9C9Z: S.c INO80

S.c INO80 in complex with Xenopus 0/80 nucleosome, INO80 Core. Determined by electron microscopy at 2.55 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 2.55 Å
Organism: Saccharomyces cerevisiae
Chains: 10
Atoms: 28,632
Mol. weight: 619.88 kDa
Ligands: ADP
Released: 16 Jul 2025

Explore 9C9Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C9Z contains 185 α-helices and 216 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 Q: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	949	1	1
β-strand	952-954	3	2
α-helix	958-971	14
α-helix	975-984	10
α-helix	1001-1012	12
α-helix	1014-1017	4
β-strand	1023	1	3
β-strand	1026-1027	2	4
β-strand	1030	1	5
β-strand	1071-1073	3	6
β-strand	1078	1	5
β-strand	1082-1084	3	7
α-helix	1087-1089	3
α-helix	1090-1094	5
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1122-1132	11
β-strand	1136	1	8
α-helix	1139-1144	6
α-helix	1148-1153	6
α-helix	1170-1177	8
α-helix	1186-1190	5
α-helix	1194-1200	7
α-helix	1206-1208	3
β-strand	1214-1215	2	4
β-strand	1216	1	9
α-helix	1217-1219	3
β-strand	1220-1222	3	7
α-helix	1227-1237	11
α-helix	1240-1245	6
α-helix	1251-1255	5
α-helix	1256-1260	5
α-helix	1265-1267	3
α-helix	1269-1270	2
α-helix	1275-1277	3
β-strand	1287	1	3
α-helix	1291-1297	7
α-helix	1299-1310	12
β-strand	1317-1318	2	10
α-helix	1327-1334	8
β-strand	1342	1	11
α-helix	1357-1363	7
β-strand	1369	1	11
β-strand	1389-1390	2	10
β-strand	1391	1	12
α-helix	1398-1405	8
β-strand	1419	1	1
β-strand	1421	1	12
β-strand	1422-1424	3	2
α-helix	1428-1434	7

Chain R: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	40-44	5	13
β-strand	49-52	4	13
β-strand	61-63	3	13
β-strand	67	1	14
β-strand	70	1	15
β-strand	79	1	15
β-strand	82	1	14
α-helix	84-87	4
α-helix	90-94	5
β-strand	97	1	14
β-strand	100	1	16
β-strand	105	1	16
α-helix	108-121	14
α-helix	124-126	3
β-strand	134-135	2	13
β-strand	136-137	2	17
α-helix	144-158	15
β-strand	162-163	2	18
β-strand	165-166	2	17
α-helix	168-176	9
β-strand	184-189	6	19
β-strand	194-200	7	19
β-strand	203-204	2	19
α-helix	206-208	3
β-strand	210-212	3	19
α-helix	217-230	14
α-helix	237-239	3
α-helix	240-250	11
α-helix	270-273	4
β-strand	277-278	2	20
α-helix	590-596	7
α-helix	606-610	5
β-strand	611-612	2	20
α-helix	620-623	4
α-helix	628-630	3
α-helix	638-648	11
β-strand	653	1	21
β-strand	656	1	21
α-helix	659-665	7
β-strand	668-671	4	19
α-helix	673-676	4
α-helix	680-691	12
β-strand	693	1	22
β-strand	700-701	2	19
α-helix	709-719	11
α-helix	721-724	4
β-strand	729-730	2	18
α-helix	731-737	7

Chain S: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	30-37	8
α-helix	65-82	18
β-strand	104	1	19
α-helix	105-108	4
α-helix	111-114	4
β-strand	115	1	23
β-strand	122	1	23
β-strand	125-126	2	24
β-strand	133-134	2	24
α-helix	137-139	3
α-helix	140-144	5
α-helix	147-148	2
α-helix	152-158	7

Chain T: 21 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	25
β-strand	35	1	26
α-helix	40	1
β-strand	41	1	26
α-helix	42	1
β-strand	44-45	2	27
β-strand	48-49	2	27
α-helix	52-67	16
β-strand	70	1	28
β-strand	74-79	6	29
α-helix	85-96	12
β-strand	102-106	5	29
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-150	22	22
β-strand	165-172	8	22
β-strand	175-181	7	22
α-helix	183-191	9
β-strand	198-203	6	22
β-strand	209-215	7	22
α-helix	216-218	3
β-strand	224	1	24
β-strand	229-230	2	22
α-helix	231-233	3
β-strand	238-248	11	22
α-helix	249-255	7
α-helix	270-271	2
α-helix	282-297	16
β-strand	301-305	5	22
β-strand	307-311	5	29
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-340	6	29
β-strand	342	1	30
β-strand	344-346	3	31
α-helix	347	1
β-strand	354-356	3	31
α-helix	361-364	4
β-strand	367-372	6	29
α-helix	377-390	14
β-strand	394-395	2	32
α-helix	397-409	13
α-helix	412-428	17
β-strand	433-434	2	32
α-helix	436-445	10
β-strand	447	1	33
α-helix	449-458	10

