9CAN: S.c INO80
S.c INO80 in complex with Xenopus 0/40 nucleosome. Determined by electron microscopy at 3.3 Å resolution. Released 16 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae
- Chains
- 20
- Atoms
- 42,187
- Mol. weight
- 869.2 kDa
- Ligands
- ADP
- Released
- 16 Jul 2025
Explore 9CAN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9CAN contains 235 α-helices and 224 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, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83 | 1 | 1 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain B: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-41 | 11 | |
| α-helix | 50-75 | 26 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 84-92 | 9 | |
| β-strand | 97 | 1 | 2 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42 | 1 | 3 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 4 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 5 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 4 |
| α-helix | 53-79 | 27 | |
| β-strand | 85 | 1 | 3 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-56 | 11 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45 | 1 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-92 | 10 | |
| β-strand | 97-98 | 2 | 5 |
Chain G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 28-35 | 8 | |
| α-helix | 46-73 | 28 | |
| β-strand | 77 | 1 | 8 |
| α-helix | 80-87 | 8 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101 | 1 | 2 |
Chain H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50 | 1 | 8 |
| α-helix | 53-80 | 28 | |
| α-helix | 88-97 | 10 | |
| α-helix | 103-120 | 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 |
|---|
| Histone H3 | A, E | protein | 136 | Xenopus laevis | A0A310TTQ1 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | A0A8J1LTD2 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 123 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (227-mer) | I | DNA | 227 | synthetic construct | |
| DNA (227-mer) | J | DNA | 227 | synthetic construct | |
| Chromatin-remodeling ATPase INO80 | Q | protein | 1489 | Saccharomyces cerevisiae | P53115 |
| Actin-related protein 5 | R | protein | 755 | Saccharomyces cerevisiae | P53946 |
| Chromatin-remodeling complex subunit IES6 | S | protein | 166 | Saccharomyces cerevisiae | P32617 |
| RuvB-like protein 1 | T, V, X | protein | 463 | Saccharomyces cerevisiae | Q03940 |
| RuvB-like protein 2 | U, W, Y | protein | 460 | Saccharomyces cerevisiae | Q12464 |
| Ino eighty subunit 2 | Z | protein | 320 | Saccharomyces cerevisiae | P40154 |
Sequence of entity 1 (A, E), FASTA
>9CAN_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9CAN_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9CAN_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>9CAN_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 5 (I), FASTA
>9CAN_5 DNA (227-MER) (chains I)
TCGGTACCCGGGGATCCTCTAGAGTGGGAGCTCGGAACACTATCCGACTGGCACCGGCAA
GGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 6 (J), FASTA
>9CAN_6 DNA (227-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACCTTGCCGGTGCCAG
TCGGATAGTGTTCCGAGCTCCCACTCTAGAGGATCCCCGGGTACCGA
