EMDB-54078: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL...

Basic information

Entry

Database: EMDB / ID: EMD-54078

• Title: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2
• Map data: Full map

Sample

• Complex: BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6
  • Complex: Nucleosome core particle
    • Protein or peptide: x 4 types
    • DNA: x 2 types
  • Complex: BAF complex
    • Protein or peptide: x 8 types
  • Complex: OCT4/SOX2 heterodimer
    • Protein or peptide: x 2 types

• Keywords: Chromatin / remodeler / transcription / GENE REGULATION

Function / homology

Function:

negative regulation of myeloid progenitor cell differentiation / glial cell fate commitment / single stranded viral RNA replication via double stranded DNA intermediate / Formation of the posterior neural plate / cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / Positive Regulation of CDH1 Gene Transcription / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / positive regulation of glucose mediated signaling pathway / pituitary gland development / blastocyst development / heart induction / bBAF complex / negative regulation of cell cycle G1/S phase transition / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / neuronal stem cell population maintenance / Specification of primordial germ cells / nBAF complex / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / npBAF complex / brahma complex / positive regulation of norepinephrine uptake / positive regulation of telomere maintenance in response to DNA damage / Transcriptional regulation of pluripotent stem cells / regulation of DNA strand elongation / perichromatin fibrils / negative regulation of androgen receptor signaling pathway / GBAF complex / Transcriptional Regulation by MECP2 / Germ layer formation at gastrulation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / eye development / 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 / response to growth factor / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / RSC-type complex / Formation of annular gap junctions / XY body / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / somatic stem cell population maintenance / 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 / histone H3K14ac reader activity / dense body / Tat protein binding / RNA polymerase I preinitiation complex assembly / Folding of actin by CCT/TriC / cellular response to fatty acid / Regulation of CDH1 Function / Ino80 complex / postsynaptic actin cytoskeleton / host-mediated activation of viral transcription / forebrain development / 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 / nucleosome disassembly / negative regulation of neuron differentiation / ATP-dependent chromatin remodeler activity / miRNA binding / 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 / inner ear development / regulation of nucleotide-excision repair / nuclear chromosome / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of chromosome organization / regulation of norepinephrine uptake / Recycling pathway of L1

Domain/homology:

SWI/SNF-like complex subunit BAF250a / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / DPF1-3, N-terminal domain / DPF1-3, N-terminal / Transcription factor SOX / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SOX transcription factor / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / : / SWI/SNF Subunit INI1, DNA binding domain / SWIB domain / SWI complex, BAF60b domains / Chromatin-remodeling complex component Sfh1/SNF5 / : / SWIFT domain / SWI/SNF complex subunit BRG1 / : / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / 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 / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / HSA domain / Homeobox, conserved site / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / 'Homeobox' domain signature. / Helicase/SANT-associated domain / HSA domain profile. / SWIB/MDM2 domain superfamily / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / HMG (high mobility group) box / SANT domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / SANT domain / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / PHD-finger / BRCT domain superfamily / Zinc finger C2H2 type domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Green fluorescent protein, GFP / Zinc finger C2H2 type domain signature.

Component:

AT-rich interactive domain-containing protein 1A / Actin-like protein 6A / Histone H2A type 1-B/E / Histone H2B type 1-J / Green fluorescent protein / Transcription factor SOX-2 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF complex subunit SMARCC2 / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

• Biological species: Homo sapiens (human) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 4.1 Å
• Authors: Vecchia L / Weiss J / Cavadini S / Kempf G / Kater L / Pathare G / Thoma NH

Funding support

European Union, Switzerland, 5 items

Organization	Grant number	Country
European Research Council (ERC)		European Union
Swiss National Science Foundation		Switzerland
European Molecular Biology Organization (EMBO)		European Union
Other private
Other private

• Citation: Journal: Mol Cell / Year: 2026; Title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4-SOX2.; Authors: Joscha Weiss / Luca Vecchia / David Domjan / Simone Cavadini / Anton Sabantsev / Georg Kempf / Ganesh R Pathare / Klaus Brackmann / Alicia K Michael / Lukas Kater / Eric Hietter-Pfeiffer / Mina Haddawi / Urja P Kuber / Sandra Mühlhäusser / Ralph S Grand / Michael B Stadler / Sebastian Deindl / Nicolas H Thomä / ; Abstract: Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4-SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4-SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4-SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes.

