9C9S: S.c INO80
S.c INO80 in complex with S.c 0/40 nucleosome, Class 1. Determined by electron microscopy at 3.09 Å resolution. Released 16 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 3.09 Å
- Organisms
- Saccharomyces cerevisiae, Xenopus laevis, synthetic construct
- Chains
- 20
- Atoms
- 43,163
- Mol. weight
- 873.63 kDa
- Ligands
- ADP
- Released
- 16 Jul 2025
Explore 9C9S in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9C9S contains 241 α-helices and 230 β-strands across 18 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 | 46-56 | 11 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 62 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 63 |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-41 | 10 | |
| β-strand | 46 | 1 | 63 |
| α-helix | 51-76 | 26 | |
| β-strand | 81 | 1 | 62 |
| α-helix | 84-94 | 11 | |
| β-strand | 98 | 1 | 64 |
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 | 65 |
| α-helix | 47-72 | 26 | |
| β-strand | 78-79 | 2 | 66 |
| α-helix | 81-89 | 9 | |
| α-helix | 92-97 | 6 | |
| β-strand | 102 | 1 | 67 |
| α-helix | 103 | 1 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 66 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 65 |
| α-helix | 94-103 | 10 | |
| α-helix | 107-126 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 68 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 69 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46 | 1 | 69 |
| α-helix | 51-76 | 26 | |
| β-strand | 81 | 1 | 68 |
| α-helix | 84-94 | 11 | |
| β-strand | 98 | 1 | 67 |
Chain G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 70 |
| α-helix | 47-72 | 26 | |
| β-strand | 78-79 | 2 | 71 |
| α-helix | 81-90 | 10 | |
| α-helix | 93-97 | 5 | |
| β-strand | 102 | 1 | 64 |
| α-helix | 103 | 1 | |
| α-helix | 114-116 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-51 | 11 | |
| β-strand | 56-57 | 2 | 71 |
| α-helix | 59-86 | 28 | |
| β-strand | 91-92 | 2 | 70 |
| α-helix | 94-104 | 11 | |
| α-helix | 107-124 | 18 | |
10 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 |
|---|
| Chromatin-remodeling ATPase INO80 | Q | protein | 1489 | Saccharomyces cerevisiae | P53115 (AlphaFold model) |
| Actin-related protein 5 | R | protein | 755 | Saccharomyces cerevisiae | P53946 (AlphaFold model) |
| Chromatin-remodeling complex subunit IES6 | S | protein | 166 | Saccharomyces cerevisiae | P32617 (AlphaFold model) |
| RuvB-like protein 1 | T, V, X | protein | 463 | Saccharomyces cerevisiae | Q03940 (AlphaFold model) |
| RuvB-like protein 2 | U, W, Y | protein | 471 | Saccharomyces cerevisiae | Q12464 |
| Ino eighty subunit 2 | Z | protein | 320 | Saccharomyces cerevisiae | P40154 |
| Histone H3 | A, E | protein | 136 | Saccharomyces cerevisiae | P61830 |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 |
| Histone H2A | C, G | protein | 132 | Saccharomyces cerevisiae | P04911 |