Sequence of entity 7 (Q), FASTA
>9CAN_7 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 8 (R), FASTA
>9CAN_8 Actin-related protein 5 (chains R)
MSSRDASLTPLKAVVIDDPPLRQTPEPFDEQSAYNPQSPIAIDFGSSKLRAGFVNHATPT
HIFPNALTKFRDRKLNKNFTFVGNDTLLDQAVRSQSRSPFDGPFVTNWNLTEEILDYTFH
HLGVVPDNGIPNPILLTERLATVQSQRTNWYQILFETYNVPGVTFGIDSLFSFYNYNPSG
NKTGLVISCGHEDTNVIPVVDGAGILTDAKRINWGGHQAVDYLNDLMALKYPYFPTKMSY
LQYETMYKDYCYVSRNYDEDIEKILTLENLDTNDVVVEAPFTEVLQPQKTEEELRIQAEK
RKETGKRLQEQARLKRMEKLVQKQEEFEYFSKVRDQLIDEPKKKVLSVLQNAGFDDERDF
KKYLHSLEQSLKKAQMVEAEDDSHLDEMNEDKTAQKFDLLDIADEDLNEDQIKEKRKQRF
LKASQDARQKAKEEKERVAKEEEEKKLKEQQWRETDLNGWIKDKRLKLNKLIKRRKEKLK
LRDEMKDRKSQVSQNRMKNLASLAEDNVKQGAKRNRHQATIDNDPNDTFGANDEDWLIYT
DITQNPEAFEEALEYEYKDIVELERLLLEHDPNFTEEDTLEAQYDWRNSILHLFLRGPRP
HDSENIHEQHQMHLNVERIRVPEVIFQPTMGGQDQAGICELSETILLKKFGSQPGKLSQT
SIDMVNNVLITGGNAKVPGLKERIVKEFTGFLPTGTNITVNMSSDPSLDAWKGMAALARN
EEQYRKTVISKKEYEEYGPEYIKEHKLGNTKYFED
Sequence of entity 9 (S), FASTA
>9CAN_9 Chromatin-remodeling complex subunit IES6 (chains S)
MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRH
KSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTG
LKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK
Sequence of entity 10 (T, V, X), FASTA
>9CAN_10 RuvB-like protein 1 (chains T, V, X)
MVAISEVKENPGVNSSNSGAVTRTAAHTHIKGLGLDESGVAKRVEGGFVGQIEAREACGV
IVDLIKAKKMSGRAILLAGGPSTGKTALALAISQELGPKVPFCPLVGSELYSVEVKKTET
LMENFRRAIGLRIKETKEVYEGEVTELTPEDAENPLGGYGKTISHVIVGLKSAKGTKTLR
LDPTIYESIQREKVSIGDVIYIEANTGAVKRVGRSDAYATEFDLETEEYVPLPKGEVHKK
KEIVQDVTLHDLDVANARPQGGQDVISMMGQLLKPKKTEITEKLRQEVNKVVAKYIDQGV
AELIPGVLFIDEVNMLDIEIFTYLNKALESNIAPVVVLASNRGMTTVRGTEDVISPHGVP
PDLIDRLLIVRTLPYDKDEIRTIIERRATVERLQVESSALDLLATMGTETSLRYALQLLA
PCGILAQTSNRKEIVVNDVNEAKLLFLDAKRSTKILETSANYL
Sequence of entity 11 (U, W, Y), FASTA
>9CAN_11 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK
Sequence of entity 12 (Z), FASTA
>9CAN_12 Ino eighty subunit 2 (chains Z)
MDSEASDIEAELSDSVSAGGEEYIDDDDYTEDIDDQIVTAKSSRRTARRSVPKGVRTSKR
IRDKELSVEVDEDYDEEEDVLSPSKKRHLHTRSMDKRQVAATASEKSDIGDSKGNDGEIE
DGILEEEESLEKELNRGGGKEVEKSEESYYAQNDVGQKGEEEQDGESGGYEDNEPSISKE
SDELVSVVNGNGNEEDDEVEATKENTTDSTRSTTTRSKMLLDLLEDGGSKKKLTDEEIQL
RRAENARKRKNLSEKRLEEEKQDTINKLLKKRAGKSRSHLPNDDEKNDGSSSFVKPRRPY
NSEGMTRILRRYEEDLFCTF
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 A0A310TTQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
- 9JNP 2.3 Å, Structure of isw1-nucleosome complex in ATP state
- 8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
- 9JNU 2.5 Å, Structure of isw1-nucleosome complex in ADP state
- 9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
- 9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
- 9JNT 2.7 Å, Structure of isw1-nucleosome complex in ADP* state
- 9LIU 2.7 Å, Structure of isw1-nucleosome double-bound complex in ATP-ATP state
- 28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
- 9JO5 2.8 Å, Structure of isw1-nucleosome complex in ADP-B state
- 9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
- 9C9X 2.83 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome
Browse structure collections
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