History

Deposition	Jun 19, 2025	-
Header (metadata) release	Feb 11, 2026	-
Map release	Feb 11, 2026	-
Update	Sep 9, 2026	-
Current status	Sep 9, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_54078.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Full map
• Voxel size: X=Y=Z: 1.69 Å

Density

Contour Level	By AUTHOR: 0.4
Minimum - Maximum	-1.7982454 - 4.792322
Average (Standard dev.)	-0.0012102686 (±0.13900559)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 240 240 240 Spacing 240 240 240
Cell	A=B=C: 405.6 Å α=β=γ: 90.0 °

Supplemental data

Half map: Half-map B

• File: emd_54078_half_map_1.map
• Annotation: Half-map B

Half map: Half-map A

• File: emd_54078_half_map_2.map
• Annotation: Half-map A

Sample components

Entire : BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6

• Entire: Name: BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6

Components

• Complex: BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6
  • Complex: Nucleosome core particle
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
  • Complex: BAF complex
    • Protein or peptide: Transcription activator BRG1
    • Protein or peptide: Actin-like protein 6A
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Protein or peptide: AT-rich interactive domain-containing protein 1A
    • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
    • Protein or peptide: SWI/SNF complex subunit SMARCC2
    • Protein or peptide: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
    • Protein or peptide: Zinc finger protein ubi-d4
  • Complex: OCT4/SOX2 heterodimer
    • Protein or peptide: Green fluorescent protein,POU domain, class 5, transcription factor 1
    • Protein or peptide: Transcription factor SOX-2

Supramolecule #1: BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6

• Supramolecule: Name: BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6; type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #2: Nucleosome core particle

• Supramolecule: Name: Nucleosome core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #15-#16
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #3: BAF complex

• Supramolecule: Name: BAF complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#12
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #4: OCT4/SOX2 heterodimer

• Supramolecule: Name: OCT4/SOX2 heterodimer / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #13-#14
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: Histone H3.1

• Macromolecule: Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.719445 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.1

Macromolecule #2: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.676703 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

Macromolecule #3: Histone H2A type 1-B/E

• Macromolecule: Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.447825 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

Macromolecule #4: Histone H2B type 1-J

• Macromolecule: Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 14.088336 KDa
• Recombinant expression: Organism: Escherichia coli (E. coli)

Sequence

String:

GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSA

UniProtKB: Histone H2B type 1-J

Macromolecule #5: Transcription activator BRG1

• Macromolecule: Name: Transcription activator BRG1 / type: protein_or_peptide / ID: 5 / 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: 184.923828 KDa

Sequence

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 QDESRHCSTG SGSASFAHTA PPPAG VNPD LEEPPLKEED EVPDDETVNQ MIARHEEEFD LFMRMDLDRR REEARNPKRK PRLMEEDELP SWIIKDDAEV ERLTCE EEE EKMFGRGSRH RKEVDYSDSL TEKQWLKAIE EGTLEEIEEE VRQKKSSRKR KRDSDAGSST PTTSTRSRDK DDESKKQ KK RGRPPAEKLS PNPPNLTKKM KKIVDAVIKY KDSSSGRQLS EVFIQLPSRK ELPEYYELIR KPVDFKKIKE RIRNHKYR S LNDLEKDVML LCQNAQTFNL EGSLIYEDSI VLQSVFTSVR QKIEKEDDSE GEESEEEEEG EEEGSESESR SVKVKIKLG RKEKAQDRLK GGRRRPSRGS RAKPVVSDDD SEEEQEEDRS GSGSEED

