8A5A: Chromatin-remodeling ATPase INO80

Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80. Determined by electron microscopy at 3.3 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 5
Atoms: 13,191
Mol. weight: 283.83 kDa
Ligands: ATP, MG
Released: 14 Dec 2022

Explore 8A5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A5A contains 95 α-helices and 72 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	459-478	20
α-helix	479-485	7
α-helix	486-513	28
α-helix	514-518	5
α-helix	522-559	38

Chain U: 43 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	167-177	11
α-helix	197-199	3
β-strand	206	1	1
α-helix	216-227	12
β-strand	268-272	5	2
β-strand	277-281	5	2
β-strand	289-292	4	2
β-strand	295-298	4	3
α-helix	299-301	3
α-helix	309-310	2
α-helix	321-340	20
α-helix	349-359	11
α-helix	362	1
β-strand	363-365	3	4
α-helix	367-369	3
β-strand	377	1	5
β-strand	384-385	2	3
α-helix	386-391	6
β-strand	392	1	5
β-strand	397-400	4	3
β-strand	403-404	2	6
β-strand	407-408	2	6
α-helix	418-433	16
α-helix	445-447	3
β-strand	449-454	6	2
α-helix	460-468	9
α-helix	469-473	5
β-strand	478-483	6	2
α-helix	484-492	9
β-strand	498-503	6	7
β-strand	508-514	7	7
β-strand	517-518	2	7
α-helix	520-522	3
β-strand	524-526	3	7
α-helix	530-543	14
α-helix	556-569	14
α-helix	574-576	3
β-strand	580-585	6	4
β-strand	593-600	8	4
α-helix	603-609	7
α-helix	610-612	3
α-helix	615-620	6
α-helix	630-632	3
α-helix	635-637	3
β-strand	638	1	8
β-strand	645	1	8
α-helix	651-657	7
α-helix	662-664	3
α-helix	668-675	8
α-helix	678-687	10
α-helix	689-692	4
α-helix	703-715	13
α-helix	720-722	3
α-helix	723-727	5
β-strand	730-732	3	7
α-helix	735-738	4
α-helix	742-753	12
α-helix	756-759	4
β-strand	760	1	9
α-helix	763-780	18
α-helix	789-815	27
α-helix	819-822	4
β-strand	824	1	9
α-helix	825-826	2
β-strand	829-830	2	7
α-helix	841-850	10
α-helix	853-857	5
β-strand	860-861	2	2
α-helix	862-868	7
α-helix	869-874	6

Chain V: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	10
β-strand	16-21	6	10
β-strand	29-32	4	10
β-strand	35-38	4	11
β-strand	53-54	2	11
α-helix	55-60	6
α-helix	62-64	3
β-strand	65-68	4	11
β-strand	71-72	2	12
β-strand	75-76	2	12
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	10
α-helix	113-127	15
β-strand	131-136	6	10
α-helix	137-143	7
β-strand	150-155	6	13
β-strand	160-166	7	13
β-strand	169-170	2	13
α-helix	172-174	3
β-strand	176-178	3	13
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	14
β-strand	247-250	4	14
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	13
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	13
α-helix	338-346	9
β-strand	349	1	1
α-helix	352-355	4
β-strand	357-358	2	10
α-helix	359-365	7
α-helix	366-371	6

Chain W: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	15
β-strand	17-20	4	16
β-strand	25-30	6	16
β-strand	38-41	4	16
β-strand	43-47	5	17
β-strand	55-56	2	17
β-strand	69-73	5	17
β-strand	75-76	2	18
β-strand	79-80	2	18
α-helix	83-96	14
β-strand	107-110	4	16
α-helix	118-125	8
α-helix	126-131	6
β-strand	136-139	4	16
α-helix	142-150	9
β-strand	155-160	6	19
β-strand	165-171	7	19
β-strand	174-175	2	19
β-strand	181-183	3	19
α-helix	187-196	10
α-helix	206-208	3
β-strand	209-211	3	20
β-strand	217-218	2	20
α-helix	227-235	9
α-helix	238-245	8
α-helix	259-264	6
α-helix	266-268	3
β-strand	270-271	2	21
α-helix	276	1
β-strand	277-278	2	21
α-helix	282-290	9
α-helix	305-306	2
α-helix	308-310	3
α-helix	317-319	3
α-helix	385-395	11
α-helix	398-400	3
α-helix	401-405	5
β-strand	408-409	2	22
β-strand	410-411	2	19
α-helix	420-431	12
β-strand	439-440	2	22
α-helix	447-461	15
α-helix	465-468	4
β-strand	471	1	16
α-helix	472-478	7
α-helix	480-486	7

