8OOS: Chromatin-remodeling ATPase Ino80

CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2. Determined by electron microscopy at 3.29 Å resolution. Released 26 Jul 2023.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Thermochaetoides thermophila, synthetic construct, Homo sapiens
Chains: 9
Atoms: 12,307
Mol. weight: 351.96 kDa
Ligands: MG, ADP, ALF
Released: 26 Jul 2023

Explore 8OOS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OOS contains 52 α-helices and 32 β-strands across 7 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 G: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	966-968	3
α-helix	971-973	3
α-helix	974-988	15
β-strand	993-995	3	1
α-helix	997-998	2
α-helix	1003-1018	16
β-strand	1024-1028	5	1
α-helix	1030-1032	3
α-helix	1033-1043	11
β-strand	1049-1052	4	1
α-helix	1056-1062	7
α-helix	1063-1065	3
β-strand	1081-1085	5	1
α-helix	1088-1091	4
α-helix	1093-1096	4
β-strand	1101	1	2
β-strand	1103-1106	4	1
α-helix	1109-1112	4
α-helix	1118-1123	6
β-strand	1128	1	2
β-strand	1131-1134	4	1
α-helix	1144-1153	10
α-helix	1190-1192	3
β-strand	1198-1199	2	1
β-strand	1214-1217	4	3
β-strand	1220	1	4
α-helix	1224-1239	16
α-helix	1257-1269	13
α-helix	1271-1273	3
α-helix	1545-1550	6
α-helix	1553-1568	16
β-strand	1572-1576	5	3
α-helix	1580-1590	11
β-strand	1596-1599	4	3
α-helix	1605-1617	13
β-strand	1623-1627	5	3
β-strand	1642-1645	4	3
α-helix	1652-1662	11
β-strand	1672-1675	4	3
β-strand	1678	1	4
α-helix	1682-1700	19
β-strand	1705	1	1

Chain M: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-75	12
β-strand	83-84	2	5
α-helix	86-113	28
β-strand	118-119	2	6
α-helix	121-131	11

Chain N: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	6
α-helix	50-75	26
β-strand	80-81	2	5
α-helix	82	1
α-helix	83-92	10

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	7
α-helix	47-72	26
β-strand	77-78	2	8
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	9
α-helix	113-115	3
α-helix	117-118	2

Chain P: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	8
α-helix	53-81	29
β-strand	85-86	2	7
α-helix	88-98	11
α-helix	101-118	18

Chain Q: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-76	13
β-strand	84	1	10
α-helix	86-113	28
β-strand	118-119	2	11
α-helix	121-131	11

Chain R: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	11
α-helix	50-75	26
β-strand	81	1	10
α-helix	83-92	10
β-strand	96-98	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromatin-remodeling ATPase Ino80	G	protein	1134	Thermochaetoides thermophila
DNA strand 1	K	DNA	226	synthetic construct
DNA Strand 2	L	DNA	226	synthetic construct
Histone H3.1	M, Q	protein	135	Homo sapiens	P68431 (AlphaFold model)
Histone H4	N, R	protein	102	Homo sapiens	P62805 (AlphaFold model)
Histone H2A	O	protein	129	Homo sapiens	Q93077 (AlphaFold model)
Histone H2B	P	protein	125	Homo sapiens	P62807 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>8OOS_1 Chromatin-remodeling ATPase Ino80 (chains G)
LELKFQSKGYNQIYDQIWRDLARKDVSKVFRLATDSYATKASNLKKTAILASKEAKRWQL
RTNKGTKDLQARAKRVMRDMMGFWKRNEREERDLRKAAERLELENARKEEADREAARQRR
KLNFLISQTELYSHFISKKIKTHEVERSTDHPDVATDEKDKIPEPTLNINVPEPTGPIAP
KVTDFNSLDFDNEDESALQAAAMANAQNAIAEAQKKAREFNKDETKLDEDGEMNFQHPEL
TEFEVAQPKLLNCQLKEYQLKGLNWLVNLYEQGINGILADEMGLGKTVQSISVMAYLAER
YDIWGPFLVVAPASTLHNWQQEVSKFVPDFKVLPYWGTAADRKVLRKFWDRKHTTYKKDS
PFHVMITSYQLVVSDVAYFQKMKWQYMILDEAQAIKSSQSSRWKCLLGFHCRNRLLLTGT
PIQNNMQELWALLHFIMPSLFDSHDEFSEWFSKDIESHAQSNTKLNEDQLKRLHMILKPF
MLRRVKKHVQKELGDKIEIDVFCELSYRQRAMYQSLRNQISIMDLIEKATVGDNEDSATL
MNLVMQFRKVCNHPDLFERADTSSPFFCGHFAETGSFLREGTNVALGYSTRSLVEYRLPR
LIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPENIRSSLEGIENFTWLRFVDTSLQE
AYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEIT
TEGVLRDLMNIARVKYRELGLCRLEKAARPRASAPPIEVVCDSRSAVIERENIMFHPAMR
KALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPSMARFVTDSGKLAK
LDELLRELKEGGHRVLLYFQMTRMIDLMEEYLTYRNYKYCRLDGSTKLEDRRDTVADFQT
RPEIFIFLLSTRAGGLGINLTTADTVIFYDSDWNPTIDSQAMDRAHRLGQTKQVTVYRLI
TRGTIEERIRKRALQKEEVQRVVITGTGSVDFSGRRPPENRNRDIAMWLADDEQAEMIER
REKELIESGEYDKIMQQRRKGGKRKRGAANGDTVPSLEDMYHEGEGHFDDNKGSGAATPV
DADSLGRGGKRKKAGGSKKAKTTKQRLAIADGEIDIDYKDDDDKGTDYKDDDDK

Sequence of entity 2 (K), FASTA

>8OOS_2 DNA strand 1 (chains K)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAG
TCGGATAGTGTTCCGAGCTCCCACTCTAGAGGATCCCCGGGTACCG

Sequence of entity 3 (L), FASTA

>8OOS_3 DNA Strand 2 (chains L)
CGGTACCCGGGGATCCTCTAGAGTGGGAGCTCGGAACACTATCCGACTGGCACCGGCAAG
GTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAG
TAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAG
AGCTTGCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 4 (M, Q), FASTA

>8OOS_4 Histone H3.1 (chains M, Q)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 5 (N, R), FASTA

>8OOS_5 Histone H4 (chains N, R)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 6 (O), FASTA

>8OOS_6 Histone H2A (chains O)
SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 7 (P), FASTA

>8OOS_7 Histone H2B (chains P)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ALF	Tetrafluoroaluminate ion	Al F4	1

Primary citation

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Zhang, M., Jungblut, A., Kunert, F. et al. Science (2023) 381:313-319. DOI 10.1126/science.adf6287 · 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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