9LIU: Histone H3

Structure of isw1-nucleosome double-bound complex in ATP-ATP 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: 12
Atoms: 19,587
Mol. weight: 445.68 kDa
Ligands: ATP, MG
Released: 9 Apr 2025

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

Secondary structure: helices and β-sheets

9LIU contains 86 α-helices and 44 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
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	96-98	3	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	46-71	26
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6

Chains D and H: 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	101-120	20

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	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	46-71	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chains K and N: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	198-213	16
β-strand	218-219	2	11
α-helix	221-222	2
α-helix	227-240	14
β-strand	248-252	5	11
α-helix	254-256	3
α-helix	257-267	11
β-strand	273-275	3	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	326-329	4
α-helix	335-340	6
β-strand	345-351	7	11
α-helix	361-370	10
α-helix	379-383	5
α-helix	398-405	8
β-strand	409-410	2	11
α-helix	422-424	3
β-strand	425-431	7	12
α-helix	435-445	11
α-helix	468-477	10
α-helix	479-481	3
α-helix	496-499	4
α-helix	502-517	16
β-strand	521-524	4	12
α-helix	528-541	14
α-helix	554-564	11
β-strand	573-575	3	12
β-strand	592-595	4	12
α-helix	602-610	9
β-strand	622-628	7	12
α-helix	632-648	17

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, N	protein	1061	Saccharomyces cerevisiae S288C	P38144

Sequence of entity 1 (A, E), FASTA

>9LIU_1 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9LIU_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9LIU_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9LIU_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>9LIU_5 DNA (146-MER) (chains I)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>9LIU_6 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGA

Sequence of entity 7 (K, N), FASTA

>9LIU_7 ISWI chromatin-remodeling complex ATPase ISW1 (chains K, N)
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
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	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
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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