9W6E: Histone H3.1

Cryo-EM structure of a stacked human nucleosome core particle dimer assembled with DNA truncated at SHL-4.5. Determined by electron microscopy at 3.7 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 20
Atoms: 20,759
Mol. weight: 364.48 kDa
Released: 12 Aug 2026

Explore 9W6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W6E contains 68 α-helices and 32 β-strands across 16 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 A: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-76	13
α-helix	86-114	29
β-strand	118-119	2	1
α-helix	121-131	11

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	1
α-helix	50-75	26
α-helix	83-93	11
β-strand	96-97	2	2

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-35	9
β-strand	42-43	2	3
α-helix	46-72	27
β-strand	77-78	2	4
α-helix	80-88	9
α-helix	92-96	5
β-strand	100-102	3	5

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	4
α-helix	56-83	28
β-strand	88-89	2	3
α-helix	91-101	11
α-helix	106-123	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	84-93	10
β-strand	96-98	3	5

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-35	8
β-strand	42-43	2	8
α-helix	46-73	28
β-strand	77-78	2	9
α-helix	80-89	10
α-helix	92-96	5
β-strand	100-101	2	2

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	9
α-helix	58-83	26
β-strand	88-89	2	8
α-helix	91-101	11
α-helix	105-121	17

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1	A, E, K, O	protein	135	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F, L, P	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-D	C, G, M, Q	protein	129	Homo sapiens	P20671 (AlphaFold model)
Histone H2B type 2-E	D, H, N, R	protein	125	Homo sapiens	Q16778 (AlphaFold model)
DNA (119-mer)	I, S	DNA	119	Escherichia coli
DNA (119-mer)	J, T	DNA	119	Escherichia coli

Sequence of entity 1 (A, E, K, O), FASTA

>9W6E_1 Histone H3.1 (chains A, E, K, O)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F, L, P), FASTA

>9W6E_2 Histone H4 (chains B, F, L, P)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G, M, Q), FASTA

>9W6E_3 Histone H2A type 1-D (chains C, G, M, Q)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 4 (D, H, N, R), FASTA

>9W6E_4 Histone H2B type 2-E (chains D, H, N, R)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 5 (I, S), FASTA

>9W6E_5 DNA (119-MER) (chains I, S)
ATCGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTT
TAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 6 (J, T), FASTA

>9W6E_6 DNA (119-MER) (chains J, T)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCGAT

Primary citation

Structural basis for nucleosome stacking diversity mediated by solvent-exposed histone interfaces. Mu, Z., Huang, J. To be published.

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

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