9LJ2: Histone H3
Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state. Determined by electron microscopy at 2.98 Å resolution. Released 9 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 2.98 Å
- Organisms
- Xenopus laevis, Escherichia coli K-12, Saccharomyces cerevisiae S288C
- Chains
- 12
- Atoms
- 21,131
- Mol. weight
- 441.59 kDa
- Ligands
- MG, ADP
- Released
- 9 Apr 2025
Explore 9LJ2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9LJ2 contains 103 α-helices and 57 β-strands across 10 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: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-74 | 11 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 87-113 | 27 | |
| 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 | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 78 | 1 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 6 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 51 | 1 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-129 | 9 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
2 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 | A, E | protein | 98 | Xenopus laevis | A0A310TTQ1 (AlphaFold model) |
| Histone H4 | B, F | protein | 88 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 107 | Xenopus laevis | Q6AZJ8 (AlphaFold model) |
| Histone H2B | D, H | protein | 93 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | Escherichia coli K-12 | |
| DNA (147-mer) | J | DNA | 147 | Escherichia coli K-12 | |
| ISWI chromatin-remodeling complex ATPase ISW1 | K, N | protein | 1129 | Saccharomyces cerevisiae S288C | P38144 |
Sequence of entity 1 (A, E), FASTA
>9LJ2_1 Histone H3 (chains A, E)
KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEAS
EAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B, F), FASTA
>9LJ2_2 Histone H4 (chains B, F)
AKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE
HAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9LJ2_3 Histone H2A (chains C, G)
AKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAAR
DNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK
Sequence of entity 4 (D, H), FASTA
>9LJ2_4 Histone H2B (chains D, H)
TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 5 (I), FASTA
>9LJ2_5 DNA (147-MER) (chains I)
TCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>9LJ2_6 DNA (147-MER) (chains J)
TCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 7 (K, N), FASTA
>9LJ2_7 ISWI chromatin-remodeling complex ATPase ISW1 (chains K, N)
MAYMLAIANFHFFKFYTRMRKKHENNSCNEKDKDENLFKIILAIFLQEKKKYDCISSGSI
MTASEEYLENLKPFQVGLPPHDPESNKKRYLLKDANGKKFDLEGTTKRFEHLLSLSGLFK
HFIESKAAKDPKFRQVLDVLEENKANGKGKGKHQDVRRRKTEHEEDAELLKEEDSDDDES
IEFQFRESPAYVNGQLRPYQIQGVNWLVSLHKNKIAGILADEMGLGKTLQTISFLGYLRY
IEKIPGPFLVIAPKSTLNNWLREINRWTPDVNAFILQGDKEERAELIQKKLLGCDFDVVI
ASYEIIIREKSPLKKINWEYIIIDEAHRIKNEESMLSQVLREFTSRNRLLITGTPLQNNL
HELWALLNFLLPDIFSDAQDFDDWFSSESTEEDQDKIVKQLHTVLQPFLLRRIKSDVETS
LLPKKELNLYVGMSSMQKKWYKKILEKDLDAVNGSNGSKESKTRLLNIMMQLRKCCNHPY
LFDGAEPGPPYTTDEHLVYNAAKLQVLDKLLKKLKEEGSRVLIFSQMSRLLDILEDYCYF
RNYEYCRIDGSTAHEDRIQAIDDYNAPDSKKFVFLLTTRAGGLGINLTSADVVVLYDSDW
NPQADLQAMDRAHRIGQKKQVKVFRLVTDNSVEEKILERATQKLRLDQLVIQQNRTSLKK
KENKADSKDALLSMIQHGAADVFKSGTSTGSAGTPEPGSGEKGDDIDLDELLLKSENKTK
SLNAKYETLGLDDLQKFNQDSAYEWNGQDFKKKIQRDIISPLLLNPTKRERKENYSIDNY
YKDVLNTGRSSTPSHPRMPKPHVFHSHQLQPPQLKVLYEKERMWTAKKTGYVPTMDDVKA
AYGDISDEEEKKQKLELLKLSVNNSQPLTEEEEKMKADWESEGFTNWNKLEFRKFITVSG
KYGRNSIQAIARELAPGKTLEEVRAYAKAFWSNIERIEDYEKYLKIIENEEEKIKRVKMQ
QEALRRKLSEYKNPFFDLKLKHPPSSNNKRTYSEEEDRFILLMLFKYGLDRDDVYELVRD
EIRDCPLFELDFYFRSRTPVELARRGNTLLQCLEKEFNAGIVLDDATKDRMKKEDENGKR
IREEFADQTANEKENVDGVESKKAKIEDTSNVGTEQLVAEKIPENETTH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
Primary citation
Structural insights into chromatin remodeling by ISWI during active ATP hydrolysis. Sia, Y., Pan, H., Chen, K. et al. Science (2025) 388:eadu5654-eadu5654. DOI 10.1126/science.adu5654 · PubMed
Other PDB entries of the same protein (UniProt A0A310TTQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
- 9JNP 2.3 Å, Structure of isw1-nucleosome complex in ATP state
- 8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
- 9JNU 2.5 Å, Structure of isw1-nucleosome complex in ADP state
- 9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
- 9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
- 9JNT 2.7 Å, Structure of isw1-nucleosome complex in ADP* state
- 9LIU 2.7 Å, Structure of isw1-nucleosome double-bound complex in ATP-ATP state
- 28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
- 9JO5 2.8 Å, Structure of isw1-nucleosome complex in ADP-B state
- 9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
- 9C9X 2.83 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome
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