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

Macromolecule #6: Actin-like protein 6A

• Macromolecule: Name: Actin-like protein 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 47.509812 KDa

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 RKCP

UniProtKB: Actin-like protein 6A

Macromolecule #7: Actin, cytoplasmic 1, N-terminally processed

• Macromolecule: Name: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 41.78266 KDa

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 PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

Macromolecule #8: AT-rich interactive domain-containing protein 1A

• Macromolecule: Name: AT-rich interactive domain-containing protein 1A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 242.250312 KDa

Sequence

String:

MAAQVAPAAA SSLGNPPPPP PSELKKAEQQ QREEAGGEAA AAAAAERGEM KAAAGQESEG PAVGPPQPLG KELQDGAESN GGGGGGGAG SGGGPGAEPD LKNSNGNAGP RPALNNNLTE PPGGGGGGSS DGVGAPPHSA AAALPPPAYG FGQPYGRSPS A VAAAAAAV FHQQHGGQQS PGLAALQSGG GGGLEPYAGP QQNSHDHGFP NHQYNSYYPN RSAYPPPAPA YALSSPRGGT PG SGAAAAA GSKPPPSSSA SASSSSSSFA QQRFGAMGGG GPSAAGGGTP QPTATPTLNQ LLTSPSSARG YQGYPGGDYS GGP QDGGAG KGPADMASQC WGAAAAAAAA AAASGGAQQR SHHAPMSPGS SGGGGQPLAR TPQPSSPMDQ MGKMRPQPYG GTNP YSQQQ GPPSGPQQGH GYPGQPYGSQ TPQRYPMTMQ GRAQSAMGGL SYTQQIPPYG QQGPSGYGQQ GQTPYYNQQS PHPQQ QQPP YSQQPPSQTP HAQPSYQQQP QSQPPQLQSS QPPYSQQPSQ PPHQQSPAPY PSQQSTTQQH PQSQPPYSQP QAQSPY QQQ QPQQPAPSTL SQQAAYPQPQ SQQSQQTAYS QQRFPPPQEL SQDSFGSQAS SAPSMTSSKG GQEDMNLSLQ SRPSSLP DL SGSIDDLPMG TEGALSPGVS TSGISSSQGE QSNPAQSPFS PHTSPHLPGI RGPSPSPVGS PASVAQSRSG PLSPAAVP G NQMPPRPPSG QSDSIMHPSM NQSSIAQDRG YMQRNPQMPQ YSSPQPGSAL SPRQPSGGQI HTGMGSYQQN SMGSYGPQG GQYGPQGGYP RQPNYNALPN ANYPSAGMAG GINPMGAGGQ MHGQPGIPPY GTLPPGRMSH ASMGNRPYGP NMANMPPQVG SGMCPPPGG MNRKTQETAV AMHVAANSIQ NRPPGYPNMN QGGMMGTGPP YGQGINSMAG MINPQGPPYS MGGTMANNSA G MAASPEMM GLGDVKLTPA TKMNNKADGT PKTESKSKKS SSSTTTNEKI TKLYELGGEP ERKMWVDRYL AFTEEKAMGM TN LPAVGRK PLDLYRLYVS VKEIGGLTQV NKNKKWRELA TNLNVGTSSS AASSLKKQYI QCLYAFECKI ERGEDPPPDI FAA ADSKKS QPKIQPPSPA GSGSMQGPQT PQSTSSSMAE GGDLKPPTPA STPHSQIPPL PGMSRSNSVG IQDAFNDGSD STFQ KRNSM TPNPGYQPSM NTSDMMGRMS YEPNKDPYGS MRKAPGSDPF MSSGQGPNGG MGDPYSRAAG PGLGNVAMGP RQHYP YGGP YDRVRTEPGI GPEGNMSTGA PQPNLMPSNP DSGMYSPSRY PPQQQQQQQQ RHDSYGNQFS TQGTPSGSPF PSQQTT MYQ QQQQNYKRPM DGTYGPPAKR HEGEMYSVPY STGQGQPQQQ QLPPAQPQPA SQQQAAQPSP QQDVYNQYGN AYPATAT AA TERRPAGGPQ NQFPFQFGRD RVSAPPGTNA QQNMPPQMMG GPIQASAEVA QQGTMWQGRN DMTYNYANRQ STGSAPQG P AYHGVNRTDE MLHTDQRANH EGSWPSHGTR QPPYGPSAPV PPMTRPPPSN YQPPPSMQNH IPQVSSPAPL PRPMENRTS PSKSPFLHSG MKMQKAGPPV PASHIAPAPV QPPMIRRDIT FPPGSVEATQ PVLKQRRRLT MKDIGTPEAW RVMMSLKSGL LAESTWALD TINILLYDDN SIMTFNLSQL PGLLELLVEY FRRCLIEIFG ILKEYEVGDP GQRTLLDPGR FSKVSSPAPM E GGEEEEEL LGPKLEEEEE EEVVENDEEI AFSGKDKPAS ENSEEKLISK FDKLPVKIVQ KNDPFVVDCS DKLGRVQEFD SG LLHWRIG GGDTTEHIQT HFESKTELLP SRPHAPCPPA PRKHVTTAEG TPGTTDQEGP PPDGPPEKRI TATMDDMLST RSS TLTEDG AKSSEAIKES SKFPFGISPA QSHRNIKILE DEPHSKDETP LCTLLDWQDS LAKRCVCVSN TIRSLSFVPG NDFE MSKHP GLLLILGKLI LLHHKHPERK QAPLTYEKEE EQDQGVSCNK VEWWWDCLEM LRENTLVTLA NISGQLDLSP YPESI CLPV LDGLLHWAVC PSAEAQDPFS TLGPNAVLSP QRLVLETLSK LSIQDNNVDL ILATPPFSRL EKLYSTMVRF LSDRKN PVC REMAVVLLAN LAQGDSLAAR AIAVQKGSIG NLLGFLEDSL AATQFQQSQA SLLHMQNPPF EPTSVDMMRR AARALLA LA KVDENHSEFT LYESRLLDIS VSPLMNSLVS QVICDVLFLI GQS

