9WC0: NCP-RA module of ncBAF-nucleosome complex

The structure of NCP-RA module of ncBAF-nucleosome complex. Determined by electron microscopy at 2.4 Å resolution. Released 18 Feb 2026.

Method: Electron microscopy
Resolution: 2.4 Å
Organisms: Xenopus laevis, synthetic construct, Homo sapiens
Chains: 11
Atoms: 12,431
Mol. weight: 259.43 kDa
Released: 18 Feb 2026

Explore 9WC0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9WC0 contains 37 α-helices and 20 β-strands across 9 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	31-40	10
β-strand	45-46	2	1
α-helix	50-75	26
β-strand	80-81	2	2
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-123	19

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3

Chain K: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-48	4
α-helix	49-52	4
α-helix	64-78	15
β-strand	83-84	2	2
α-helix	86-113	28
β-strand	118-119	2	1
α-helix	121-131	11

Chain O: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	129	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B 1.1	D, H	protein	125	Xenopus laevis	P02281 (AlphaFold model)
Histone H3.2	E, K	protein	135	Xenopus laevis	P84233 (AlphaFold model)
DNA (207-mer)	I	DNA	207	synthetic construct
DNA (207-mer)	J	DNA	207	synthetic construct
B-cell CLL/lymphoma 7 protein family member A	O	protein	210	Homo sapiens	Q4VC05

Sequence of entity 1 (B, F), FASTA

>9WC0_1 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 2 (C, G), FASTA

>9WC0_2 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 3 (D, H), FASTA

>9WC0_3 Histone H2B 1.1 (chains D, H)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 4 (E, K), FASTA

>9WC0_4 Histone H3.2 (chains E, K)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 5 (I), FASTA

>9WC0_5 DNA (207-MER) (chains I)
GGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGAATCACCCCACGAA
GTACTAGAGGATCATAATCAGCCATAC

Sequence of entity 6 (J), FASTA

>9WC0_6 DNA (207-MER) (chains J)
GTATGGCTGATTATGATCCTCTAGTACTTCGTGGGGTGATTCAGGATGTATATATCTGAC
ACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTA
CGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGAT
TCTCCAGGGCGGCCGCGTATAGGGTCC

Sequence of entity 7 (O), FASTA

>9WC0_7 B-cell CLL/lymphoma 7 protein family member A (chains O)
MSGRSVRAETRSRAKDDIKRVMAAIEKVRKWEKKWVTVGDTSLRIYKWVPVTEPKVDDKN
KNKKKGKDEKCGSEVTTPENSSSPGMMDMHDDNSNQSSIADASPIKQENSSNSSPAPEPN
SAVPSDGTEAKVDEAQADGKEHPGAEDASDEQNSQSSMEHSMNSSEKVDRQPSGDSGLAA
ETSAISQDLEGVPPSKKMKLEASQQNSEEM

Primary citation

ncBAF recognizes the nucleosome through BCL7A in chromatin remodeling. Chen, K., Du, L., Liu, Y. et al. Cell Discov (2025) 11:102-102. DOI 10.1038/s41421-025-00858-1 · PubMed

Other PDB entries of the same protein (UniProt P62799 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
4ZBJ 2.25 Å, UBN1 peptide bound to H3.3/H4/Asf1
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA

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