8WH9: DDM1-nucleosome complex in ADP-BeFx state
Structure of DDM1-nucleosome complex in ADP-BeFx state. Determined by electron microscopy at 3.31 Å resolution. Released 17 Apr 2024.
- Method
- Electron microscopy
- Resolution
- 3.31 Å
- Organisms
- Arabidopsis thaliana, synthetic construct
- Chains
- 11
- Atoms
- 15,328
- Mol. weight
- 291.87 kDa
- Ligands
- BEF, ADP
- Released
- 17 Apr 2024
Explore 8WH9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WH9 contains 61 α-helices and 34 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-73 | 10 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 3 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 4 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 5 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 6 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 7 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 5 |
| α-helix | 108-110 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 63-73 | 11 | |
| β-strand | 78-79 | 2 | 7 |
| α-helix | 81-108 | 28 | |
| β-strand | 113-114 | 2 | 6 |
| α-helix | 116-126 | 11 | |
| α-helix | 129-148 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 46-54 | 9 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 4 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 3 |
| α-helix | 121-129 | 9 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| 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 | 8 |
Chain G: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-37 | 10 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 47-73 | 27 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 8 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 63-73 | 11 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-108 | 28 | |
| β-strand | 113-114 | 2 | 9 |
| α-helix | 117-126 | 10 | |
| α-helix | 129-147 | 19 | |
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 | 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.6 | D, H | protein | 150 | Arabidopsis thaliana | O23629 (AlphaFold model) |
| DNA (sense strand) | I | DNA | 147 | synthetic construct | |
| DNA (antisense strand) | J | DNA | 147 | synthetic construct | |
| ATP-dependent DNA helicase DDM1 | K | protein | 765 | Arabidopsis thaliana | Q9XFH4 |
Sequence of entity 1 (A, E), FASTA
>8WH9_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8WH9_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8WH9_3 Histone H2A.6 (chains C, G)
MAGRGKTLGSGGAKKATSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYL
AAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLLLPK
KAGASKPQED
Sequence of entity 4 (D, H), FASTA
>8WH9_4 Histone H2B.6 (chains D, H)
MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSV
ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREI
QTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sequence of entity 5 (I), FASTA
>8WH9_5 DNA (sense strand) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTAACCGCCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>8WH9_6 DNA (antisense strand) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGGCGGTTA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 7 (K), FASTA
>8WH9_7 ATP-dependent DNA helicase DDM1 (chains K)
SMVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKNGD
SSLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFLLE
KMEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETINSD
LTEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQTIG
FLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMPKT
VGPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNKLL
LTGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVVSK
LHGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAIRG
QGWKGKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLFAN
NHKVLIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLS
TRAGGLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVL
KRAYSKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDADLD
RLLDRSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
Primary citation
Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. Liu, Y., Zhang, Z., Hu, H. et al. Nat Plants (2024) 10:374-380. DOI 10.1038/s41477-024-01640-z · 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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