UniProtKB: AT-rich interactive domain-containing protein 1A

Macromolecule #9: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

• Macromolecule: Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1; type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 44.199188 KDa

Sequence

String:

MMMMALSKTF GQKPVKFQLE DDGEFYMIGS EVGNYLRMFR GSLYKRYPSL WRRLATVEER KKIVASSHGK KTKPNTKDHG YTTLATSVT LLKASEVEEI LDGNDEKYKA VSISTEPPTY LREQKAKRNS QWVPTLPNSS HHLDAVPCST TINRNRMGRD K KRTFPLCF DDHDPAVIHE NASQPEVLVP IRLDMEIDGQ KLRDAFTWNM NEKLMTPEMF SEILCDDLDL NPLTFVPAIA SA IRQQIES YPTDSILEDQ SDQRVIIKLN IHVGNISLVD QFEWDMSEKE NSPEKFALKL CSELGLGGEF VTTIAYSIRG QLS WHQKTY AFSENPLPTV EIAIRNTGDA DQWCPLLETL TDAEMEKKIR DQDRNTRRMR RLANTAPAW

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

Macromolecule #10: SWI/SNF complex subunit SMARCC2

• Macromolecule: Name: SWI/SNF complex subunit SMARCC2 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 133.048109 KDa

Sequence

String:

