9C9X: S.c INO80

S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome. Determined by electron microscopy at 2.83 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 2.83 Å
Organisms: Xenopus laevis, synthetic construct
Chains: 10
Atoms: 11,799
Mol. weight: 249.31 kDa
Released: 16 Jul 2025

Explore 9C9X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C9X contains 36 α-helices and 20 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 A: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-57	12
α-helix	65-76	12
β-strand	84-85	2	1
α-helix	87-114	28
β-strand	119-120	2	2
α-helix	122-132	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-41	10
β-strand	46-47	2	2
α-helix	51-76	26
β-strand	81-82	2	1
α-helix	85-93	9
β-strand	97-99	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	28-36	9
β-strand	43-44	2	4
α-helix	47-72	26
β-strand	78-79	2	5
α-helix	81-90	10
α-helix	94-97	4
β-strand	101-103	3	6
α-helix	114-116	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	5
α-helix	54-81	28
β-strand	86-87	2	4
α-helix	89-99	11
α-helix	102-120	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-43	2
α-helix	47-56	10
α-helix	65-77	13
β-strand	84-85	2	7
α-helix	87-114	28
β-strand	119-120	2	8
α-helix	122-131	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-41	10
β-strand	46-47	2	8
α-helix	52-76	25
β-strand	81-82	2	7
α-helix	84-93	10
β-strand	97-99	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-22	5
α-helix	29-36	8
β-strand	43-44	2	10
α-helix	47-73	27
β-strand	78-79	2	9
α-helix	81-89	9
α-helix	92-97	6
β-strand	101-103	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-46	11
β-strand	51-52	2	9
α-helix	54-81	28
β-strand	86-87	2	10
α-helix	89-99	11
α-helix	102-121	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	136	Xenopus laevis	A0A310TTQ1 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281 (AlphaFold model)
DNA (227-mer)	I	DNA	227	synthetic construct
DNA (227-mer)	J	DNA	227	synthetic construct

Sequence of entity 1 (A, E), FASTA

>9C9X_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9C9X_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9C9X_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9C9X_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 5 (I), FASTA

>9C9X_5 DNA (227-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAG
TCGGATAGTGTTCCGAGCTCCCACTCTAGAGGATCCCCGGGTACCGA

Sequence of entity 6 (J), FASTA

>9C9X_6 DNA (227-MER) (chains J)
TCGGTACCCGGGGATCCTCTAGAGTGGGAGCTCGGAACACTATCCGACTGGCACCGGCAA
GGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

Primary citation

Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning. Kaur, U., Wu, H., Cheng, Y. et al. Science (2025) 389:eadr3831-eadr3831. DOI 10.1126/science.adr3831 · 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…
36IV 2.89 Å, Cryo-EM structure of BRD4 BD1 bound to acetylated nucleosomes

Browse structure collections

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