Chain U: 18 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	28
β-strand	31	1	34
β-strand	37	1	34
β-strand	40-41	2	35
β-strand	44-45	2	35
α-helix	48-63	16
β-strand	66	1	36
β-strand	70-74	5	37
α-helix	81-91	11
β-strand	98-102	5	37
α-helix	103-105	3
α-helix	113-122	10
β-strand	125-146	22	8
β-strand	155-161	7	8
β-strand	166-171	6	8
α-helix	173-181	9
β-strand	188-193	6	8
β-strand	199	1	8
β-strand	203-205	3	8
β-strand	214	1	22
β-strand	221-222	2	8
α-helix	223-225	3
β-strand	230-240	11	8
α-helix	241-249	9
α-helix	256-259	4
α-helix	267-282	16
β-strand	287-290	4	8
β-strand	292-296	5	37
β-strand	302	1	38
α-helix	303-312	10
β-strand	320-325	6	37
β-strand	329-331	3	39
α-helix	332	1
β-strand	333	1	38
β-strand	338-340	3	39
α-helix	345-349	5
β-strand	351-355	5	37
α-helix	356	1
α-helix	361-374	14
β-strand	379	1	40
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	40
α-helix	420-429	10
β-strand	431	1	29
α-helix	433-442	10
β-strand	448	1	30

Chain V: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	36
α-helix	35-36	2
α-helix	40-42	3
β-strand	44-45	2	41
β-strand	48-49	2	41
α-helix	52-66	15
β-strand	70	1	42
β-strand	74-78	5	43
α-helix	85-96	12
β-strand	102-106	5	43
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-151	23	44
α-helix	152	1
β-strand	163-171	9	44
β-strand	176-181	6	44
α-helix	185-191	7
β-strand	198-203	6	44
β-strand	213-215	3	44
β-strand	224	1	8
β-strand	229-230	2	44
α-helix	231-234	4
β-strand	238-248	11	44
α-helix	249-257	9
α-helix	265-272	8
α-helix	282-297	16
β-strand	301-305	5	44
β-strand	307-311	5	43
α-helix	313-315	3
β-strand	317	1	45
α-helix	318-327	10
β-strand	335-340	6	43
β-strand	342	1	46
β-strand	344-346	3	47
α-helix	347	1
β-strand	348	1	45
β-strand	354-356	3	47
α-helix	361-365	5
β-strand	367-371	5	43
α-helix	373-375	3
α-helix	377-390	14
β-strand	394-395	2	48
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-427	9
β-strand	433-434	2	48
α-helix	435	1
α-helix	436-445	10
β-strand	447	1	37
α-helix	449-458	10

Chain W: 19 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	42
β-strand	31	1	49
β-strand	37	1	49
β-strand	40-41	2	50
β-strand	44-45	2	50
α-helix	48-63	16
β-strand	66	1	51
β-strand	70-74	5	52
α-helix	81-91	11
β-strand	98-102	5	52
α-helix	113-122	10
β-strand	126-147	22	44
β-strand	154-161	8	44
β-strand	166-171	6	44
α-helix	173-180	8
β-strand	188-193	6	44
β-strand	198-204	7	44
α-helix	219-220	2
β-strand	221	1	44
α-helix	223-225	3
β-strand	230-240	11	44
α-helix	241-249	9
α-helix	253-259	7
α-helix	267-283	17
β-strand	286-289	4	44
β-strand	292-296	5	52
α-helix	298-300	3
α-helix	303-312	10
β-strand	320-325	6	52
β-strand	329-331	3	53
α-helix	332	1
β-strand	338-340	3	53
α-helix	345-349	5
β-strand	351-355	5	52
α-helix	361-374	14
β-strand	379	1	54
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	54
α-helix	420-429	10
β-strand	431	1	43
α-helix	433-442	10
α-helix	444-446	3
β-strand	448	1	46

Chain X: 21 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	51
β-strand	35	1	55
β-strand	41	1	55
β-strand	44-45	2	56
β-strand	48-49	2	56
α-helix	52-67	16
β-strand	70	1	57
β-strand	74-78	5	58
α-helix	85-96	12
β-strand	102-106	5	58
α-helix	107-110	4
α-helix	117-127	11
β-strand	129-151	23	6
β-strand	163-172	10	6
β-strand	175-181	7	6
α-helix	183-190	8
β-strand	198-203	6	6
β-strand	209-215	7	6
β-strand	223	1	44
β-strand	229-230	2	6
α-helix	232-233	2
β-strand	239-248	10	6
α-helix	249-257	9
β-strand	261	1	9
α-helix	265-272	8
α-helix	274-275	2
α-helix	282-297	16
β-strand	301-305	5	6
β-strand	307-311	5	58
α-helix	313-315	3
β-strand	317	1	59
α-helix	318-327	10
β-strand	335-340	6	58
β-strand	342	1	60
β-strand	344-346	3	61
α-helix	347	1
β-strand	348	1	59
β-strand	354-356	3	61
α-helix	361-364	4
β-strand	369-371	3	58
α-helix	373-375	3
α-helix	377-390	14
β-strand	394-395	2	62
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-428	10
β-strand	433-434	2	62
α-helix	436-445	10
β-strand	447	1	52
α-helix	449-457	9

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
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	460	Saccharomyces cerevisiae	Q12464
Ino eighty subunit 2	Z	protein	320	Saccharomyces cerevisiae	P40154

Sequence of entity 1 (Q), FASTA

>9C9Z_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

>9C9Z_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

>9C9Z_3 Chromatin-remodeling complex subunit IES6 (chains S)
MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRH
KSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTG
LKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK

Sequence of entity 4 (T, V, X), FASTA

>9C9Z_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

>9C9Z_5 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK

Sequence of entity 6 (Z), FASTA

>9C9Z_6 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 P53115 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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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