9K46: Histone H3.3
Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry). Determined by electron microscopy at 2.85 Å resolution. Released 12 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 2.85 Å
- Organism
- Arabidopsis thaliana
- Chains
- 10
- Atoms
- 11,844
- Mol. weight
- 209.35 kDa
- Released
- 12 Nov 2025
Explore 9K46 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9K46 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 | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-130 | 10 | |
Chains B and 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 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 36-45 | 10 | |
| β-strand | 51-52 | 2 | 4 |
| α-helix | 56-81 | 26 | |
| β-strand | 86-87 | 2 | 5 |
| α-helix | 89-97 | 9 | |
| α-helix | 100-105 | 6 | |
| β-strand | 109-111 | 3 | 6 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-58 | 3 | |
| α-helix | 61-71 | 11 | |
| β-strand | 76-77 | 2 | 5 |
| α-helix | 79-106 | 28 | |
| β-strand | 111-112 | 2 | 4 |
| α-helix | 114-124 | 11 | |
| α-helix | 128-146 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-30 | 5 | |
| α-helix | 36-45 | 10 | |
| β-strand | 51-52 | 2 | 9 |
| α-helix | 56-81 | 26 | |
| β-strand | 86-87 | 2 | 10 |
| α-helix | 89-97 | 9 | |
| α-helix | 100-105 | 6 | |
| β-strand | 109-111 | 3 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-71 | 11 | |
| β-strand | 76-77 | 2 | 10 |
| α-helix | 79-106 | 28 | |
| β-strand | 111-112 | 2 | 9 |
| α-helix | 114-124 | 11 | |
| α-helix | 128-146 | 19 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.3 | A, E | protein | 136 | Arabidopsis thaliana | P59169 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Arabidopsis thaliana | P59259 (AlphaFold model) |
| Probable histone H2A.7 | C, G | protein | 150 | Arabidopsis thaliana | Q9FJE8 (AlphaFold model) |
| Histone H2B.1 | D, H | protein | 148 | Arabidopsis thaliana | Q9LQQ4 (AlphaFold model) |
| 15.2.2 DNA (147-mer) | I | DNA | 147 | Arabidopsis thaliana | |
| 15.2.2 DNA (147-mer) | J | DNA | 147 | Arabidopsis thaliana | |
Sequence of entity 1 (A, E), FASTA
>9K46_1 Histone H3.3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9K46_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9K46_3 Probable histone H2A.7 (chains C, G)
MESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVY
MAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGVLPN
INSVLLPKKSATKPAEEKATKSPVKSPKKA
Sequence of entity 4 (D, H), FASTA
>9K46_4 Histone H2B.1 (chains D, H)
MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEAGDKKKKRSKKNVET
YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQT
AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sequence of entity 5 (I), FASTA
>9K46_5 15.2.2 DNA (147-MER) (chains I)
ACCTTTATTGACTCCATAATTGACCAATTGAGCGGCTCGATTCAACTGTCAATAACTTCA
AATGAAGCAAGAGCCTTATCGTATTCTCCGCACGATGGTGCTTTAATCCACCGCAACTTT
CCTCTTTAATAAAGGCACAAGCATTAA
Sequence of entity 6 (J), FASTA
>9K46_6 15.2.2 DNA (147-MER) (chains J)
TTAATGCTTGTGCCTTTATTAAAGAGGAAAGTTGCGGTGGATTAAAGCACCATCGTGCGG
AGAATACGATAAGGCTCTTGCTTCATTTGAAGTTATTGACAGTTGAATCGAGCCGCTCAA
TTGGTCAATTATGGAGTCAATAAAGGT
Primary citation
Functional redundancy of core histone H2A and its variants in Arabidopsis. Wang, Y., Dong, A. To be published.
Other PDB entries of the same protein (UniProt P59169 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4PLI 1.65 Å, Structure of the chromodomain of MRG2 in complex with H3K36me3
- 4PL6 1.68 Å, Structure of the chromodomain of MRG2 in complex with H3K4me3
- 8XAG 1.75 Å, Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone…
- 4PLL 2.6 Å, Structure of the chromodaomain of MRG2 in complex with H3K36me3
- 9K45 2.71 Å, Cryo-EM structure of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native…
- 7UX9 3.2 Å, Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA)
- 9K44 3.22 Å, Cryo-EM structure of Arabidopsis thaliana H2A-H3.3-nucleosome with Arabidopsis native…
Browse structure collections
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