MAVRKKDGGP NVKYYEAADT VTQFDNVRLW LGKNYKKYIQ AEPPTNKSLS SLVVQLLQFQ EEVFGKHVSN APLTKLPIKC FLDFKAGGS LCHILAAAYK FKSDQGWRRY DFQNPSRMDR NVEMFMTIEK SLVQNNCLSR PNIFLCPEIE PKLLGKLKDI I KRHQGTVT EDKNNASHVV YPVPGNLEEE EWVRPVMKRD KQVLLHWGYY PDSYDTWIPA SEIEASVEDA PTPEKPRKVH AK WILDTDT FNEWMNEEDY EVNDDKNPVS RRKKISAKTL TDEVNSPDSD RRDKKGGNYK KRKRSPSPSP TPEAKKKNAK KGP STPYTK SKRGHREEEQ EDLTKDMDEP SPVPNVEEVT LPKTVNTKKD SESAPVKGGT MTDLDEQEDE SMETTGKDED ENST GNKGE QTKNPDLHED NVTEQTHHII IPSYAAWFDY NSVHAIERRA LPEFFNGKNK SKTPEIYLAY RNFMIDTYRL NPQEY LTST ACRRNLAGDV CAIMRVHAFL EQWGLINYQV DAESRPTPMG PPPTSHFHVL ADTPSGLVPL QPKTPQQTSA SQQMLN FPD KGKEKPTDMQ NFGLRTDMYT KKNVPSKSKA AASATREWTE QETLLLLEAL EMYKDDWNKV SEHVGSRTQD ECILHFL RL PIEDPYLEDS EASLGPLAYQ PIPFSQSGNP VMSTVAFLAS VVDPRVASAA AKSALEEFSK MKEEVPTALV EAHVRKVE E AAKVTGKADP AFGLESSGIA GTTSDEPERI EESGNDEARV EGQATDEKKE PKEPREGGGA IEEEAKEKTS EAPKKDEEK GKEGDSEKES EKSDGDPIVD PEKEKEPKEG QEEVLKEVVE SEGERKTKVE RDIGEGNLST AAAAALAAAA VKAKHLAAVE ERKIKSLVA LLVETQMKKL EIKLRHFEEL ETIMDREREA LEYQRQQLLA DRQAFHMEQL KYAEMRARQQ HFQQMHQQQQ Q PPPALPPG SQPIPPTGAA GPPAVHGLAV APASVVPAPA GSGAPPGSLG PSEQIGQAGS TAGPQQQQPA GAPQPGAVPP GV PPPGPHG PSPFPNQQTP PSMMPGAVPG SGHPGVAGNA PLGLPFGMPP PPPPPAPSII PFGSLADSIS INLPAPPNLH GHH HHLPFA PGTLPPPNLP VSMANPLHPN LPATTTMPSS LPLGPGLGSA AAQSPAIVAA VQGNLLPSAS PLPDPGTPLP PDPT APSPG TVTPVPPPQ

UniProtKB: SWI/SNF complex subunit SMARCC2

Macromolecule #11: SWI/SNF-related matrix-associated actin-dependent regulator of ch...

• Macromolecule: Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1; type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 58.311391 KDa

Sequence

String:

MAARAGFQSV APSGGAGASG GAGAAAALGP GGTPGPPVRM GPAPGQGLYR SPMPGAAYPR PGMLPGSRMT PQGPSMGPPG YGGNPSVRP GLAQSGMDQS RKRPAPQQIQ QVQQQAVQNR NHNAKKKKMA DKILPQRIRE LVPESQAYMD LLAFERKLDQ T IMRKRLDI QEALKRPIKQ KRKLRIFISN TFNPAKSDAE DGEGTVASWE LRVEGRLLED SALSKYDATK QKRKFSSFFK SL VIELDKD LYGPDNHLVE WHRTATTQET DGFQVKRPGD VNVRCTVLLM LDYQPPQFKL DPRLARLLGI HTQTRPVIIQ ALW QYIKTH KLQDPHEREF VICDKYLQQI FESQRMKFSE IPQRLHALLM PPEPIIINHV ISVDPNDQKK TACYDIDVEV DDTL KTQMN SFLLSTASQQ EIATLDNKIH ETIETINQLK TQREFMLSFA RDPQGFINDW LQSQCRDLKT MTDVVGNPEE ERRAE FYFQ PWAQEAVCRY FYSKVQQRRQ ELEQALGIRN T

