8SKZ: DDM1-HELLS chimera
Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome. Determined by electron microscopy at 3.5 Å resolution. Released 20 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organisms
- Arabidopsis thaliana, Homo sapiens, Xenopus laevis
- Chains
- 11
- Atoms
- 17,251
- Mol. weight
- 323.87 kDa
- Ligands
- BEF, ADP
- Released
- 20 Nov 2024
Explore 8SKZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8SKZ contains 84 α-helices and 37 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: 40 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 182-193 | 12 | |
| α-helix | 201-203 | 3 | |
| α-helix | 204-218 | 15 | |
| β-strand | 223-225 | 3 | 1 |
| α-helix | 227-228 | 2 | |
| α-helix | 233-246 | 14 | |
| β-strand | 253-256 | 4 | 1 |
| α-helix | 259-261 | 3 | |
| α-helix | 262-272 | 11 | |
| β-strand | 278-280 | 3 | 1 |
| α-helix | 285-295 | 11 | |
| α-helix | 304-305 | 2 | |
| β-strand | 306-309 | 4 | 1 |
| α-helix | 311-316 | 6 | |
| α-helix | 322-324 | 3 | |
| β-strand | 329-332 | 4 | 1 |
| α-helix | 335-338 | 4 | |
| α-helix | 345-348 | 4 | |
| α-helix | 349-351 | 3 | |
| β-strand | 357-360 | 4 | 1 |
| α-helix | 370-379 | 10 | |
| α-helix | 387-392 | 6 | |
| α-helix | 408-424 | 17 | |
| α-helix | 425-427 | 3 | |
| β-strand | 428-429 | 2 | 1 |
| α-helix | 433-436 | 4 | |
| β-strand | 443-450 | 8 | 2 |
| α-helix | 454-465 | 12 | |
| α-helix | 468-472 | 5 | |
| β-strand | 482 | 1 | 3 |
| α-helix | 487 | 1 | |
| β-strand | 488 | 1 | 3 |
| α-helix | 489-490 | 2 | |
| α-helix | 543-552 | 10 | |
| α-helix | 554-556 | 3 | |
| β-strand | 566 | 1 | 4 |
| α-helix | 570-576 | 7 | |
| α-helix | 578-591 | 14 | |
| β-strand | 597-601 | 5 | 2 |
| α-helix | 604-617 | 14 | |
| β-strand | 622-624 | 3 | 2 |
| α-helix | 630-641 | 12 | |
| β-strand | 649-653 | 5 | 2 |
| α-helix | 654-657 | 4 | |
| β-strand | 668-671 | 4 | 2 |
| α-helix | 678-685 | 8 | |
| α-helix | 686-688 | 3 | |
| β-strand | 697-704 | 8 | 2 |
| α-helix | 708-718 | 11 | |
| α-helix | 720-726 | 7 | |
| α-helix | 760-763 | 4 | |
| α-helix | 765-768 | 4 | |
| α-helix | 769-775 | 7 | |
| α-helix | 779-781 | 3 | |
| α-helix | 783-785 | 3 | |
| α-helix | 788-793 | 6 | |
| β-strand | 798-799 | 2 | 2 |
| β-strand | 802-804 | 3 | 2 |
Chain B: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 5 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 6 |
| α-helix | 121-131 | 11 | |
Chain C: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 8 |
| α-helix | 113-115 | 3 | |
| α-helix | 117-118 | 2 | |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 7 |
| α-helix | 53-80 | 28 | |
| α-helix | 88-98 | 11 | |
| α-helix | 102-119 | 18 | |
Chain E: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-39 | 3 | |
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 65-75 | 11 | |
| β-strand | 83-84 | 2 | 9 |
| α-helix | 88-112 | 25 | |
| β-strand | 118-119 | 2 | 10 |
| α-helix | 121-131 | 11 | |
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 | 10 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 9 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 8 |
Chain G: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 11 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 12 |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 13 |
| α-helix | 113-115 | 3 | |
