8ATF: Nucleosome-bound Ino80 ATPase
Nucleosome-bound Ino80 ATPase. Determined by electron microscopy at 3.45 Å resolution. Released 14 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 3.45 Å
- Organisms
- Thermochaetoides thermophila, DNA molecule, Homo sapiens
- Chains
- 12
- Atoms
- 15,719
- Mol. weight
- 433.75 kDa
- Ligands
- ADP
- Released
- 14 Dec 2022
Explore 8ATF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8ATF contains 65 α-helices and 33 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 G: 27 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 963-965 | 3 | |
| α-helix | 971-973 | 3 | |
| α-helix | 974-989 | 16 | |
| β-strand | 993-995 | 3 | 1 |
| α-helix | 997-998 | 2 | |
| α-helix | 1003-1017 | 15 | |
| β-strand | 1024-1028 | 5 | 1 |
| α-helix | 1030-1032 | 3 | |
| α-helix | 1033-1043 | 11 | |
| β-strand | 1049-1052 | 4 | 1 |
| α-helix | 1056-1063 | 8 | |
| β-strand | 1081-1085 | 5 | 1 |
| α-helix | 1086-1091 | 6 | |
| α-helix | 1093-1096 | 4 | |
| β-strand | 1101-1106 | 6 | 1 |
| α-helix | 1109-1112 | 4 | |
| α-helix | 1118-1123 | 6 | |
| β-strand | 1128-1134 | 7 | 1 |
| α-helix | 1143-1153 | 11 | |
| α-helix | 1161-1165 | 5 | |
| α-helix | 1184-1193 | 10 | |
| β-strand | 1198-1199 | 2 | 1 |
| α-helix | 1203-1205 | 3 | |
| α-helix | 1211-1213 | 3 | |
| β-strand | 1214-1220 | 7 | 2 |
| α-helix | 1224-1235 | 12 | |
| α-helix | 1261-1269 | 9 | |
| α-helix | 1271-1273 | 3 | |
| α-helix | 1545-1550 | 6 | |
| α-helix | 1553-1568 | 16 | |
| β-strand | 1572-1576 | 5 | 2 |
| α-helix | 1579-1591 | 13 | |
| β-strand | 1596-1599 | 4 | 2 |
| α-helix | 1605-1617 | 13 | |
| β-strand | 1623-1627 | 5 | 2 |
| α-helix | 1628-1631 | 4 | |
| β-strand | 1642-1645 | 4 | 2 |
| α-helix | 1652-1659 | 8 | |
| β-strand | 1672-1678 | 7 | 2 |
| α-helix | 1682-1701 | 20 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 390-415 | 26 | |
Chain M: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 3 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 4 |
| α-helix | 121-131 | 11 | |
Chain N: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 4 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 3 |
| α-helix | 82 | 1 | |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 5 |
Chain O: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 6 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 7 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 8 |
| α-helix | 113-115 | 3 | |
Chain P: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 7 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 6 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain Q: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 9 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 10 |
| 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 | 10 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 9 |
| α-helix | 83-90 | 8 | |
| β-strand | 96-98 | 3 | 8 |
2 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 ATPase | G | protein | 1139 | Thermochaetoides thermophila | |
| PAPA-1 domain-containing protein | H | protein | 492 | Thermochaetoides thermophila | G0RY01 (AlphaFold model) |
| DNA (227-mer) | K | DNA | 227 | DNA molecule | |
| DNA (226-mer) | L | DNA | 226 | DNA molecule | |
| Histone H3.2 | M, Q | protein | 135 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | N, R | protein | 102 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A | O, S | protein | 129 | Homo sapiens | P0C0S8 (AlphaFold model) |
| Histone H2B type 1-C/E/F/G/I | P, T | protein | 125 | Homo sapiens | P62807 |
