EMDB-68040: Cryo-EM structure of ncBAF bound to the nucleosome

Basic information

Entry

Database: EMDB / ID: EMD-68040

• Title: Cryo-EM structure of ncBAF bound to the nucleosome
• Map data: The overal map for SMARCA4-ARP-NCP processed by cryoSPARC

Sample

• Complex: The ncBAF-NCP complex
  • Complex: The ncBAF complex
    • Complex: The ATPase domain of SMARCA4
      • Protein or peptide: x 1 types
    • Complex: The ARP module
      • Protein or peptide: x 3 types
  • Complex: Nucleosome
    • Protein or peptide: x 4 types
    • DNA: x 2 types
• Ligand: x 3 types

• Keywords: Chromatin remodeling complex / ncBAF complex / nucleosome / SMARCA4 / BCL7 / ARP / NUCLEAR PROTEIN/DNA / NUCLEAR PROTEIN-DNA complex

Function / homology

Function:

regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / morphogenesis of a polarized epithelium / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Gap junction degradation / Formation of the non-canonical BAF (ncBAF) 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 / Ino80 complex / postsynaptic actin cytoskeleton / RSC-type complex / blastocyst formation / Regulation of CDH1 Function / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / regulation of nucleotide-excision repair / Adherens junctions interactions / adherens junction assembly / RHOF GTPase cycle / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / tight junction / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / Interaction between L1 and Ankyrins / apical junction complex / spinal cord development / regulation of chromosome organization / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / regulation of norepinephrine uptake / transporter regulator activity / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair / 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / nitric-oxide synthase binding / brush border / 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 / ATP-dependent activity, acting on DNA / regulation of DNA repair / 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 / EPHB-mediated forward signaling / substantia nigra development / telomere maintenance / calyx of Held / nitric-oxide synthase regulator activity / positive regulation of DNA repair / helicase activity / cell motility / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / negative regulation of cell growth / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton

Domain/homology:

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. / ATPase, nucleotide binding domain / Histone H3 signature 2. / 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

Component:

Histone H3 / Histone H2B / Actin-like protein 6A / Actin, cytoplasmic 1 / Histone H4 / B-cell CLL/lymphoma 7 protein family member A / Histone H2A / SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4

• Biological species: Homo sapiens (human) / Xenopus laevis (African clawed frog)
• Method: single particle reconstruction / cryo EM / Resolution: 4.7 Å
• Authors: Xu W / Cheng J / Chen Y

Funding support

China, 1 items

Organization	Grant number	Country
Ministry of Science and Technology (MoST, China)	2023YFA1800403	China

• Citation: Journal: J Mol Cell Biol / Year: 2026; Title: Structural basis of complex assembly and nucleosome recognition by the chromatin remodeling ncBAF complex.; Authors: Wancheng Xu / Shengsheng Ma / Yi Li / Muchun Li / Chihang Li / Yue Yin / Qingrun Li / Jingdong Cheng / Yong Chen / ; Abstract: BRG1/BRM-associated factor (BAF)-family chromatin remodelers regulate transcription and genome organization by repositioning nucleosomes. The human non-canonical BAF (ncBAF) complex is uniquely defined by the presence of BRD9 and GLTSCR1/GLTSCR1L, as well as the absence of the ARID1/2 scaffold and the canonical nucleosome-binding module found in cBAF and PBAF. How ncBAF assembles and engages nucleosomes remains elusive. Here, we present a cryo-EM structure of ncBAF bound to a nucleosome, integrated with biochemical assays and crosslinking mass spectrometry analyses. The ncBAF complex adopts a three-module architecture comprising an ATPase motor module, a repositioned actin-related protein (ARP) module, and a highly flexible Base module. The ncBAF-specific subunits BRD9 and GLTSCR1L are largely dispensable for complex assembly and nucleosome remodeling. Instead, BCL7A directly engages the H2A-H2B acidic patch and the H2A N-terminal tail, providing a structural substitute for SMARCB1 in stimulating remodeling activity. These findings reveal how ncBAF compensates for the loss of the canonical nucleosome-binding module through modular reorganization, providing a structural framework for understanding ncBAF-mediated chromatin regulation and its roles in development and disease.

