1AOI: Histone H3
Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment. Determined by X-ray diffraction at 2.8 Å resolution. Released 30 Sept 1998.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organism
- Xenopus laevis
- Chains
- 10
- Atoms
- 12,385
- Mol. weight
- 184.55 kDa
- Ligands
- MN
- Released
- 30 Sept 1998
Explore 1AOI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1AOI 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 | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| 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 | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 6 |
| α-helix | 113-115 | 3 | |
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 | 101-119 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| 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 | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Palindromic 146 bp DNA repeat 8/9 from human X-chromosome alpha satellite DNA | I, J | DNA | 146 | | |
| Histone H3 | A, E | protein | 116 | Xenopus laevis | P02302 (AlphaFold model) |
| Histone H4 | B, F | protein | 87 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 116 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B | D, H | protein | 99 | Xenopus laevis | P02281 (AlphaFold model) |
Sequence of entity 1 (I, J), FASTA
>1AOI_1 PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
Sequence of entity 2 (A, E), FASTA
>1AOI_2 HISTONE H3 (chains A, E)
LATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK
TDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 3 (B, F), FASTA
>1AOI_3 HISTONE H4 (chains B, F)
KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH
AKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (C, G), FASTA
>1AOI_4 HISTONE H2A (chains C, G)
GKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEIL
ELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
Sequence of entity 5 (D, H), FASTA
>1AOI_5 HISTONE H2B (chains D, H)
KKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKR
STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MN | Manganese (II) ion | Mn | 6 |
Primary citation
Crystal structure of the nucleosome core particle at 2.8 A resolution. Luger, K., Mader, A.W., Richmond, R.K. et al. Nature (1997) 389:251-260. DOI 10.1038/38444 · PubMed
Other PDB entries of the same protein (UniProt P02302 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
- 1M18 2.45 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 1M1A 2.65 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
- 8ETV 3.16 Å, Class2 of the INO80-Hexasome complex
- 8U5H 3.23 Å, Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
- 6PX1 3.3 Å, Set2 bound to nucleosome
- 8DU4 3.55 Å, Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
- 7M1X 3.7 Å, Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
- 6NZO 3.8 Å, Set2 bound to nucleosome
- 6PX3 4.1 Å, Set2 bound to nucleosome
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