Chain X: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-40	5
β-strand	41-51	11	15
β-strand	57-65	9	15
α-helix	66-72	7

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

>8A5A_1 Chromatin-remodeling ATPase INO80 (chains G)
MSLAVLLNKEDKDISDFSKTTAGKSAKKNSRERVADVAPTRVLDKKQAYLSQLNSEFNRI
KRRDSIEQLYQDWKFINLQEFELISEWNQQSKDWQFDNTNDSQDLHFKKLYRDMSMINKE
WAEYQSFKNANLSDIINEKDADEDEEDDEDELEDGEEDMEEDEASTGRHTNGKSMRGNGI
QKSRKKDAAAAAAIGKAIKDDQTHADTVVTVNGDENEDGNNGEDEDNDNDNENNNDNDND
NENENDNDSDNDDEEENGEEDEEEEEIEDLDEEDFAAFEEQDDNDDEDFNPDVEKRRKRS
SSSSSSTKLSMNSLSLITSKKINKNITINSDRPKIVRELIKMCNKNKHQKIKKRRFTNCI
VTDYNPIDSKLNIKITLKQYHVKRLKKLINDAKREREREEALKNNVGLDGNDLDNDEDGS
ESHKRRKLNNNTANGADDANKRKFNTRHGLPTYGMKMNAKEARAIQRHYDNTYTTIWKDM
ARKDSTKMSRLVQQIQSIRSTNFRKTSSLCAREAKKWQSKNFKQIKDFQTRARRGIREMS
NFWKKNEREERDLKKKIEKEAMEQAKKEEEEKESKRQAKKLNFLLTQTELYSHFIGRKDY
KDDDDKGTDYKDDDDK

Sequence of entity 2 (U), FASTA

>8A5A_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

>8A5A_3 Actin (chains V)
MDSEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGIMVGMGQKDSYVGDEAQS
KRGILTLRYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPMNPKSNREKMT
QIMFETFNVPAFYVSIQAVLSLYSSGRTTGIVLDSGDGVTHVVPIYAGFSLPHAILRIDL
AGRDLTDYLMKILSERGYSFSTTAEREIVRDIKEKLCYVALDFEQEMQTAAQSSSIEKSY
ELPDGQVITIGNERFRAPEALFHPSVLGLESAGIDQTTYNSIMKCDVDVRKELYGNIVMS
GGTTMFPGIAERMQKEITALAPSSMKVKIIAPPERKYSVWIGGSILASLTTFQQMWISKQ
EYDESGPSIVHHKCF

Sequence of entity 4 (W), FASTA

>8A5A_4 Actin-related protein 4 (chains W)
MSNAALQVYGGDEVSAVVIDPGSYTTNIGYSGSDFPQSILPSVYGKYTADEGNKKIFSEQ
SIGIPRKDYELKPIIENGLVIDWDTAQEQWQWALQNELYLNSNSGIPALLTEPVWNSTEN
RKKSLEVLLEGMQFEACYLAPTSTCVSFAAGRPNCLVVDIGHDTCSVSPIVDGMTLSKST
RRNFIAGKFINHLIKKALEPKEIIPLFAIKQRKPEFIKKTFDYEVDKSLYDYANNRGFFQ
ECKETLCHICPTKTLEETKTELSSTAKRSIESPWNEEIVFDNETRYGFAEELFLPKEDDI
PANWPRSNSGVVKTWRNDYVPLKRTKPSGVNKSDKKVTPTEEKEQEAVSKSTSPAANSAD
TPNETGKRPLEEEKPPKENNELIGLADLVYSSIMSSDVDLRATLAHNVVLTGGTSSIPGL
SDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQLWVGKKEYEEVGV
ERLLNDRFR

Sequence of entity 5 (X), FASTA

>8A5A_5 Ino eighty subunit 4 (chains X)
MSQESSVLSESQEQLANNPKIEDTSPPSANSRDNSKPVLPWDYKNKAIEIKSFSGYKVNF
TGWIRRDVREERQRGSEFTASDVKGSDDKATRKKEPADEDPEVKQLEKEGEDGLDS

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
MG	Magnesium ion	Mg	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
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
9CAN 3.3 Å, S.c INO80 in complex with Xenopus 0/40 nucleosome

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