History

Deposition	Dec 31, 2025	-
Header (metadata) release	May 13, 2026	-
Map release	May 13, 2026	-
Update	Jul 15, 2026	-
Current status	Jul 15, 2026	Processing site: PDBc / Status: Released

Map

• File: Download / File: emd_68040.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: The overal map for SMARCA4-ARP-NCP processed by cryoSPARC
• Voxel size: X=Y=Z: 1.1 Å

Density

Contour Level	By AUTHOR: 0.0075
Minimum - Maximum	-0.0663502 - 0.08802954
Average (Standard dev.)	0.00009154299 (±0.0016502528)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 396.0 Å α=β=γ: 90.0 °

Supplemental data

Additional map: multibody refined map focusing on the ARP module

• File: emd_68040_additional_1.map
• Annotation: multibody refined map focusing on the ARP module

Additional map: multibody refined map focusing on the ATPase domain

• File: emd_68040_additional_2.map
• Annotation: multibody refined map focusing on the ATPase domain

Additional map: multibody refined map focusing on NCP

• File: emd_68040_additional_3.map
• Annotation: multibody refined map focusing on NCP

Half map: Half map B processed by cryoSPARC

• File: emd_68040_half_map_1.map
• Annotation: Half map B processed by cryoSPARC

Half map: Half map A processed by cryoSPARC

• File: emd_68040_half_map_2.map
• Annotation: Half map A processed by cryoSPARC

Sample components

Entire : The ncBAF-NCP complex

• Entire: Name: The ncBAF-NCP complex

Components

• Complex: The ncBAF-NCP complex
  • Complex: The ncBAF complex
    • Complex: The ATPase domain of SMARCA4
      • Protein or peptide: SMARCA4 isoform 2
    • Complex: The ARP module
      • Protein or peptide: B-cell CLL/lymphoma 7 protein family member A
      • Protein or peptide: Actin, cytoplasmic 1
      • Protein or peptide: Actin-like protein 6A
  • Complex: Nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
• Ligand: BERYLLIUM TRIFLUORIDE ION
• Ligand: MAGNESIUM ION
• Ligand: ADENOSINE-5'-DIPHOSPHATE

Supramolecule #1: The ncBAF-NCP complex

• Supramolecule: Name: The ncBAF-NCP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 / Details: The ncBAF complex bound to a nucleosome
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 900 KDa

Supramolecule #2: The ncBAF complex

• Supramolecule: Name: The ncBAF complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5, #8-#10; Details: Only BCL7A, SMARCA4,ACTB, and ACT6A are observed in density map.
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 700 KDa

Supramolecule #3: Nucleosome

• Supramolecule: Name: Nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#7; Details: The nucleosome core particle composed of Histones H2A, H2B, H3, H4, and double-stranded DNA. BCL7 finger helix is also included.
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 200 KDa

Supramolecule #4: The ATPase domain of SMARCA4

• Supramolecule: Name: The ATPase domain of SMARCA4 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #8 / Details: It includes ATPase domain of SMARCA4
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 190 KDa

Supramolecule #5: The ARP module

• Supramolecule: Name: The ARP module / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #5, #8-#10; Details: The ARP module is composed of ACTB, ACTL6A, ABM of BCL7A,and HSA of SMARCA4
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 110 KDa

Macromolecule #1: Histone H3

• Macromolecule: Name: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 15.30393 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

Macromolecule #2: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 11.263231 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

Macromolecule #3: Histone H2A

• Macromolecule: Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 13.978241 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

Macromolecule #4: Histone H2B

• Macromolecule: Name: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Xenopus laevis (African clawed frog)
• Molecular weight: Theoretical: 13.848097 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B

