9GF6: Human INO80 core-nucleosome complex state N-6

CryoEM structure of the human INO80 core-nucleosome complex state N-6. Determined by electron microscopy at 3.8 Å resolution. Released 20 Aug 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: synthetic construct, Homo sapiens
Chains: 11
Atoms: 11,865
Mol. weight: 241.65 kDa
Released: 20 Aug 2025

Explore 9GF6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GF6 contains 39 α-helices and 20 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 H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	143-158	16
α-helix	173-175	3
α-helix	178-188	11

Chain M: 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 N: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	49-75	27
β-strand	80-81	2	1
α-helix	82	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain O: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	43	1	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-97	7
β-strand	101	1	6
α-helix	111-112	2

Chain P: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	89	1	4
α-helix	91-101	11
α-helix	104-124	21

Chain Q: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118	1	8
α-helix	121-131	11

Chain R: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45	1	8
α-helix	48-75	28
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97	1	6

Chain S: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	43	1	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	93-96	4
β-strand	100-102	3	3

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
Nucleosomal DNA Strand 1	K	DNA	152	synthetic construct
Nucleosomal DNA Strand 2	L	DNA	152	synthetic construct
Histone H3.1	M, Q	protein	136	Homo sapiens	P68431 (AlphaFold model)
Histone H4	N, R	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	O, S	protein	129	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 2-E	P, T	protein	125	Homo sapiens	Q16778 (AlphaFold model)
INO80 complex subunit B	H	protein	356	Homo sapiens	Q9C086

Sequence of entity 1 (K), FASTA

>9GF6_1 Nucleosomal DNA Strand 1 (chains K)
CAATATCCCGAGTACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAG
TAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAG
AGCTGTCTACGACCAATTGAGCGGCCTCGGCA

Sequence of entity 2 (L), FASTA

>9GF6_2 Nucleosomal DNA Strand 2 (chains L)
TGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGC
TGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGAT
ATATACATCCTGTGCATGTACTCGGGATATTG

Sequence of entity 3 (M, Q), FASTA

>9GF6_3 Histone H3.1 (chains M, Q)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (N, R), FASTA

>9GF6_4 Histone H4 (chains N, R)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (O, S), FASTA

>9GF6_5 Histone H2A type 1-B/E (chains O, S)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 6 (P, T), FASTA

>9GF6_6 Histone H2B type 2-E (chains P, T)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 7 (H), FASTA

>9GF6_7 INO80 complex subunit B (chains H)
MSKLWRRGSTSGAMEAPEPGEALELSLAGAHGHGVHKKKHKKHKKKHKKKHHQEEDAGPT
QPSPAKPQLKLKIKLGGQVLGTKSVPTFTVIPEGPRSPSPLMVVDNEEEPMEGVPLEQYR
AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQRWLDALEKGELDDNGDLKKEINERLLTARQ
RALLQKARSQPSPMLPLPVAEGCPPPALTEEMLLKREERARKRRLQAARRAEEHKNQTIE
RLTKTAATSGRGGRGGARGERRGGRAAAPAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRP
SPSGPPPRCSVPGCPHPRRYACSRTGQALCSLQCYRINLQMRLGGPEGPGSPLLAT

Primary citation

Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Aggarwal, P., Sharma, M., Woike, S. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag138 · PubMed

Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail

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