9JNT: Isw1-nucleosome complex in ADP* state

Structure of isw1-nucleosome complex in ADP* state. Determined by electron microscopy at 2.7 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Xenopus laevis, Escherichia coli K-12, Saccharomyces cerevisiae S288C
Chains: 11
Atoms: 16,283
Mol. weight: 321.89 kDa
Ligands: ADP, MG
Released: 9 Apr 2025

Explore 9JNT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JNT contains 67 α-helices and 36 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
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	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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	101-102	2	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-119	18

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-74	11
α-helix	75-77	3
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-87	8
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	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

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	A, E	protein	135	Xenopus laevis	A0A310TTQ1 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	A0A8J1LTD2 (AlphaFold model)
Histone H2A	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B	D, H	protein	122	Xenopus laevis	P02281 (AlphaFold model)
DNA (146-mer)	I	DNA	146	Escherichia coli K-12
DNA (146-mer)	J	DNA	146	Escherichia coli K-12
ISWI chromatin-remodeling complex ATPase ISW1	K	protein	1061	Saccharomyces cerevisiae S288C	P38144

Sequence of entity 1 (A, E), FASTA

>9JNT_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9JNT_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9JNT_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9JNT_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>9JNT_5 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>9JNT_6 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 7 (K), FASTA

>9JNT_7 ISWI chromatin-remodeling complex ATPase ISW1 (chains K)
ENLKPFQVGLPPHDPESNKKRYLLKDANGKKFDLEGTTKRFEHLLSLSGLFKHFIESKAA
KDPKFRQVLDVLEENKANGKGKGKHQDVRRRKTEHEEDAELLKEEDSDDDESIEFQFRES
PAYVNGQLRPYQIQGVNWLVSLHKNKIAGILADEMGLGKTLQTISFLGYLRYIEKIPGPF
LVIAPKSTLNNWLREINRWTPDVNAFILQGDKEERAELIQKKLLGCDFDVVIASYEIIIR
EKSPLKKINWEYIIIDEAHRIKNEESMLSQVLREFTSRNRLLITGTPLQNNLHELWALLN
FLLPDIFSDAQDFDDWFSSESTEEDQDKIVKQLHTVLQPFLLRRIKSDVETSLLPKKELN
LYVGMSSMQKKWYKKILEKDLDAVNGSNGSKESKTRLLNIMMQLRKCCNHPYLFDGAEPG
PPYTTDEHLVYNAAKLQVLDKLLKKLKEEGSRVLIFSQMSRLLDILEDYCYFRNYEYCRI
DGSTAHEDRIQAIDDYNAPDSKKFVFLLTTRAGGLGINLTSADVVVLYDSDWNPQADLQA
MDRAHRIGQKKQVKVFRLVTDNSVEEKILERATQKLRLDQLVIQQNRTSLKKKENKADSK
DALLSMIQHGAADVFKSGTSTGSAGTPEPGSGEKGDDIDLDELLLKSENKTKSLNAKYET
LGLDDLQKFNQDSAYEWNGQDFKKKIQRDIISPLLLNPTKRERKENYSIDNYYKDVLNTG
RSSTPSHPRMPKPHVFHSHQLQPPQLKVLYEKERMWTAKKTGYVPTMDDVKAAYGDISDE
EEKKQKLELLKLSVNNSQPLTEEEEKMKADWESEGFTNWNKLEFRKFITVSGKYGRNSIQ
AIARELAPGKTLEEVRAYAKAFWSNIERIEDYEKYLKIIENEEEKIKRVKMQQEALRRKL
SEYKNPFFDLKLKHPPSSNNKRTYSEEEDRFILLMLFKYGLDRDDVYELVRDEIRDCPLF
ELDFYFRSRTPVELARRGNTLLQCLEKEFNAGIVLDDATKDRMKKEDENGKRIREEFADQ
TANEKENVDGVESKKAKIEDTSNVGTEQLVAEKIPENETTH

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

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
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
36IV 2.89 Å, Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes

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