Macromolecule #5: B-cell CLL/lymphoma 7 protein family member A

• Macromolecule: Name: B-cell CLL/lymphoma 7 protein family member A / type: protein_or_peptide / ID: 5 / Details: BCL7A full length with a C-terminal 6xHis tag / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 23.671818 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MSGRSVRAET RSRAKDDIKR VMAAIEKVRK WEKKWVTVGD TSLRIYKWVP VTEPKVDDKN KNKKKGKDEK CGSEVTTPEN SSSPGMMDM HDDNSNQSSI ADASPIKQEN SSNSSPAPEP NSAVPSDGTE AKVDEAQADG KEHPGAEDAS DEQNSQSSME H SMNSSEKV DRQPSGDSGL AAETSAISQD LEGVPPSKKM KLEASQQNSE EMHHHHHH

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

Macromolecule #8: SMARCA4 isoform 2

• Macromolecule: Name: SMARCA4 isoform 2 / type: protein_or_peptide / ID: 8 ; Details: SMARCA4 full length with an N-terminal 10aa linker and a C-terminal 3xFlag tag; Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 191.867219 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

GPGGSGGSGT MSTPDPPLGG TPRPGPSPGP GPSPGAMLGP SPGPSPGSAH SMMGPSPGPP SAGHPIPTQG PGGYPQDNMH QMHKPMESM HEKGMSDDPR YNQMKGMGMR SGGHAGMGPP PSPMDQHSQG YPSPLGGSEH ASSPVPASGP SSGPQMSSGP G GAPLDGAD PQALGQQNRG PTPFNQNQLH QLRAQIMAYK MLARGQPLPD HLQMAVQGKR PMPGMQQQMP TLPPPSVSAT GP GPGPGPG PGPGPGPAPP NYSRPHGMGG PNMPPPGPSG VPPGMPGQPP GGPPKPWPEG PMANAAAPTS TPQKLIPPQP TGR PSPAPP AVPPAASPVM PPQTQSPGQP AQPAPMVPLH QKQSRITPIQ KPRGLDPVEI LQEREYRLQA RIAHRIQELE NLPG SLAGD LRTKATIELK ALRLLNFQRQ LRQEVVVCMR RDTALETALN AKAYKRSKRQ SLREARITEK LEKQQKIEQE RKRRQ KHQE YLNSILQHAK DFKEYHRSVT GKIQKLTKAV ATYHANTERE QKKENERIEK ERMRRLMAED EEGYRKLIDQ KKDKRL AYL LQQTDEYVAN LTELVRQHKA AQVAKEKKKK KKKKKAENAE GQTPAIGPDG EPLDETSQMS DLPVKVIHVE SGKILTG TD APKAGQLEAW LEMNPGYEVA PRSDSEESGS EEEEEEEEEE QPQAAQPPTL PVEEKKKIPD PDSDDVSEVD ARHIIENA K QDVDDEYGVS QALARGLQSY YAVAHAVTER VDKQSALMVN GVLKQYQIKG LEWLVSLYNN NLNGILADEM GLGKTIQTI ALITYLMEHK RINGPFLIIV PLSTLSNWAY EFDKWAPSVV KVSYKGSPAA RRAFVPQLRS GKFNVLLTTY EYIIKDKHIL AKIRWKYMI VDEGHRMKNH HCKLTQVLNT HYVAPRRLLL TGTPLQNKLP ELWALLNFLL PTIFKSCSTF EQWFNAPFAM T GEKVDLNE EETILIIRRL HKVLRPFLLR RLKKEVEAQL PEKVEYVIKC DMSALQRVLY RHMQAKGVLL TDGSEKDKKG KG GTKTLMN TIMQLRKICN HPYMFQHIEE SFSEHLGFTG GIVQGLDLYR ASGKFELLDR ILPKLRATNH KVLLFCQMTS LMT IMEDYF AYRGFKYLRL DGTTKAEDRG MLLKTFNEPG SEYFIFLLST RAGGLGLNLQ SADTVIIFDS DWNPHQDLQA QDRA HRIGQ QNEVRVLRLC TVNSVEEKIL AAAKYKLNVD QKVIQAGMFD QKSSSHERRA FLQAILEHEE QDESRHCSTG SGSAS FAHT APPPAGVNPD LEEPPLKEED EVPDDETVNQ MIARHEEEFD LFMRMDLDRR REEARNPKRK PRLMEEDELP SWIIKD DAE VERLTCEEEE EKMFGRGSRH RKEVDYSDSL TEKQWLKKIT GKDIHDTASS VARGLQFQRG LQFCTRASKA IEEGTLE EI EEEVRQKKSS RKRKRDSDAG SSTPTTSTRS RDKDDESKKQ KKRGRPPAEK LSPNPPNLTK KMKKIVDAVI KYKDSSSG R QLSEVFIQLP SRKELPEYYE LIRKPVDFKK IKERIRNHKY RSLNDLEKDV MLLCQNAQTF NLEGSLIYED SIVLQSVFT SVRQKIEKED DSEGEESEEE EEGEEEGSES ESRSVKVKIK LGRKEKAQDR LKGGRRRPSR GSRAKPVVSD DDSEEEQEED RSGSGSEED DYKDHDGDYK DHDIDYKDDD DK