| α-helix | 117-118 | 2 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-42 | 8 | |
| β-strand | 50-51 | 2 | 12 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 11 |
| α-helix | 88-98 | 11 | |
| α-helix | 103-119 | 17 | |
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 |
|---|
| ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera | A | protein | 821 | Arabidopsis thaliana, Homo sapiens | Q9NRZ9 (AlphaFold model), Q9XFH4 (AlphaFold model) |
| Histone H3.2 | B, E | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H2A | C, G | protein | 133 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 123 | Xenopus laevis | P02281 |
| Histone H4 | F, I | protein | 110 | Xenopus laevis | A0A8J1LTD2 |
| DNA (192-mer) | J | DNA | 192 | Homo sapiens | |
| DNA (192-mer) | K | DNA | 192 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>8SKZ_1 ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera (chains A)
SNAMVSLRSRKVIPASEMVSDGKTEKDASGDSPTSVLNEEENCEEKSVTVVEEEILLAKN
GDSSLISEAMAQEEEQLLKLREDEEKANNAGSAVAPNLNETQFTKLDELLTQTQLYSEFL
LEKMEDITINGIESESQKAEPEKTGRGRKRKAASQYNNTKAKRAVAAMISRSKEDGETIN
SDLTEEETVIKLQNELCPLLTGGQLKSYQLKGVKWLISLWQNGLNGILADQMGLGKTIQT
IGFLSHLKGNGLDGPYLVIAPLSTLSNWFNEIARFTPSINAIIYHGDKNQRDELRRKHMP
KTVGPKFPIVITSYEVAMNDAKRILRHYPWKYVVIDEGHRLKNHKCKLLRELKHLKMDNK
LLLTGTPLQNNLSELWSLLNFILPDIFTSHDEFESWFDFSEKNKNEATKEEEEKRRAQVV
SKLHGILRPFILRRMKCDVELSLPRKKEIIMYATMTDHQKKFQEHLVNNTLEAHLGENAI
RGIELSPTGRPKRRTRKSINYSKIDDFPNELEKLISQIQPEVDRERAVVEVNIPVEQGWK
GKLNNLVIQLRKNCNHPDLLQGQIDGSYLYPPVEEIVGQCGKFRLLERLLVRLFANNHKV
LIFSQWTKLLDIMDYYFSEKGFEVCRIDGSVKLDERRRQIKDFSDEKSSCSIFLLSTRAG
GLGINLTAADTCILYDSDWNPQMDLQAMDRCHRIGQTKPVHVYRLSTAQSIETRVLKRAY
SKLKLEHVVIGQGQFHQERAKSSTPLEEEDILALLKEDETAEDKLIQTDISDADLDRLLD
RSDLTITAPGETQAAEAFPVKGPGWEVVLPSSGGMLSSLNS
Sequence of entity 2 (B, E), FASTA
>8SKZ_2 Histone H3.2 (chains B, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 3 (C, G), FASTA
>8SKZ_3 Histone H2A (chains C, G)
SNAMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLL
PKKTESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>8SKZ_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 5 (F, I), FASTA
>8SKZ_5 Histone H4 (chains F, I)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGGSENLYFQ
Sequence of entity 6 (J), FASTA
>8SKZ_6 DNA (192-MER) (chains J)
GAAAACCTGTACTTCCAATCCAATAGGCCTCTGGAGAATCCCGGTGCCGAGGCCGCTCAA
TTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTA
ACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCA
TGTATTGAACAG
Sequence of entity 7 (K), FASTA
>8SKZ_7 DNA (192-MER) (chains K)
CTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAAT
CCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCT
GTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGAGGCCTATTGGATTGGAA
GTACAGGTTTTC
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
Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome. Nartey, W., Williams, G.J. To be published.
Other PDB entries of the same protein (UniProt Q9NRZ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9Z05 2.86 Å, Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state (D3)
- 9Z04 2.99 Å, Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state
- 9Z06 3.39 Å, Structure of human lymphoid-specific helicase HELLS in its auto-inhibitory state
Browse structure collections
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