9JO2: Isw1-nucleosome complex in Apo* state

Structure of isw1-nucleosome complex in Apo* state. Determined by electron microscopy at 3.0 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Xenopus laevis, Escherichia coli K-12, Saccharomyces cerevisiae S288C
Chains: 11
Atoms: 16,225
Mol. weight: 321.48 kDa
Released: 9 Apr 2025

Explore 9JO2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JO2 contains 67 α-helices and 35 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	45-54	10
α-helix	65-75	11
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chains B and 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	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	17-20	4
α-helix	28-36	9
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	78	1	5
α-helix	80-89	10
α-helix	92-96	5
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	102-119	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	65-74	10
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 G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-73	28
β-strand	77-78	2	10
α-helix	80-88	9
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	54-80	27
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	102-120	19

Chain K: 30 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	83-90	8
α-helix	102-113	12
α-helix	117-120	4
α-helix	121-129	9
α-helix	131-137	7
α-helix	188-189	2
α-helix	198-200	3
α-helix	201-211	11
β-strand	217-219	3	11
α-helix	228-242	15
β-strand	248-252	5	11
α-helix	254-256	3
α-helix	257-267	11
α-helix	280-286	7
α-helix	287-291	5
β-strand	298-302	5	11
α-helix	303-308	6
α-helix	310-313	4
β-strand	318-323	6	11
α-helix	326-328	3
α-helix	335-342	8
β-strand	345-351	7	11
α-helix	360-370	11
α-helix	378-385	8
α-helix	393-405	13
β-strand	409-410	2	11
α-helix	422-424	3
β-strand	425	1	12
β-strand	428-431	4	13
α-helix	435-445	11
α-helix	470-477	8
α-helix	479-481	3
α-helix	502-515	14
β-strand	521	1	12
α-helix	528-541	14
β-strand	548	1	14
α-helix	554-565	12
β-strand	573	1	12
β-strand	576	1	14
β-strand	592	1	12
α-helix	602-613	12
β-strand	622	1	12
β-strand	625-628	4	13
α-helix	632-650	19
α-helix	654-657	4

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

>9JO2_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9JO2_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9JO2_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9JO2_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>9JO2_5 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>9JO2_6 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 7 (K), FASTA

>9JO2_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

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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