8A5O: Chromatin-remodeling ATPase INO80
Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80. Determined by electron microscopy at 3.2 Å resolution. Released 14 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Saccharomyces cerevisiae S288C
- Chains
- 5
- Atoms
- 12,571
- Mol. weight
- 283.88 kDa
- Ligands
- MG, AGS
- Released
- 14 Dec 2022
Explore 8A5O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8A5O contains 94 α-helices and 68 β-strands across 5 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: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 459-479 | 21 | |
| α-helix | 480-485 | 6 | |
| α-helix | 486-517 | 32 | |
| α-helix | 522-558 | 37 | |
Chain U: 41 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 268-272 | 5 | 1 |
| β-strand | 277-281 | 5 | 1 |
| β-strand | 289-292 | 4 | 1 |
| β-strand | 295-298 | 4 | 2 |
| α-helix | 299-301 | 3 | |
| α-helix | 304-306 | 3 | |
| α-helix | 313-316 | 4 | |
| α-helix | 321-340 | 20 | |
| α-helix | 349-359 | 11 | |
| α-helix | 362 | 1 | |
| β-strand | 363-365 | 3 | 3 |
| β-strand | 377 | 1 | 4 |
| β-strand | 384-385 | 2 | 2 |
| α-helix | 386-390 | 5 | |
| β-strand | 392 | 1 | 4 |
| β-strand | 397-400 | 4 | 2 |
| β-strand | 403-404 | 2 | 5 |
| β-strand | 407-408 | 2 | 5 |
| α-helix | 418-433 | 16 | |
| α-helix | 442-447 | 6 | |
| β-strand | 449-454 | 6 | 1 |
| α-helix | 460-468 | 9 | |
| α-helix | 469-473 | 5 | |
| β-strand | 478-483 | 6 | 1 |
| α-helix | 484-492 | 9 | |
| β-strand | 498-503 | 6 | 6 |
| β-strand | 508-514 | 7 | 6 |
| β-strand | 517-518 | 2 | 6 |
| α-helix | 520-522 | 3 | |
| β-strand | 524-526 | 3 | 6 |
| α-helix | 532-543 | 12 | |
| α-helix | 556-569 | 14 | |
| α-helix | 574-576 | 3 | |
| β-strand | 580-586 | 7 | 3 |
| β-strand | 593-600 | 8 | 3 |
| α-helix | 603-609 | 7 | |
| α-helix | 610-612 | 3 | |
| α-helix | 615-619 | 5 | |
| α-helix | 622-625 | 4 | |
| α-helix | 628-633 | 6 | |
| α-helix | 635-637 | 3 | |
| β-strand | 638 | 1 | 7 |
| β-strand | 645 | 1 | 7 |
| α-helix | 651-658 | 8 | |
| α-helix | 662-664 | 3 | |
| α-helix | 668-687 | 20 | |
| α-helix | 703-715 | 13 | |
| α-helix | 720-722 | 3 | |
| α-helix | 723-727 | 5 | |
| β-strand | 730-733 | 4 | 6 |
| α-helix | 735-738 | 4 | |
| α-helix | 742-753 | 12 | |
| α-helix | 756-759 | 4 | |
| α-helix | 763-780 | 18 | |
| α-helix | 782-783 | 2 | |
| α-helix | 789-815 | 27 | |
| β-strand | 829-830 | 2 | 6 |
| α-helix | 831-832 | 2 | |
| α-helix | 833-835 | 3 | |
| α-helix | 841-849 | 9 | |
| α-helix | 853-857 | 5 | |
| α-helix | 859 | 1 | |
| β-strand | 860-861 | 2 | 1 |
| α-helix | 862-868 | 7 | |
| α-helix | 869-874 | 6 | |
Chain V: 25 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-7 | 2 | |
| β-strand | 8-11 | 4 | 8 |
| β-strand | 16-21 | 6 | 8 |
| β-strand | 22 | 1 | 9 |
| β-strand | 24 | 1 | 9 |
| β-strand | 29-32 | 4 | 8 |
| β-strand | 35-38 | 4 | 10 |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-60 | 5 | |
| α-helix | 62-64 | 3 | |
| β-strand | 65-68 | 4 | 10 |
| β-strand | 71-72 | 2 | 11 |
| β-strand | 75-76 | 2 | 11 |
| α-helix | 79-88 | 10 | |
| α-helix | 89-94 | 6 | |
| α-helix | 98-100 | 3 | |
