9PM0: Nucleosome containing histone variant macroH2A
nucleosome containing histone variant macroH2A. Determined by electron microscopy at 2.9 Å resolution. Released 24 Jun 2026.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Homo sapiens, Xenopus laevis, synthetic construct
- Chains
- 12
- Atoms
- 15,610
- Mol. weight
- 302.47 kDa
- Released
- 24 Jun 2026
Explore 9PM0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9PM0 contains 48 α-helices and 67 β-strands across 10 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: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-19 | 5 | |
| α-helix | 25-35 | 11 | |
| β-strand | 40-41 | 2 | 1 |
| α-helix | 45-70 | 26 | |
| α-helix | 78-86 | 9 | |
| α-helix | 91-94 | 4 | |
| β-strand | 99 | 1 | 2 |
| α-helix | 111-114 | 4 | |
Chain B: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-49 | 10 | |
| α-helix | 58-84 | 27 | |
| β-strand | 89-90 | 2 | 1 |
| α-helix | 92-100 | 9 | |
| α-helix | 110-124 | 15 | |
Chains C and G: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-50 | 4 | |
| α-helix | 52-57 | 6 | |
| α-helix | 65-79 | 15 | |
| β-strand | 84-85 | 2 | 5 |
| α-helix | 87-113 | 27 | |
| β-strand | 119 | 1 | 6 |
| α-helix | 122-124 | 3 | |
| α-helix | 125-132 | 8 | |
Chain D: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-42 | 10 | |
| β-strand | 46 | 1 | 6 |
| α-helix | 52-62 | 11 | |
| α-helix | 67-75 | 9 | |
| β-strand | 81-82 | 2 | 5 |
| α-helix | 85-90 | 6 | |
| α-helix | 97 | 1 | |
| β-strand | 98 | 1 | 2 |
| α-helix | 99 | 1 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-35 | 10 | |
| β-strand | 40-41 | 2 | 3 |
| α-helix | 46-70 | 25 | |
| α-helix | 78-86 | 9 | |
| α-helix | 91-94 | 4 | |
| β-strand | 99 | 1 | 4 |
| α-helix | 111-114 | 4 | |
Chain F: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-47 | 8 | |
| α-helix | 60-84 | 25 | |
| β-strand | 89-90 | 2 | 3 |
| α-helix | 92-100 | 9 | |
| α-helix | 110-113 | 4 | |
| α-helix | 116-124 | 9 | |
Chain H: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-42 | 10 | |
| β-strand | 46 | 1 | 8 |
| α-helix | 52-62 | 11 | |
| α-helix | 63-65 | 3 | |
| α-helix | 67-76 | 10 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 85-94 | 10 | |
| α-helix | 97 | 1 | |
| β-strand | 98 | 1 | 4 |
| α-helix | 99 | 1 | |
Chain M: 2 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-23 | 4 | |
| β-strand | 24-25 | 2 | 9 |
| β-strand | 31 | 1 | 10 |
| β-strand | 38-41 | 4 | 11 |
| β-strand | 42-43 | 2 | 9 |
| β-strand | 52-57 | 6 | 12 |
| β-strand | 64-68 | 5 | 12 |
| β-strand | 72 | 1 | 12 |
| β-strand | 81-84 | 4 | 11 |
| β-strand | 91-94 | 4 | 11 |
| β-strand | 104-109 | 6 | 12 |
| β-strand | 121-122 | 2 | 12 |
| β-strand | 124 | 1 | 10 |
| β-strand | 152-155 | 4 | 13 |
| β-strand | 159-161 | 3 | 14 |
| β-strand | 167-168 | 2 | 15 |
| β-strand | 171-174 | 4 | 13 |
| β-strand | 182-188 | 7 | 16 |
| β-strand | 194-201 | 8 | 16 |
| β-strand | 206-209 | 4 | 16 |
| β-strand | 217-220 | 4 | 15 |
| β-strand | 227 | 1 | 13 |
| β-strand | 229-232 | 4 | 15 |
| α-helix | 237-239 | 3 | |
| β-strand | 242-248 | 7 | 16 |
| β-strand | 263-264 | 2 | 16 |
| β-strand | 265-267 | 3 | 14 |
1 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 |
|---|
| Core histone macro-H2A.1 | A, E | protein | 161 | Homo sapiens | O75367 (AlphaFold model) |
| Histone H2B 1.1 | B, F | protein | 125 | Xenopus laevis | P02281 (AlphaFold model) |
| Histone H3.2 | C, G | protein | 135 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | D, H | protein | 102 | Xenopus laevis | P62799 (AlphaFold model) |
| DNA Widom601 (208bp) strand1 | I | DNA | 208 | synthetic construct | |
| DNA Widom601 (208bp) strand2 | J | DNA | 208 | synthetic construct | |
| scFv20 | M, N | protein | 270 | Mus musculus | |
Sequence of entity 1 (A, E), FASTA
>9PM0_1 Core histone macro-H2A.1 (chains A, E)
MSSRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEI
LELAGNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRGS
KGKLEAIITPPPAKKAKSPSQKKPVSKKAGGKKGARKSKKK
Sequence of entity 2 (B, F), FASTA
>9PM0_2 Histone H2B 1.1 (chains B, F)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK
Sequence of entity 3 (C, G), FASTA
>9PM0_3 Histone H3.2 (chains C, G)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 4 (D, H), FASTA
>9PM0_4 Histone H4 (chains D, H)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (I), FASTA
>9PM0_5 DNA Widom601 (208bp) strand1 (chains I)
ACTTATGTGATGGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCA
ATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTT
AACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGC
ATGTATTGAACAGCGACCTTGCCGGAGT
Sequence of entity 6 (J), FASTA
>9PM0_6 DNA Widom601 (208bp) strand2 (chains J)
ACTCCGGCAAGGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGG
AGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTA
AGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGC
GGCCGCGTATAGGGTCCATCACATAAGT
Sequence of entity 7 (M, N), FASTA
>9PM0_7 scFv20 (chains M, N)
MKSSHHHHHHENLYFQSNAMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWYQQKP
WKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPYTFGS
GTKLEIKRAGGGGSGGGGSGGGGSGGGGSMEVQLQQSGPELVEPGTSVKMPCKASGYTFT
SYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSED
SAVYYCARKSSRLRSTLDYWGQGTSVTVSS
Primary citation
nucleosome containing histone variant macroH2A. Tan, D., Sokolova, V. To be published.
Other PDB entries of the same protein (UniProt O75367 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3HSV 1.43 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
- 1ZR3 1.66 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form B)
- 3IVB 1.75 Å, Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3…
- 3IID 1.9 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
- 3IIF 2.1 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
- 5IIT 2.13 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
- 3HQH 2.3 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
- 2FXK 2.54 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form A)
- 2F8N 2.9 Å, 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
- 1ZR5 2.92 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.2
- 1U35 3.0 Å, Crystal structure of the nucleosome core particle containing the histone domain of…
- 7D3Y 3.11 Å, Crystal structure of the osPHR2-osSPX2 complex
Browse structure collections
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