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- PDB-9rl4: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 -

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Entry
Database: PDB / ID: 9rl4
TitleStructure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
Components
  • (DNA (148-MER)) x 2
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • (Transcription ...) x 2
  • AT-rich interactive domain-containing protein 1A
  • Actin, cytoplasmic 1, N-terminally processed
  • Actin-like protein 6A
  • Green fluorescent protein,POU domain, class 5, transcription factor 1
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
  • SWI/SNF complex subunit SMARCC2
  • Zinc finger protein ubi-d4
KeywordsGENE REGULATION / remodelling / chromatin / transcription
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / Positive Regulation of CDH1 Gene Transcription / glial cell fate commitment / single stranded viral RNA replication via double stranded DNA intermediate / regulation of myofibroblast cell apoptotic process / 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 ...negative regulation of myeloid progenitor cell differentiation / Positive Regulation of CDH1 Gene Transcription / glial cell fate commitment / single stranded viral RNA replication via double stranded DNA intermediate / regulation of myofibroblast cell apoptotic process / 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 glucose mediated signaling pathway / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / response to oxygen-glucose deprivation / adenohypophysis development / heart induction / negative regulation of cell cycle G1/S phase transition / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of primordial germ cells / Specification of the neural plate border / pituitary gland development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of norepinephrine uptake / Regulation of CDH1 Function / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / Formation of the polybromo-BAF (pBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / positive regulation of cell-cell adhesion / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Transcriptional Regulation by MECP2 / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Transcriptional regulation of pluripotent stem cells / neuronal stem cell population maintenance / Germ layer formation at gastrulation / bBAF complex / eye development / cellular response to cytochalasin B / neural retina development / npBAF complex / tissue regeneration / negative regulation of androgen receptor signaling pathway / nBAF complex / brahma complex / histone H3K14ac reader activity / EGR2 and SOX10-mediated initiation of Schwann cell myelination / blastocyst hatching / N-acetyltransferase activity / regulation of transepithelial transport / nucleosome array spacer activity / response to growth factor / hepatocyte differentiation / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Gap junction degradation / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / protein localization to adherens junction / dense body / Tat protein binding / postsynaptic actin cytoskeleton / RNA polymerase I preinitiation complex assembly / Ino80 complex / Prefoldin mediated transfer of substrate to CCT/TriC / XY body / RSC-type complex / blastocyst formation / host-mediated activation of viral transcription / ATP-dependent chromatin remodeler activity / cellular response to fatty acid / regulation of nucleotide-excision repair / regulation of double-strand break repair / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / nucleosome disassembly / apical protein localization / germ cell nucleus / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / miRNA binding / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear androgen receptor binding / apical junction complex / nuclear chromosome / negative regulation of neuron differentiation / positive regulation of double-strand break repair / spinal cord development / maintenance of blood-brain barrier
Similarity search - Function
SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal ...SWI/SNF-like complex subunit BAF250a / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWIB domain / SWI complex, BAF60b domains / DPF1-3, N-terminal domain / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / DPF1-3, N-terminal / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / Transcription factor SOX / SOX transcription factor / : / SWI/SNF Subunit INI1, DNA binding domain / SWI/SNF complex subunit BRG1 / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / : / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / 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 / : / 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 / 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 / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Homeobox, conserved site / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / 'Homeobox' domain signature. / 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 / SNF2, N-terminal / SNF2-related domain / Lambda repressor-like, DNA-binding domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / PHD-finger / BRCT domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Zinc finger C2H2 type domain profile. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Green fluorescent protein, GFP / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Actin / Actin family / Actin
Similarity search - Domain/homology
PENTANEDIAL / DNA / DNA (> 10) / DNA (> 100) / 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 ...PENTANEDIAL / DNA / DNA (> 10) / DNA (> 100) / 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 E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Aequorea victoria (jellyfish)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVecchia, L. / Weiss, J. / Cavadini, S. / Kempf, G. / Kater, L. / Pathare, G. / Thoma, N.H.
Funding supportEuropean Union, Switzerland, 5items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
European Molecular Biology Organization (EMBO)European Union
Other private
Other private
CitationJournal: To be published
Title: Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
Authors: Lastname, F.M.
History
DepositionJun 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: Transcription activator BRG1
J: Actin-like protein 6A
K: Actin, cytoplasmic 1, N-terminally processed
L: AT-rich interactive domain-containing protein 1A
M: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
N: SWI/SNF complex subunit SMARCC2
O: SWI/SNF complex subunit SMARCC2
P: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Q: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
R: Zinc finger protein ubi-d4
V: Green fluorescent protein,POU domain, class 5, transcription factor 1
W: Transcription factor SOX-2
X: DNA (148-MER)
Y: DNA (148-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,317,50339
Polymers1,315,83622
Non-polymers1,66717
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 10 types, 15 molecules AEBFCGDHJKLNORV

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15719.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14088.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#6: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 47509.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: O96019
#7: Protein Actin, cytoplasmic 1, N-terminally processed


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: P60709
#8: Protein AT-rich interactive domain-containing protein 1A / ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated ...ARID domain-containing protein 1A / B120 / BRG1-associated factor 250 / BAF250 / BRG1-associated factor 250a / BAF250A / Osa homolog 1 / hOSA1 / SWI-like protein / SWI/SNF complex protein p270 / SWI/SNF-related / matrix-associated / actin-dependent regulator of chromatin subfamily F member 1 / hELD


Mass: 242250.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: O14497
#10: Protein SWI/SNF complex subunit SMARCC2 / BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2


Mass: 133048.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q8TAQ2
#13: Protein Zinc finger protein ubi-d4 / Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D / D4 / zinc and double ...Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D / D4 / zinc and double PHD fingers family 2 / Protein requiem


Mass: 48554.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2, BAF45D, REQ, UBID4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q92785
#14: Protein Green fluorescent protein,POU domain, class 5, transcription factor 1 / Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding ...Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding transcription factor 3 / OTF-3


Mass: 70735.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, POU5F1, OCT3, OCT4, OTF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P42212, UniProt: Q01860

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Transcription ... , 2 types, 2 molecules IW

#5: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 184923.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#15: Protein Transcription factor SOX-2


Mass: 12718.679 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOX2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48431

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SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ

#9: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47 / Integrase interactor 1 protein / SNF5 homolog / hSNF5


Mass: 44199.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q12824
#11: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / 60 kDa BRG-1/Brm-associated factor subunit A / BRG1-associated factor 60A / BAF60A / SWI/SNF ...60 kDa BRG-1/Brm-associated factor subunit A / BRG1-associated factor 60A / BAF60A / SWI/SNF complex 60 kDa subunit


Mass: 58311.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q96GM5
#12: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / BRG1-associated factor 57 / BAF57


Mass: 46710.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q969G3

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DNA chain , 2 types, 2 molecules XY

#16: DNA chain DNA (148-MER)


Mass: 69816.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain DNA (148-MER)


Mass: 70362.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 17 molecules

#18: Chemical
ChemComp-PTD / PENTANEDIAL


Mass: 100.116 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C5H8O2
#19: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1BAF in complex with a OCT4/SOX2-bound nucleosomeCOMPLEX#1-#170MULTIPLE SOURCES
2Nucleosome core particleCOMPLEX#1-#4, #16-#171NATURAL
3BAF complexCOMPLEX#5-#131NATURAL
4OCT4/SOX2 heterodimerCOMPLEX#14-#151RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606HEK293
44Homo sapiens (human)9606
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
7ISOLDEmodel fitting
8PHENIXmodel refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179373 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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