| β-strand | 103-107 | 5 | 8 |
| α-helix | 113-125 | 13 | |
| β-strand | 131-136 | 6 | 8 |
| α-helix | 137-143 | 7 | |
| β-strand | 150-155 | 6 | 12 |
| β-strand | 160-166 | 7 | 12 |
| β-strand | 169-170 | 2 | 12 |
| α-helix | 172-174 | 3 | |
| β-strand | 176-178 | 3 | 12 |
| α-helix | 182-195 | 14 | |
| α-helix | 203-216 | 14 | |
| α-helix | 223-232 | 10 | |
| α-helix | 234-236 | 3 | |
| β-strand | 238-241 | 4 | 13 |
| β-strand | 247-250 | 4 | 13 |
| α-helix | 253-259 | 7 | |
| α-helix | 264-267 | 4 | |
| α-helix | 274-282 | 9 | |
| α-helix | 287-289 | 3 | |
| α-helix | 290-294 | 5 | |
| β-strand | 297-300 | 4 | 12 |
| α-helix | 302-305 | 4 | |
| α-helix | 309-320 | 12 | |
| β-strand | 329-330 | 2 | 12 |
| α-helix | 338-347 | 10 | |
| α-helix | 350-354 | 5 | |
| β-strand | 357-358 | 2 | 8 |
| α-helix | 359-365 | 7 | |
| α-helix | 367-369 | 3 | |
| α-helix | 370-373 | 4 | |
Chain W: 23 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-20 | 4 | 14 |
| β-strand | 25-30 | 6 | 14 |
| β-strand | 38-41 | 4 | 14 |
| β-strand | 43-47 | 5 | 15 |
| β-strand | 55-56 | 2 | 15 |
| α-helix | 59-62 | 4 | |
| β-strand | 69-73 | 5 | 15 |
| β-strand | 75-76 | 2 | 16 |
| β-strand | 79-80 | 2 | 16 |
| α-helix | 83-96 | 14 | |
| β-strand | 107-112 | 6 | 14 |
| α-helix | 118-126 | 9 | |
| α-helix | 127-131 | 5 | |
| β-strand | 136-141 | 6 | 14 |
| α-helix | 142-150 | 9 | |
| β-strand | 155-160 | 6 | 17 |
| β-strand | 165-171 | 7 | 17 |
| β-strand | 174-175 | 2 | 17 |
| β-strand | 181-183 | 3 | 17 |
| α-helix | 187-196 | 10 | |
| α-helix | 206-208 | 3 | |
| β-strand | 209-211 | 3 | 18 |
| β-strand | 217-218 | 2 | 18 |
| α-helix | 227-234 | 8 | |
| α-helix | 235-239 | 5 | |
| α-helix | 240-245 | 6 | |
| α-helix | 255-264 | 10 | |
| β-strand | 269-271 | 3 | 19 |
| α-helix | 276 | 1 | |
| β-strand | 277-279 | 3 | 19 |
| α-helix | 282-290 | 9 | |
| α-helix | 305-306 | 2 | |
| α-helix | 385-394 | 10 | |
| α-helix | 401-405 | 5 | |
| β-strand | 408-411 | 4 | 17 |
| α-helix | 413-416 | 4 | |
| α-helix | 420-431 | 12 | |
| β-strand | 439 | 1 | 17 |
| α-helix | 447-461 | 15 | |
| α-helix | 463-468 | 6 | |
| α-helix | 469 | 1 | |
| β-strand | 470-471 | 2 | 14 |
| α-helix | 472-478 | 7 | |
| α-helix | 480-486 | 7 | |
Chain X: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-40 | 5 | |
| β-strand | 41-51 | 11 | 20 |
| β-strand | 57-65 | 9 | 20 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Chromatin-remodeling ATPase INO80 | G | protein | 616 | Saccharomyces cerevisiae S288C | P53115 (AlphaFold model) |
| Actin-like protein ARP8 | U | protein | 881 | Saccharomyces cerevisiae S288C | Q12386 (AlphaFold model) |
| Actin | V | protein | 375 | Saccharomyces cerevisiae S288C | P60010 (AlphaFold model) |
| Actin-related protein 4 | W | protein | 489 | Saccharomyces cerevisiae S288C | P80428 (AlphaFold model) |
| Ino eighty subunit 4 | X | protein | 116 | Saccharomyces cerevisiae S288C | Q08561 |
Sequence of entity 1 (G), FASTA
>8A5O_1 Chromatin-remodeling ATPase INO80 (chains G)
MSLAVLLNKEDKDISDFSKTTAGKSAKKNSRERVADVAPTRVLDKKQAYLSQLNSEFNRI
KRRDSIEQLYQDWKFINLQEFELISEWNQQSKDWQFDNTNDSQDLHFKKLYRDMSMINKE