UniProtKB: SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4

Macromolecule #9: Actin, cytoplasmic 1

• Macromolecule: Name: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 9 / Details: ACTB full length with a C-terminal 6xHis tag / 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 weight: Theoretical: 42.611527 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

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 PSIVHRKCFH HHHHH

UniProtKB: Actin, cytoplasmic 1

Macromolecule #10: Actin-like protein 6A

• Macromolecule: Name: Actin-like protein 6A / type: protein_or_peptide / ID: 10 / Details: ACTL6A full length with a C-terminal 6xHis tag / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 48.33868 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

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 RKCPHHHHHH

UniProtKB: Actin-like protein 6A

Macromolecule #6: DNA (167-MER)

• Macromolecule: Name: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 51.333703 KDa

Sequence

String:

(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG) (DC)(DG)(DA)(DC)(DC)

Macromolecule #7: DNA (167-MER)

• Macromolecule: Name: DNA (167-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 51.773973 KDa

Sequence

String:

(DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC) (DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC) (DT)(DC)(DC)(DA)(DG)

Macromolecule #11: BERYLLIUM TRIFLUORIDE ION

• Macromolecule: Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: BEF
• Molecular weight: Theoretical: 66.007 Da

Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

Macromolecule #12: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 1.5 mg/mL

Buffer

pH: 8
Component:

Concentration	Formula	Name
100.0 mM	KCl	Potasium Chloride
20.0 mM	HEPES	4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
2.0 mM	MgCl2	Magnesium Chloride
2.0 mM	DTT	Dithiothreitol
0.5 mM	ADP	Adenosine diphosphate
8.0 mM	NaF	Sodium Floride
1.0 mM	BeSO4	Beryllium sulfate

Details: 20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.

• Grid: Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 14128693
• CTF correction: Software - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Startup model

Type of model: EMDB MAP
EMDB ID:

31925

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 22221
• Initial angle assignment: Type: OTHER / Details: Relion
• Final angle assignment: Type: OTHER / Details: Relion

Atomic model buiding 1

Initial model

PDB ID	Chain
7y8r	source_name: PDB, initial_model_type: experimental model
	source_name: AlphaFold, initial_model_type: in silico model

• Details: We docked the AlphaFold3-predicted ARP module and refined ATPase-NCP model by rigid body fit, due to the limited resolution.
• Refinement: Protocol: RIGID BODY FIT

Output model

PDB-21vv:
Cryo-EM structure of ncBAF bound to the nucleosome