9W6O: Histone H3.1
Cryo-EM structure of a stacked human nucleosome core particle dimer (type 6, top NCP) assembled with DNA truncated at SHL-5.5. Determined by electron microscopy at 4.08 Å resolution. Released 12 Aug 2026.
- Method
- Electron microscopy
- Resolution
- 4.08 Å
- Organisms
- Homo sapiens, Escherichia coli
- Chains
- 10
- Atoms
- 10,846
- Mol. weight
- 188.42 kDa
- Released
- 12 Aug 2026
Explore 9W6O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9W6O contains 33 α-helices and 14 β-strands across 8 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, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45 | 1 | 2 |
| α-helix | 49-76 | 28 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 96-97 | 2 | 3 |
Chain C: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-35 | 9 | |
| α-helix | 46-70 | 25 | |
| α-helix | 80-89 | 10 | |
| α-helix | 94-96 | 3 | |
| β-strand | 100 | 1 | 4 |
Chain D: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-47 | 10 | |
| α-helix | 57-83 | 27 | |
| α-helix | 91-101 | 11 | |
| α-helix | 105-122 | 18 | |
Chain E: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 5 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| α-helix | 51-75 | 25 | |
| β-strand | 80 | 1 | 5 |
| α-helix | 83-93 | 11 | |
| β-strand | 96 | 1 | 4 |
Chain G: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 6 |
| α-helix | 46-72 | 27 | |
| β-strand | 77 | 1 | 7 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-48 | 9 | |
| β-strand | 53 | 1 | 7 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 6 |
| α-helix | 91-100 | 10 | |
| α-helix | 105-121 | 17 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 135 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-D | C, G | protein | 129 | Homo sapiens | P20671 (AlphaFold model) |
| Histone H2B type 2-E | D, H | protein | 125 | Homo sapiens | Q16778 (AlphaFold model) |
| DNA (129-mer) | I | DNA | 129 | Escherichia coli | |
| DNA (129-mer) | J | DNA | 129 | Escherichia coli | |
Sequence of entity 1 (A, E), FASTA
>9W6O_1 Histone H3.1 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9W6O_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9W6O_3 Histone H2A type 1-D (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>9W6O_4 Histone H2B type 2-E (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK
Sequence of entity 5 (I), FASTA
>9W6O_5 DNA (129-MER) (chains I)
ATCCGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCG
TACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGG
ATTCTCGAT
Sequence of entity 6 (J), FASTA
>9W6O_6 DNA (129-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGGAT
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
Browse structure collections
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