WAEYQSFKNANLSDIINEKDADEDEEDDEDELEDGEEDMEEDEASTGRHTNGKSMRGNGI
QKSRKKDAAAAAAIGKAIKDDQTHADTVVTVNGDENEDGNNGEDEDNDNDNENNNDNDND
NENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDFNPDVEKRRKRS
SSSSSSTKLSMNSLSLITSKKINKNITINSDRPKIVRELIKMCNKNKHQKIKKRRFTNCI
VTDYNPIDSKLNIKITLKQYHVKRLKKLINDAKREREREEALKNNVGLDGNDLDNDEDGS
ESHKRRKLNNNTANGADDANKRKFNTRHGLPTYGMKMNAKEARAIQRHYDNTYTTIWKDM
ARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMS
NFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKDY
KDDDDKGTDYKDDDDK
Sequence of entity 2 (U), FASTA
>8A5O_2 Actin-like protein ARP8 (chains U)
MSQEEAESSIIYEEPIDIPLEDDDDEDELEEENSVPLSSQADQENAENESDDSVDNVVGS
ETPRSVTGLSVDPRDVADEEDEDEEGEDEDEDEDDNDVDNEDENDNDNANENENELGSSR
DKRAPPAVQTSKRYKKYPKLDPAKAPPGKKVPLHLLEKRRLGRIKAAEEFAKTLKKIGIE
KVETTTLPATGLFQPLMLINQKNYSSDYLKKDDQIFALRDRKFLRNNNTSQISSTNTPDV
IDLKSLPHSEASAAPLNDEIDLNDPTATIVIHPGSNSIKIGFPKDDHPVVVPNCVAVPKK
WLDLENSEHVENVCLQREQSEEFNNIKSEMEKNFRERMRYYKRKVPGNAHEQVVSFNENS
KPEIISEKNDPSPIEWIFDDSKLYYGSDALRCVDEKFVIRKPFRGGSFNVKSPYYKSLAE
LISDVTKLLEHALNSETLNVKPTKFNQYKVVLVIPDIFKKSHVETFIRVLLTELQFQAVA
IIQESLATCYGAGISTSTCVVNIGAAETRIACVDEGTVLEHSAITLDYGGDDITRLFALF
LLQSDFPLQDWKIDSKHGWLLAERLKKNFTTFQDADVAVQLYNFMNRSPNQPTEKYEFKL
FDEVMLAPLALFFPQIFKLIRTSSHKNSSLEFQLPESRDLFTNELNDWNSLSQFESKEGN
LYCDLNDDLKILNRILDAHNIIDQLQDKPENYGNTLKENFAPLEKAIVQSIANASITADV
TRMNSFYSNILIVGGSSKIPALDFILTDRINIWRPSLLSSASFPQFYKKLTKEIKDLEGH
YVNAPDKTEDENKQILQAQIKEKIVEELEEQHQNIEHQNGNEHIFPVSIIPPPRDMNPAL
IIWKGASVLAQIKLVEELFITNSDWDVHGSRILQYKCIFTY
Sequence of entity 3 (V), FASTA
>8A5O_3 Actin (chains V)
MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQS
KRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMT
QIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDL
AGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSY
ELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMS
GGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQ
EYDESGPSIVHHKCF
Sequence of entity 4 (W), FASTA
>8A5O_4 Actin-related protein 4 (chains W)
MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQ
SIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTEN
RKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKST
RRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQ
ECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDI
PANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSAD
TPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGL
SDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGV
ERLLNDRFR
Sequence of entity 5 (X), FASTA
>8A5O_5 Ino eighty subunit 4 (chains X)
MSQESSVLSESQEQLANNPKIEDTSPPSANSRDNSKPVLPWDYKNKAIEIKSFSGYKVNF
TGWIRRDVREERQRGSEFTASDVKGSDDKATRKKEPADEDPEVKQLEKEGEDGLDS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 3 |
| AGS | Phosphothiophosphoric acid-adenylate ester | C10 H16 N5 O12 P3 S | 3 |
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 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
- 9C9S 3.09 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 1
- 9C9T 3.16 Å, S.c INO80 in complex with S.c 0/40 nucleosome, Class 2
- 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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