9GFM: Human INO80 core-nucleosome complex state N-7

CryoEM structure of the human INO80 core-nucleosome complex state N-7. Determined by electron microscopy at 3.8 Å resolution. Released 20 Aug 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 12,125
Mol. weight: 177.24 kDa
Released: 20 Aug 2025

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

Secondary structure: helices and β-sheets

9GFM contains 43 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	142-158	17
α-helix	167-168	2
α-helix	173-175	3
α-helix	178-187	10

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	121-131	11

Chain N: 4 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	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain O: 7 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	100-102	3	6
α-helix	110-112	3
α-helix	113-115	3

Chain P: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
α-helix	38-45	8
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	104-124	21

Chain Q: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-56	11
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	88-113	26
β-strand	118-119	2	8
α-helix	121-130	10

Chain R: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
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	83-92	10
β-strand	96-98	3	6

Chain S: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	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
INO80 complex subunit B	H	protein	50	Homo sapiens	Q9C086 (AlphaFold model)
Nucleosomal DNA strand 1	K	DNA	139	synthetic construct
Nucleosomal DNA strand 2	L	DNA	139	synthetic construct
Histone H3.1	M	protein	93	Homo sapiens	P68431 (AlphaFold model)
Histone H4	N	protein	82	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	O	protein	106	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 2-E	P	protein	96	Homo sapiens	Q16778
Histone H3.1	Q	protein	100	Homo sapiens	P68431 (AlphaFold model)
Histone H4	R	protein	79	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	S	protein	111	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 2-E	T	protein	93	Homo sapiens	Q16778

Sequence of entity 1 (H), FASTA

>9GFM_1 INO80 complex subunit B (chains H)
GLGGQEEEEEQRWLDALEKGELDDNGDLKKEINERLLTARQRALLQKARS

Sequence of entity 2 (K), FASTA

>9GFM_2 Nucleosomal DNA strand 1 (chains K)
ACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGC
GGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGAC
CAATTGAGCGGCCTCGGCA

Sequence of entity 3 (L), FASTA

>9GFM_3 Nucleosomal DNA strand 2 (chains L)
TGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGC
TGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGAT
ATATACATCCTGTGCATGT

Sequence of entity 4 (M), FASTA

>9GFM_4 Histone H3.1 (chains M)
PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVG
LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 5 (N), FASTA

>9GFM_5 Histone H4 (chains N)
VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT
VTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (O), FASTA

>9GFM_6 Histone H2A type 1-B/E (chains O)
KAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARD
NKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Sequence of entity 7 (P), FASTA

>9GFM_7 Histone H2B type 2-E (chains P)
KRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTI
TSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 8 (Q), FASTA

>9GFM_8 Histone H3.1 (chains Q)
KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEA
CEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 9 (R), FASTA

>9GFM_9 Histone H4 (chains R)
DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTA
MDVVYALKRQGRTLYGFGG

Sequence of entity 10 (S), FASTA

>9GFM_10 Histone H2A type 1-B/E (chains S)
GKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAG
NAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Sequence of entity 11 (T), FASTA

>9GFM_11 Histone H2B type 2-E (chains T)
RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS

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 Q9C086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZI4 3.2 Å, Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
9GE5 3.35 Å, CryoEM structure of the human INO80-Hexasome complex
9GCG 3.43 Å, CryoEM structure of the human INO80 core- H2A.Z nucleosome complex
9GEV 3.47 Å, CryoEM structure of the human INO80 core-nucleosome complex state N-6
9GFB 3.55 Å, CryoEM structure of the human INO80 core-nucleosome complex state N-7
9GF6 3.8 Å, CryoEM structure of the human INO80 core-nucleosome complex state N-6
6HTS 4.8 Å, Cryo-EM structure of the human INO80 complex bound to nucleosome

Browse structure collections

About this viewer

MolViewer shows 9GFM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.