| Histone H2B | D, H | protein | 131 | Saccharomyces cerevisiae | P02293 |
| DNA (227-mer) | I | DNA | 227 | synthetic construct | |
| DNA (227-mer) | J | DNA | 227 | synthetic construct | |
Sequence of entity 1 (Q), FASTA
>9C9S_1 Chromatin-remodeling ATPase INO80 (chains Q)
MSLAVLLNKEDKDISDFSKTTAGKSAKKNSRERVADVAPTRVLDKKQAYLSQLNSEFNRI
KRRDSIEQLYQDWKFINLQEFELISEWNQQSKDWQFDNTNDSQDLHFKKLYRDMSMINKE
WAEYQSFKNANLSDIINEKDADEDEEDDEDELEDGEEDMEEDEASTGRHTNGKSMRGNGI
QKSRKKDAAAAAAIGKAIKDDQTHADTVVTVNGDENEDGNNGEDEDNDNDNENNNDNDND
NENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDFNPDVEKRRKRS
SSSSSSTKLSMNSLSLITSKKINKNITINSDRPKIVRELIKMCNKNKHQKIKKRRFTNCI
VTDYNPIDSKLNIKITLKQYHVKRLKKLINDAKREREREEALKNNVGLDGNDLDNDEDGS
ESHKRRKLNNNTANGADDANKRKFNTRHGLPTYGMKMNAKEARAIQRHYDNTYTTIWKDM
ARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMS
NFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKIK
TNELEGNNVSSNDSESQKNIDISALAPNKNDFHAIDFDNENDEQLRLRAAENASNALAET
RAKAKQFDDHANAHEEEEEEDELNFQNPTSLGEITIEQPKILACTLKEYQLKGLNWLANL
YDQGINGILADEMGLGKTVQSISVLAHLAENHNIWGPFLVVTPASTLHNWVNEISKFLPQ
FKILPYWGNANDRKVLRKFWDRKNLRYNKNAPFHVMVTSYQMVVTDANYLQKMKWQYMIL
DEAQAIKSSQSSRWKNLLSFHCRNRLLLTGTPIQNSMQELWALLHFIMPSLFDSHDEFNE
WFSKDIESHAEANTKLNQQQLRRLHMILKPFMLRRVKKNVQSELGDKIEIDVLCDLTQRQ
AKLYQVLKSQISTNYDAIENAATNDSTSNSASNSGSDQNLINAVMQFRKVCNHPDLFERA
DVDSPFSFTTFGKTTSMLTASVANNNSSVISNSNMNLSSMSSNNISNGKFTDLIYSSRNP
IKYSLPRLIYEDLILPNYNNDVDIANKLKNVKFNIFNPSTNYELCLFLSKLTGEPSLNEF
FRVSTTPLLKRVIERTNGPKNTDSLSFKTITQELLEVTRNAPSEGVMASLLNVEKHAYER
EYLNCIQRGYHPNVSAPPVTIEVLGSSHVTNSINNELFDPLISQALSDIPAITQYNMHVK
KGIPVEDFPKTGLFPEPLNKNFSSNISMPSMDRFITESAKLRKLDELLVKLKSEGHRVLI
YFQMTKMMDLMEEYLTYRQYNHIRLDGSSKLEDRRDLVHDWQTNPEIFVFLLSTRAGGLG
INLTAADTVIFYDSDWNPTIDSQAMDRAHRLGQTRQVTVYRLLVRGTIEERMRDRAKQKE
QVQQVVMEGKTQEKNIKTIEVGENDSEVTREGSKSISQDGIKEAASALA
Sequence of entity 2 (R), FASTA
>9C9S_2 Actin-related protein 5 (chains R)
MSSRDASLTPLKAVVIDDPPLRQTPEPFDEQSAYNPQSPIAIDFGSSKLRAGFVNHATPT
HIFPNALTKFRDRKLNKNFTFVGNDTLLDQAVRSQSRSPFDGPFVTNWNLTEEILDYTFH
HLGVVPDNGIPNPILLTERLATVQSQRTNWYQILFETYNVPGVTFGIDSLFSFYNYNPSG
NKTGLVISCGHEDTNVIPVVDGAGILTDAKRINWGGHQAVDYLNDLMALKYPYFPTKMSY
LQYETMYKDYCYVSRNYDEDIEKILTLENLDTNDVVVEAPFTEVLQPQKTEEELRIQAEK
RKETGKRLQEQARLKRMEKLVQKQEEFEYFSKVRDQLIDEPKKKVLSVLQNAGFDDERDF
KKYLHSLEQSLKKAQMVEAEDDSHLDEMNEDKTAQKFDLLDIADEDLNEDQIKEKRKQRF
LKASQDARQKAKEEKERVAKEEEEKKLKEQQWRETDLNGWIKDKRLKLNKLIKRRKEKLK
LRDEMKDRKSQVSQNRMKNLASLAEDNVKQGAKRNRHQATIDNDPNDTFGANDEDWLIYT
DITQNPEAFEEALEYEYKDIVELERLLLEHDPNFTEEDTLEAQYDWRNSILHLFLRGPRP
HDSENIHEQHQMHLNVERIRVPEVIFQPTMGGQDQAGICELSETILLKKFGSQPGKLSQT
SIDMVNNVLITGGNAKVPGLKERIVKEFTGFLPTGTNITVNMSSDPSLDAWKGMAALARN
EEQYRKTVISKKEYEEYGPEYIKEHKLGNTKYFED
Sequence of entity 3 (S), FASTA
>9C9S_3 Chromatin-remodeling complex subunit IES6 (chains S)
MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRH
KSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTG
LKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK
Sequence of entity 4 (T, V, X), FASTA
