9TG1 | pdb_00009tg1

Structure of endogenous human ncBAF bound to nucleosome

PDB DOI: https://doi.org/10.2210/pdb9TG1/pdb
EM Map EMD-55887: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens, Xenopus laevis, unidentified plasmid
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-11-28 Released: 2026-11-04
Deposition Author(s): Arias Pinto, C., Guan, Y., Concordet, J.P., Ben-Shem, A., Papai, G.
Funding Organization(s): La ligue contre le cancer

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.75 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Insight into mechanism and vulnerability from structure of endogenous human non-canonical BAF bound to nucleosome

Arias Pinto, C., Guan, Y., Brion, A., Werderer, M., Forciniti, C., Schnitzler, C., Eberling, P., Crucifix, C., Poterszman, A., Schultz, P., Concordet, J.P., Papai, G., Ben-Shem, A.

To be published.

Macromolecule Content

Total Structure Weight: 555.33 kDa
Atom Count: 23,460
Modeled Residue Count: 2,516
Deposited Residue Count: 4,510
Unique protein chains: 9
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription activator BRG1	A [auth K]	1,647	Homo sapiens	Mutation(s): 0 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51532 (Homo sapiens) Explore P51532 Go to UniProtKB: P51532
PHAROS: P51532 GTEx: ENSG00000127616
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51532
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	B [auth A], F [auth E]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C [auth B], G [auth F]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	D [auth C], H [auth G]	130	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	E [auth D], I [auth H]	126	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	L	597	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens) Explore Q9H8M2 Go to UniProtKB: Q9H8M2
PHAROS: Q9H8M2 GTEx: ENSG00000028310
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H8M2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell CLL/lymphoma 7 protein family member A	M [auth O]	210	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q4VC05 (Homo sapiens) Explore Q4VC05 Go to UniProtKB: Q4VC05
PHAROS: Q4VC05 GTEx: ENSG00000110987
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4VC05
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, cytoplasmic 1, N-terminally processed	N [auth M]	375	Homo sapiens	Mutation(s): 0 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens) Explore P60709 Go to UniProtKB: P60709
PHAROS: P60709 GTEx: ENSG00000075624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60709
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-like protein 6A	O [auth N]	429	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O96019 (Homo sapiens) Explore O96019 Go to UniProtKB: O96019
PHAROS: O96019 GTEx: ENSG00000136518
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O96019
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Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
DNA (131-MER)	J [auth I]	131	unidentified plasmid
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
DNA (131-MER)	K [auth J]	131	unidentified plasmid
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain P [auth K] MOL2 format, chain P [auth K] mmCIF format, chain P [auth K]	P [auth K]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain P [auth K] Interactions & Density Focus chain P [auth K]
BEF Query on BEF Download:Ideal Coordinates CCD File SDF format, chain R [auth K] MOL2 format, chain R [auth K] mmCIF format, chain R [auth K]	R [auth K]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain R [auth K] Interactions & Density Focus chain R [auth K]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth K] MOL2 format, chain Q [auth K] mmCIF format, chain Q [auth K]	Q [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth K] Interactions & Density Focus chain Q [auth K]