9JAO: SMARCAD1
The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx. Determined by electron microscopy at 3.1 Å resolution. Released 30 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organisms
- Homo sapiens, Xenopus laevis, synthetic construct
- Chains
- 10
- Atoms
- 13,916
- Mol. weight
- 374.41 kDa
- Ligands
- BEF, ADP, MG
- Released
- 30 Apr 2025
Explore 9JAO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9JAO contains 63 α-helices and 25 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 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 | 4 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 3 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 5 |
Chain C: 36 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 380-382 | 3 | |
| α-helix | 383-395 | 13 | |
| α-helix | 398-402 | 5 | |
| α-helix | 410-417 | 8 | |
| α-helix | 424-433 | 10 | |
| α-helix | 440-475 | 36 | |
| α-helix | 499-513 | 15 | |
| β-strand | 519-520 | 2 | 1 |
| α-helix | 528-541 | 14 | |
| β-strand | 548-552 | 5 | 1 |
| α-helix | 557-567 | 11 | |
| β-strand | 573-575 | 3 | 1 |
| α-helix | 580-591 | 12 | |
| β-strand | 599-603 | 5 | 1 |
| α-helix | 611-619 | 9 | |
| β-strand | 624-628 | 5 | 1 |
| α-helix | 630-633 | 4 | |
| α-helix | 639-645 | 7 | |
| β-strand | 651-655 | 5 | 1 |
| α-helix | 664-674 | 11 | |
| α-helix | 676-679 | 4 | |
| α-helix | 683-689 | 7 | |
| α-helix | 702-715 | 14 | |
| β-strand | 719-720 | 2 | 1 |
| α-helix | 724-727 | 4 | |
| β-strand | 737-741 | 5 | 2 |
| α-helix | 745-760 | 16 | |
| α-helix | 772-774 | 3 | |
| α-helix | 776-783 | 8 | |
| α-helix | 785-787 | 3 | |
| α-helix | 794-803 | 10 | |
| α-helix | 804-806 | 3 | |
| α-helix | 808-810 | 3 | |
| α-helix | 815-823 | 9 | |
| α-helix | 827-836 | 10 | |
| α-helix | 841-843 | 3 | |
| α-helix | 844-846 | 3 | |
| α-helix | 847-850 | 4 | |
| α-helix | 854-868 | 15 | |
| β-strand | 873-877 | 5 | 2 |
| α-helix | 880-892 | 13 | |
| β-strand | 897-900 | 4 | 2 |
| α-helix | 906-908 | 3 | |
| α-helix | 909-918 | 10 | |
| β-strand | 924-928 | 5 | 2 |
| β-strand | 943-946 | 4 | 2 |
| α-helix | 953-960 | 8 | |
| β-strand | 973-979 | 7 | 2 |
| α-helix | 983-1001 | 19 | |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 3 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 4 |
| α-helix | 121-131 | 11 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-92 | 10 | |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 8 |
| α-helix | 47-72 | 26 | |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 5 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 8 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain K: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1019-1024 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing… | C, K | protein | 845 | Homo sapiens | Q9H4L7 (AlphaFold model) |
| Histone H3 | D, E | protein | 136 | Xenopus laevis | A0A310TTQ1 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | H | protein | 123 | Xenopus laevis | P02281 |
| DNA (157-mer) | I | DNA | 157 | synthetic construct | |
| DNA (157-mer) | J | DNA | 157 | synthetic construct | |
Sequence of entity 1 (C, K), FASTA
>9JAO_1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (chains C, K)
MHHHHHHHHHHHHGEFDIDAGGGPRKRKLSSSSEPYEEDEFNDDQSIKKTRLDHGEESNE
SAESSSNWEKQESIVLKLQKEFPNFDKQELREVLKEHEWMYTEALESLKVFAEDQDMQYV
SQSEVPNGKEVSSRSQNYPKNATKTKLKQKFSMKAQNGFNKKRKKNVFNPKRVVEDSEYD
SGSDVGSSLDEDYSSGEEVMEDGYKGKILHFLQDASIGELTLIPQCSQKKAQKITELRPF
NSWEALFTKMSKTNGLSEDLIWHCKTLIQERDVVIRLMNKCEDISNKLTKQVTMLTGNGG
GWNIEQPSILNQSLSLKPYQKVGLNWLALVHKHGLNGILADEMGLGKTIQAIAFLAYLYQ
EGNNGPHLIVVPASTIDNWLREVNLWCPTLKVLCYYGSQEERKQIRFNIHSRYEDYNVIV
TTYNCAISSSDDRSLFRRLKLNYAIFDEGHMLKNMGSIRYQHLMTINANNRLLLTGTPVQ
NNLLELMSLLNFVMPHMFSSSTSEIRRMFSSKTKSADEQSIYEKERIAHAKQIIKPFILR
RVKEEVLKQLPPKKDRIELCAMSEKQEQLYLGLFNRLKKSINNLEKNTEMCNVMMQLRKM
ANHPLLHRQYYTAEKLKEMSQLMLKEPTHCEANPDLIFEDMEVMTDFELHVLCKQYRHIN
NFQLDMDLILDSGKFRVLGCILSELKQKGDRVVLFSQFTMMLDILEVLLKHHQHRYLRLD
GKTQISERIHLIDEFNTDMDIFVFLLSTKAGGLGINLTSANVVILHDIDCNPYNDKQAED
RCHRVGQTKEVLVIKLISQGTIEESMLKINQQKLKLEQDMTTVDEGDEGSMPADIATLLK
TSMGL
Sequence of entity 2 (D, E), FASTA
>9JAO_2 Histone H3 (chains D, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 3 (B, F), FASTA
>9JAO_3 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (G), FASTA
>9JAO_4 Histone H2A (chains G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 5 (H), FASTA
>9JAO_5 Histone H2B 1.1 (chains H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 6 (I), FASTA
>9JAO_6 DNA (157-MER) (chains I)
CCGCCCTCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCG
CTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGT
CTCCAGGCACGTGTCAGATATATACATCCTGAAGCTT
Sequence of entity 7 (J), FASTA
>9JAO_7 DNA (157-MER) (chains J)
AAGCTTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCG
GTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACC
AATTGAGCGGCCTCGGCACCGGGATTCTCGAGGGCGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| MG | Magnesium ion | Mg | 1 |
Primary citation
Subnucleosome preference of human chromatin remodeller SMARCAD1. Hu, P., Sun, J., Sun, H. et al. Nature (2025) 644:818-826. DOI 10.1038/s41586-025-09100-0 · PubMed
Other PDB entries of the same protein (UniProt Q9H4L7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7Z36 2.8 Å, Crystal structure of the KAP1 tripartite motif in complex with the ZNF93 KRAB domain
- 6QU1 3.7 Å, Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain at…
- 6H3A 5.5 Å, Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain.
Browse structure collections
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