>9C9S_4 RuvB-like protein 1 (chains T, V, X)
MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGV
IVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTET
LMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLR
LDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK
KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGV
AELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVP
PDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLA
PCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYL
Sequence of entity 5 (U, W, Y), FASTA
>9C9S_5 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAKSADPDAMDTTE
Sequence of entity 6 (Z), FASTA
>9C9S_6 Ino eighty subunit 2 (chains Z)
MDSEASDIEAELSDSVSAGGEEYIDDDDYTEDIDDQIVTAKSSRRTARRSVPKGVRTSKR
IRDKELSVEVDEDYDEEEDVLSPSKKRHLHTRSMDKRQVAATASEKSDIGDSKGNDGEIE
DGILEEEESLEKELNRGGGKEVEKSEESYYAQNDVGQKGEEEQDGESGGYEDNEPSISKE
SDELVSVVNGNGNEEDDEVEATKENTTDSTRSTTTRSKMLLDLLEDGGSKKKLTDEEIQL
RRAENARKRKNLSEKRLEEEKQDTINKLLKKRAGKSRSHLPNDDEKNDGSSSFVKPRRPY
NSEGMTRILRRYEEDLFCTF
Sequence of entity 7 (A, E), FASTA
>9C9S_7 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI
QKKDIKLARRLRGERS
Sequence of entity 8 (B, F), FASTA
>9C9S_8 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 9 (C, G), FASTA
>9C9S_9 Histone H2A (chains C, G)
MSGGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYL
AAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPK
KSAKATKASQEL
Sequence of entity 10 (D, H), FASTA
>9C9S_10 Histone H2B (chains D, H)
MSAKAEKKPASKAPAEKKPAAKKTSTSTDGKKRSKARKETYSSYIYKVLKQTHPDTGISQ
KSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTR
AVTKYSSSTQA
Sequence of entity 11 (I), FASTA
>9C9S_11 DNA (227-MER) (chains I)
TCGGTACCCGGGGATCCTCTAGAGTGGGAGCTCGGAACACTATCCGACTGGCACCGGCAA
GGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 12 (J), FASTA
>9C9S_12 DNA (227-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAG
TCGGATAGTGTTCCGAGCTCCCACTCTAGAGGATCCCCGGGTACCGA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 6 |
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 P53115 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9C9Z 2.55 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, INO80 Core
- 8ETW 2.64 Å, Class3 of INO80-Hexasome complex
- 8ETU 2.8 Å, Class2 of the INO80-Hexasome complex
- 9CAT 2.9 Å, DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module
- 9C9G 2.91 Å, S.c INO80 in complex with S.c 0/80 nucleosome
- 9CCD 3.01 Å, DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module
- 8ETS 3.04 Å, Class1 of the INO80-Hexasome complex
- 9C9T 3.16 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 2
- 8A5O 3.2 Å, Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80
- 9OB1 3.2 Å, S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State
- 8A5A 3.3 Å, Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80
- 9CAN 3.3 Å, S.c INO80 in complex with Xenopus 0/40 nucleosome
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