9MLR: GammaH2AX containing nucleosome, Half-wrapped

GammaH2AX containing nucleosome, Half-wrapped (Class 2). Determined by electron microscopy at 3.1 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 10
Atoms: 11,077
Mol. weight: 211.42 kDa
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9MLR contains 38 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	46-57	12
α-helix	65-76	12
β-strand	84-85	2	1
α-helix	87-114	28
β-strand	119-120	2	2
α-helix	122-132	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
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: 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	4
α-helix	47-73	27
β-strand	78-79	2	5
α-helix	81-90	10
α-helix	94-97	4
β-strand	102-103	2	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	5
α-helix	54-81	28
β-strand	86-87	2	4
α-helix	89-99	11
α-helix	102-121	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	120	1	8
α-helix	122-131	10

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
α-helix	32-41	10
β-strand	47	1	8
α-helix	51-76	26
β-strand	81-82	2	7
α-helix	83	1
α-helix	84-93	10
β-strand	98-99	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	28-36	9
β-strand	43-44	2	9
α-helix	48-73	26
β-strand	78-79	2	10
α-helix	81-89	9
α-helix	94-97	4
β-strand	102-103	2	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	10
α-helix	54-81	28
β-strand	86-87	2	9
α-helix	89-99	11
α-helix	102-122	21

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 (126-mer)	I	DNA	145	synthetic construct
DNA (126-mer)	J	DNA	145	synthetic construct

Sequence of entity 1 (A, E), FASTA

>9MLR_1 Histone H3.1 (chains A, E)
MGSSHHHHHHSQDPENLYFQGMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKP
HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEA
YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9MLR_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9MLR_3 Histone H2AX (chains C, G)
MGSSHHHHHHSQDPENLYFQGMSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGH
YAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLG
GVTIAQGGVLPNIQAVLLPKKTSATVGPKAPSGGKKAEQDSQEY

Sequence of entity 4 (D, H), FASTA

>9MLR_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Sequence of entity 5 (I), FASTA

>9MLR_5 DNA (126-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT

Sequence of entity 6 (J), FASTA

>9MLR_6 DNA (126-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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