9MMK: H2AX containing nucleosome, Canonical
H2AX containing nucleosome, Canonical (Class 1). Determined by electron microscopy at 3.2 Å resolution. Released 29 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 10
- Atoms
- 11,806
- Mol. weight
- 211.42 kDa
- Released
- 29 Oct 2025
Explore 9MMK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9MMK contains 39 α-helices and 20 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 | 42-43 | 2 | |
| α-helix | 46-55 | 10 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 1 |
| α-helix | 87-113 | 27 | |
| β-strand | 119-120 | 2 | 2 |
| α-helix | 122-132 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 84-93 | 10 | |
| β-strand | 98-99 | 2 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-15 | 3 | |
| α-helix | 18-22 | 5 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-89 | 9 | |
| α-helix | 94-97 | 4 | |
| β-strand | 101-103 | 3 | 6 |
| α-helix | 114-116 | 3 | |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| β-strand | 54-55 | 2 | 5 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 92-102 | 11 | |
| α-helix | 105-124 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-43 | 2 | |
| α-helix | 46-57 | 12 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 7 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 8 |
| α-helix | 122-132 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-29 | 5 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 8 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-99 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-15 | 3 | |
| α-helix | 18-22 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-72 | 25 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-89 | 9 | |
| α-helix | 94-97 | 4 | |
| β-strand | 102-103 | 2 | 3 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 157 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2AX | C, G | protein | 164 | Homo sapiens | P16104 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (143-mer) | I | DNA | 145 | synthetic construct | |
| DNA (143-mer) | J | DNA | 145 | synthetic construct | |
Sequence of entity 1 (A, E), FASTA
>9MMK_1 Histone H3.1 (chains A, E)
MGSSHHHHHHSQDPENLYFQGMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKP
HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEA
YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9MMK_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9MMK_3 Histone H2AX (chains C, G)
MGSSHHHHHHSQDPENLYFQGMSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGH
YAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLG
GVTIAQGGVLPNIQAVLLPKKTSATVGPKAPSGGKKAEQDSQEY
Sequence of entity 4 (D, H), FASTA
>9MMK_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I), FASTA
>9MMK_5 DNA (143-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J), FASTA
>9MMK_6 DNA (143-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT
Primary citation
Structural insights into gamma H2Ax containing nucleosomes. Panigrahi, R., Edwards, R., Islam, M.T. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf1028 · PubMed
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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