9K42: Histone H3.1
Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with 147bp Widom 601 DNA (C2 symmetry). Determined by electron microscopy at 3.14 Å resolution. Released 14 May 2025.
- Method
- Electron microscopy
- Resolution
- 3.14 Å
- Organism
- Arabidopsis thaliana
- Chains
- 10
- Atoms
- 11,824
- Mol. weight
- 204.46 kDa
- Released
- 14 May 2025
Explore 9K42 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9K42 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.
Chains A and 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 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chains B and F: 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 | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 47-74 | 28 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102-103 | 2 | 6 |
| α-helix | 114-116 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-71 | 11 | |
| β-strand | 76-77 | 2 | 5 |
| α-helix | 79-107 | 29 | |
| β-strand | 111-112 | 2 | 4 |
| α-helix | 114-124 | 11 | |
| α-helix | 127-145 | 19 | |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102-103 | 2 | 3 |
| α-helix | 114-116 | 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 | 127-146 | 20 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 136 | Arabidopsis thaliana | P59226 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Arabidopsis thaliana | P59259 (AlphaFold model) |
| Histone H2A.6 | C, G | protein | 130 | Arabidopsis thaliana | Q9LD28 (AlphaFold model) |
| Histone H2B.1 | D, H | protein | 148 | Arabidopsis thaliana | Q9LQQ4 (AlphaFold model) |
| Widom 601 DNA (147-MER) | I | DNA | 147 | Arabidopsis thaliana | |
| Widom 601 DNA (147-MER) | J | DNA | 147 | Arabidopsis thaliana | |
Sequence of entity 1 (A, E), FASTA
>9K42_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9K42_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9K42_3 Histone H2A.6 (chains C, G)
MAGRGKTLGSGGAKKATSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYL
AAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLLLPK
KAGASKPQED
Sequence of entity 4 (D, H), FASTA
>9K42_4 Histone H2B.1 (chains D, H)
MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEAGDKKKKRSKKNVET
YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQT
AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sequence of entity 5 (I), FASTA
>9K42_5 Widom 601 DNA (147-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT
Sequence of entity 6 (J), FASTA
>9K42_6 Widom 601 DNA (147-MER) (chains J)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG
Primary citation
Structural and functional interrelationships of histone H2A with its variants H2A.Z and H2A.W in Arabidopsis. Wang, Y., Wu, J., Yang, S. et al. Structure (2025) 33:1240. DOI 10.1016/j.str.2025.04.015 · PubMed
Other PDB entries of the same protein (UniProt P59226 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6LQF 1.5 Å, Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide…
- 5YVX 1.59 Å, Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide
- 9M4S 1.6 Å, crystal structure of Arabidopsis thaliana ING2 PHD finger in complex with an H3K4me3…
- 9M4R 1.7 Å, crystal structure of Arabidopsis thaliana ING1 PHD finger in complex with an H3K4me3…
- 7DE9 1.71 Å, crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide
- 5ZWX 1.9 Å, Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide
- 6LQE 1.9 Å, Crystal structure of Arabidopsis ARID5 PHD finger in complex with H3K4me3 peptide
- 5HH7 1.9 Å, crystal structure of Arabidopsis ORC1b BAH-PHD cassette in complex with unmodified H3…
- 5Z8L 2.0 Å, crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide
- 5VBC 2.1 Å, Crystal structure of ATXR5 in complex with histone H3.1
- 8JG4 2.3 Å, Crystal Structure of YAF9A YEATS bound to H3K27cr peptide
- 7YTA 2.31 Å, crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide
Browse structure collections
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