9MLS: GammaH2AX containing nucleosome, Extended
GammaH2AX containing nucleosome, Extended (Class 3). Determined by electron microscopy at 3.6 Å resolution. Released 29 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 10
- Atoms
- 10,104
- Mol. weight
- 211.42 kDa
- Released
- 29 Oct 2025
Explore 9MLS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9MLS contains 37 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 | 41-42 | 2 | |
| α-helix | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 6 |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-120 | 20 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 119 | 1 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 82 | 1 | |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 6 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 | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 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 (107-mer) | I | DNA | 145 | synthetic construct | |
| DNA (107-mer) | J | DNA | 145 | synthetic construct | |
Sequence of entity 1 (A, E), FASTA
>9MLS_1 Histone H3.1 (chains A, E)
MGSSHHHHHHSQDPENLYFQGMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKP
HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEA
YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9MLS_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9MLS_3 Histone H2AX (chains C, G)
MGSSHHHHHHSQDPENLYFQGMSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGH
YAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLG
GVTIAQGGVLPNIQAVLLPKKTSATVGPKAPSGGKKAEQDSQEY
Sequence of entity 4 (D, H), FASTA
>9MLS_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I), FASTA
>9MLS_5 DNA (107-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 6 (J), FASTA
>9MLS_6 DNA (107-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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