8J90: DDM1-nucleosome complex
Cryo-EM structure of DDM1-nucleosome complex. Determined by electron microscopy at 4.71 Å resolution. Released 3 Jul 2024.
- Method
- Electron microscopy
- Resolution
- 4.71 Å
- Organisms
- Arabidopsis thaliana, synthetic construct
- Chains
- 11
- Atoms
- 13,881
- Mol. weight
- 312.07 kDa
- Released
- 3 Jul 2024
Explore 8J90 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8J90 contains 61 α-helices and 29 β-strands across 9 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: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 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 | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 36-46 | 11 | |
| β-strand | 51-52 | 2 | 4 |
| α-helix | 56-81 | 26 | |
| α-helix | 89-98 | 10 | |
| α-helix | 100-105 | 6 | |
| β-strand | 110-111 | 2 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 63-73 | 11 | |
| α-helix | 81-108 | 28 | |
| β-strand | 113-114 | 2 | 4 |
| α-helix | 116-126 | 11 | |
| α-helix | 129-148 | 20 | |
Chain E: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-78 | 15 | |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 6 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 6 |
| α-helix | 50-75 | 26 | |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 5 |
Chain G: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-46 | 11 | |
| α-helix | 56-82 | 27 | |
| β-strand | 86-87 | 2 | 7 |
| α-helix | 89-98 | 10 | |
| α-helix | 100-105 | 6 | |
| β-strand | 109-111 | 3 | 3 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 63-73 | 11 | |
| β-strand | 78-79 | 2 | 7 |
| α-helix | 81-108 | 28 | |
| α-helix | 116-126 | 11 | |
| α-helix | 129-148 | 20 | |
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 |
|---|
| Histone H3.1 | A, E | protein | 139 | Arabidopsis thaliana | P59226 (AlphaFold model) |
| Histone H4 | B, F | protein | 106 | Arabidopsis thaliana | P59259 (AlphaFold model) |
| HTA6 | C, G | protein | 153 | Arabidopsis thaliana | Q9FJE8 (AlphaFold model) |
| HTB9 | D, H | protein | 153 | Arabidopsis thaliana | O23629 (AlphaFold model) |
| DNA (169-mer) | I | DNA | 169 | synthetic construct | |
| DNA (169-mer) | J | DNA | 169 | synthetic construct | |
| ATP-dependent DNA helicase DDM1 | K | protein | 767 | Arabidopsis thaliana | Q9XFH4 |
Sequence of entity 1 (A, E), FASTA
>8J90_1 Histone H3.1 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8J90_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8J90_3 HTA6 (chains C, G)
GSHMESTGKVKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGA
PVYMAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGGV
LPNINSVLLPKKSATKPAEEKATKSPVKSPKKA
Sequence of entity 4 (D, H), FASTA
>8J90_4 HTB9 (chains D, H)
GSHMAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKK
KSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITS
REIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sequence of entity 5 (I), FASTA
>8J90_5 DNA (169-MER) (chains I)
ATCGGACCCTATCGCGAGCCAGGCCTGAGAATCCGGTGCCGAGGCCGCTCAATTGGTCGT
AGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAA
GGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>8J90_6 DNA (169-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGATTCTCAGGCCTGGCTCGCGATAGGGTCCGAT
Sequence of entity 7 (K), FASTA
>8J90_7 ATP-dependent DNA helicase DDM1 (chains K)
GPHMVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKN
GDSSLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFL
LEKMEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETIN
SDLTEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQT
IGFLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMP
KTVGPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNK
LLLTGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVV
SKLHGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAI
RGQGWKGKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLF
ANNHKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFL
LSTRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETR
VLKRAYSKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDAD
LDRLLDRSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS
Primary citation
Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1. Osakabe, A., Takizawa, Y., Horikoshi, N. et al. Nat Commun (2024) 15:5187-5187. DOI 10.1038/s41467-024-49465-w · 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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