UniProtKB: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

Macromolecule #12: Zinc finger protein ubi-d4

• Macromolecule: Name: Zinc finger protein ubi-d4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 48.554125 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MAAVVENVVK LLGEQYYKDA MEQCHNYNAR LCAERSVRLP FLDSQTGVAQ SNCYIWMEKR HRGPGLASGQ LYSYPARRWR KKRRAHPPE DPRLSFPSIK PDTDQTLKKE GLISQDGSSL EALLRTDPLE KRGAPDPRVD DDSLGEFPVT NSRARKRILE P DDFLDDLD DEDYEEDTPK RRGKGKSKGK GVGSARKKLD ASILEDRDKP YACDICGKRY KNRPGLSYHY AHSHLAEEEG ED KEDSQPP TPVSQRSEEQ KSKKGPDGLA LPNNYCDFCL GDSKINKKTG QPEELVSCSD CGRSGHPSCL QFTPVMMAAV KTY RWQCIE CKCCNICGTS ENDDQLLFCD DCDRGYHMYC LTPSMSEPPE GSWSCHLCLD LLKEKASIYQ NQNSSGTLEV LFQG PGGSG SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK

UniProtKB: Zinc finger protein ubi-d4

Macromolecule #13: Green fluorescent protein,POU domain, class 5, transcription factor 1

• Macromolecule: Name: Green fluorescent protein,POU domain, class 5, transcription factor 1; type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 70.735531 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MDWSHPQFEK SAVDENLYFQ GGGRMVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DATYGKLTLK FICTTGKLPV PWPTLVTTL TYGVQCFSRY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYKTRAEVKF EGDTLVNRIE LKGIDFKEDG N ILGHKLEY NYNSHNVYIM ADKQKNGIKV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDNHYLST QSKLSKDPNE KR DHMVLLE FVTAAGITLG MDELYKEAAA KEAAAKMAGH LASDFAFSPP PGGGGDGPGG PEPGWVDPRT WLSFQGPPGG PGI GPGVGP GSEVWGIPPC PPPYEFCGGM AYCGPQVGVG LVPQGGLETS QPEGEAGVGV ESNSDGASPE PCTVTPGAVK LEKE KLEQN PEESQDIKAL QKELEQFAKL LKQKRITLGY TQADVGLTLG VLFGKVFSQT TICRFEALQL SFKNMCKLRP LLQKW VEEA DNNENLQEIC KAETLVQARK RKRTSIENRV RGNLENLFLQ CPKPTLQQIS HIAQQLGLEK DVVRVWFCNR RQKGKR SSS DYAQREDFEA AGSPFSGGPV SFPLAPGPHF GTPGYGSPHF TALYSSVPFP EGEAFPPVSV TTLGSPMHSN LPETGGH HH HHH

UniProtKB: Green fluorescent protein, POU domain, class 5, transcription factor 1

Macromolecule #14: Transcription factor SOX-2

• Macromolecule: Name: Transcription factor SOX-2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 12.718679 KDa
• Recombinant expression: Organism: Trichoplusia ni (cabbage looper)

Sequence

String:

MDWSHPQFEK SAVDENLYFQ GGMSPDRVKR PMNAFMVWSR GQRRKMAQEN PKMHNSEISK RLGAEWKLLS ETEKRPFIDE AKRLRALHM KEHPDYKYRP RRKTKT

UniProtKB: Transcription factor SOX-2

Macromolecule #15: DNA (147-MER)

• Macromolecule: Name: DNA (147-MER) / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 69.794414 KDa

Sequence

String:

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

Macromolecule #16: DNA (147-MER)

• Macromolecule: Name: DNA (147-MER) / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 70.389781 KDa

Sequence

String:

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

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 8
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: FEI FALCON IV (4k 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: 2.5 µm / Nominal defocus min: 0.5 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Software - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27074
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT

Output model

PDB-9rn2:
Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2