EPLDETSQMS DLPVKVIHVE SGKILTGTDA PKAGQLE AW LEMNPGYEVA PRSDSEESGS EEEEEEEEEE QPQAAQPPTL PVEEKKKIPD PDSDDVSEVD ARHIIENAKQ DVDDEYGV S QALARGLQSY YAVAHAVTER VDKQSALMVN GVLKQYQIKG LEWLVSLYNN NLNGILADEM GLGKTIQTIA LITYLMEHK RINGPFLIIV PLSTLSNWAY EFDKWAPSVV KVSYKGSPAA RRAFVPQLRS GKFNVLLTTY EYIIKDKHIL AKIRWKYMIV DEGHRMKNH HCKLTQVLNT HYVAPRRLLL TGTPLQNKLP ELWALLNFLL PTIFKSCSTF EQWFNAPFAM TGEKVDLNEE E TILIIRRL HKVLRPFLLR RLKKEVEAQL PEKVEYVIKC DMSALQRVLY RHMQAKGVLL TDGSEKDKKG KGGTKTLMNT IM QLRKICN HPYMFQHIEE SFSEHLGFTG GIVQGLDLYR ASGKFELLDR ILPKLRATNH KVLLFCQMTS LMTIMEDYFA YRG FKYLRL DGTTKAEDRG MLLKTFNEPG SEYFIFLLST RAGGLGLNLQ SADTVIIFDS DWNPHQDLQA QDRAHRIGQQ NEVR VLRLC TVNSVEEKIL AAAKYKLNVD QKVIQAGMFD QKSSSHERRA FLQAILEHEE QDEEEDEVPD DETVNQMIAR HEEEF DLFM RMDLDRRREE ARNPKRKPRL MEEDELPSWI IKDDAEVERL TCEEEEEKMF GRGSRHRKEV DYSDSLTEKQ WLKAIE EGT LEEIEEEVRQ KKSSRKRKRD SDAGSSTPTT STRSRDKDDE SKKQKKRGRP PAEKLSPNPP NLTKKMKKIV DAVIKYK DS SSGRQLSEVF IQLPSRKELP EYYELIRKPV DFKKIKERIR NHKYRSLNDL EKDVMLLCQN AQTFNLEGSL IYEDSIVL Q SVFTSVRQKI EKEDDSEGEE SEEEEEGEEE GSESESRSVK VKIKLGRKEK AQDRLKGGRR RPSRGSRAKP VVSDDDSEE EQEEDRSGSG SEED

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

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 55992
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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