Sequence of entity 1 (G), FASTA
>8ATF_1 Ino80 ATPase (chains G)
LELKFQSKGYNQIYDQIWRDLARKDVSKVFRLATDSYATKASNLKKTAILASKEAKRWQL
RTNKGTKDLQARAKRVMRDMMGFWKRNEREERDLRKAAERLELENARKEEADREAARQRR
KLNFLISQTELYSHFISKKIKTHEVERSTDHPDVATDEKDKIPEPTLNINVPEPTGPIAP
KVTDFNSLDFDNEDESALQAAAMANAQNAIAEAQKKAREFNKDETKLDEDGEMNFQHPEL
TEFEVAQPKLLNCQLKEYQLKGLNWLVNLYEQGINGILADEMGLGKTVQSISVMAYLAER
YDIWGPFLVVAPASTLHNWQQEVSKFVPDFKVLPYWGTAADRKVLRKFWDRKHTTYKKDS
PFHVMITSYQLVVSDVAYFQKMKWQYMILDEAQAIKSSQSSRWKCLLGFHCRNRLLLTGT
PIQNNMQELWALLHFIMPSLFDSHDEFSEWFSKDIESHAQSNTKLNEDQLKRLHMILKPF
MLRRVKKHVQKELGDKIEIDVFCELSYRQRAMYQSLRNQISIMDLIEKATVGDNEDSATL
MNLVMQFRKVCNHPDLFERADTSSPFFCGHFAETGSFLREGTNVALGYSTRSLVEYRLPR
LIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPENIRSSLEGIENFTWLRFVDTSLQE
AYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEIT
TEGVLRDLMNIARVKYRELGLCRLEKAARPRASAPPIEVVCDSRSAVIERENIMFHPAMR
KALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPSMARFVTDSGKLAK
LDELLRELKEGGHRVLLYFQMTRMIDLMEEYLTYRNYKYCRLDGSTKLEDRRDTVADFQT
RPEIFIFLLSTRAGGLGINLTTADTVIFYDSDWNPTIDSQAMDRAHRLGQTKQVTVYRLI
TRGTIEERIRKRALQKEEVQRVVITGTGSVDFSGRRPPENRNRDIAMWLADDEQAEMIER
REKELIESGEYDKIMQQRRKGGKRKRGAANGDTVPSLEDMYHEGEGHFDDNKGSGAATPV
DADSLGRGGKRKKAGGSKKAKTTKQRLAIADGEIDDGEIDIDYKDDDDKGTDYKDDDDK
Sequence of entity 2 (H), FASTA
>8ATF_2 PAPA-1 domain-containing protein (chains H)
MSTRPRRHAAQRASQAITDLADRDRESDHSHGPISSRMSSFNSSSRSRLPGKGIASVSRS
EAGGASDPEHIHLTVKLPSSKLRQATSSSGIKKAGSVGSSSSSSGGGKAAVKRARGGKRS
RVLESSEEEEEENEVEVLGDEDEEEEEEEDEIEVREGEGYDEDEEDVEDEDEEMQDLGEE
DADGEDDEMDVDAEGEEDADGDVNMDAGVVGARATTVRAVPPAIKVTKPPKESPSNGKAA
TASKANDNAVPVKRPAPDSDDESLSSLESEPEEEVNVAGGEDAEGEDDDAEGEVDAEGEE
EEEEEEIEVADEDAEGEDVEQDEDEDEEEEDDDDEMISRAQTPDMSRLTARQRARLGEAS
GEYLKLSDEVQSKKHFTAEELSMRRAEMARRRRNLSEKRNEEIKMETVNKLLKKQAPRTT
RRAAQAAAAAEEAEEAAKQPKRPDPMMIRWVNNKMGSVVAVPEELLGTHAGVVFGAGPGK
GLPAGKMVEEVS
Sequence of entity 3 (K), FASTA
>8ATF_3 DNA (227-MER) (chains K)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAG
TCGGATAGTGTTCCGAGCTCCCACTCTAGAGGATCCCCGGGTACCGA
Sequence of entity 4 (L), FASTA
>8ATF_4 DNA (226-MER) (chains L)
TCGGTACCCGGGGATCCTCTAGAGTGGGAGCTCGGAACACTATCCGACTGGCACCGGCAA
GGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCA
Sequence of entity 5 (M, Q), FASTA
>8ATF_5 Histone H3.2 (chains M, Q)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 6 (N, R), FASTA
>8ATF_6 Histone H4 (chains N, R)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (O, S), FASTA
>8ATF_7 Histone H2A (chains O, S)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 8 (P, T), FASTA
>8ATF_8 Histone H2B type 1-C/E/F/G/I (chains P, T)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
Primary citation
Structural mechanism of extranucleosomal DNA readout by the INO80 complex. Kunert, F., Metzner, F.J., Jung, J. et al. Sci Adv (2022) 8:eadd3189-eadd3189. DOI 10.1126/sciadv.add3189 · PubMed
Other PDB entries of the same protein (UniProt G0RY01 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8OOP 2.7 Å, CryoEM Structure INO80core Hexasome complex composite model state2
- 8OO7 2.8 Å, CryoEM Structure INO80core Hexasome complex composite model state1
- 8OOR 2.87 Å, CryoEM Structure INO80core Hexasome complex Rvb core refinement state2
- 8OOC 2.93 Å, CryoEM Structure INO80core Hexasome complex Rvb core refinement state1
- 6FHS 3.75 Å, CryoEM Structure of INO80core
- 6FML 4.34 Å, CryoEM Structure INO80core Nucleosome complex
- 8AV6 4.68 Å, CryoEM structure of INO80 core nucleosome complex in closed grappler conformation
Browse structure collections
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