9MU5: Histone H2A
Structure of a native Drosophila melanogaster hexameric nucleosome. Determined by electron microscopy at 6.3 Å resolution. Released 19 Feb 2025.
- Method
- Electron microscopy
- Resolution
- 6.3 Å
- Organism
- Drosophila melanogaster
- Chains
- 8
- Atoms
- 9,666
- Mol. weight
- 143.99 kDa
- Released
- 19 Feb 2025
Explore 9MU5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9MU5 contains 24 α-helices and 14 β-strands across 6 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-50 | 5 | |
| α-helix | 65-79 | 15 | |
| β-strand | 84-85 | 2 | 4 |
| α-helix | 87-114 | 28 | |
| β-strand | 119 | 1 | 5 |
| 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 | 1 | 5 |
| α-helix | 51-75 | 25 | |
| β-strand | 81-82 | 2 | 4 |
| α-helix | 84-93 | 10 | |
| β-strand | 97-99 | 3 | 3 |
Chain e: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-79 | 15 | |
| β-strand | 84-85 | 2 | 6 |
| α-helix | 87-114 | 28 | |
| β-strand | 119 | 1 | 7 |
| α-helix | 122-132 | 11 | |
Chain f: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46 | 1 | 7 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 6 |
| α-helix | 84-93 | 10 | |
Chain g: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 1 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 2 |
| α-helix | 80-87 | 8 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
Chain h: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-46 | 11 | |
| β-strand | 51-52 | 2 | 2 |
| α-helix | 54-81 | 28 | |
| β-strand | 86-87 | 2 | 1 |
| α-helix | 89-99 | 11 | |
| α-helix | 103-121 | 19 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H2A | g | protein | 105 | Drosophila melanogaster | P84051 (AlphaFold model) |
| Histone H2B | h | protein | 97 | Drosophila melanogaster | P02283 (AlphaFold model) |
| Histone H3 | a, e | protein | 92 | Drosophila melanogaster | P02299 (AlphaFold model) |
| Histone H4 | b, f | protein | 80 | Drosophila melanogaster | P84040 (AlphaFold model) |
| DNA (133-mer) | N | DNA | 133 | Drosophila melanogaster | |
| DNA (133-mer) | T | DNA | 133 | Drosophila melanogaster | |
Sequence of entity 1 (g), FASTA
>9MU5_1 Histone H2A (chains g)
AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN
KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPK
Sequence of entity 2 (h), FASTA
>9MU5_2 Histone H2B (chains h)
KKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRST
ITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sequence of entity 3 (a, e), FASTA
>9MU5_3 Histone H3 (chains a, e)
GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGL
FEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 4 (b, f), FASTA
>9MU5_4 Histone H4 (chains b, f)
RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVT
AMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (N), FASTA
>9MU5_5 DNA (133-MER) (chains N)
CCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGC
GTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTTA
TATATATATATAT
Sequence of entity 6 (T), FASTA
>9MU5_6 DNA (133-MER) (chains T)
ATATATATATATATAAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTA
GCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTC
CCTAGTCTCCAGG
Primary citation
Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster. Venette-Smith, N.L., Vishwakarma, R.K., Venkatakrishnan, V. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-75963-0 · PubMed
Other PDB entries of the same protein (UniProt P84051 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
- 2NQB 2.3 Å, Drosophila Nucleosome Structure
- 9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
- 2PYO 2.43 Å, Drosophila nucleosome core
- 8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
- 8PP7 2.91 Å, human RYBP-PRC1 bound to mononucleosome
- 6DZT 2.99 Å, Cryo-EM structure of nucleosome in complex with a single chain antibody fragment
- 8PP6 3.18 Å, human RYBP-PRC1 bound to H2AK118ub1 nucleosome
- 9ZQA 3.28 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2
- 9MU4 3.29 Å, Structure of a native Drosophila melanogaster octameric nucleosome
- 9ZQ9 3.3 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1
- 4X23 3.5 Å, Crystal structure of cenp-C in complex with the nucleosome core particle
Browse structure collections
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