9CAT: DeltaArp8 INO80

DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module. Determined by electron microscopy at 2.9 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 10
Atoms: 30,518
Mol. weight: 619.88 kDa
Ligands: ADP
Released: 16 Jul 2025

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

Secondary structure: helices and β-sheets

9CAT contains 198 α-helices and 221 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: 43 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	710-723	14
β-strand	728-729	2	1
α-helix	731-732	2
α-helix	737-751	15
β-strand	759-761	3	1
α-helix	764-766	3
α-helix	767-777	11
β-strand	783	1	2
α-helix	790-799	10
β-strand	815	1	2
β-strand	816-818	3	1
α-helix	820-825	6
β-strand	838-841	4	1
α-helix	843-846	4
α-helix	852-857	6
β-strand	866-868	3	1
α-helix	879-887	9
α-helix	895-900	6
α-helix	922-927	6
β-strand	948-954	7	3
α-helix	958-970	13
α-helix	1004-1012	9
α-helix	1014-1016	3
β-strand	1023	1	4
β-strand	1026-1027	2	5
β-strand	1030	1	6
β-strand	1071-1073	3	7
β-strand	1078	1	6
β-strand	1082-1084	3	8
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	9
α-helix	1139-1143	5
α-helix	1148-1154	7
α-helix	1170-1177	8
α-helix	1186-1190	5
α-helix	1193-1200	8
α-helix	1203-1205	3
α-helix	1206-1208	3
β-strand	1214-1215	2	5
β-strand	1216	1	10
α-helix	1217-1219	3
β-strand	1220-1222	3	8
α-helix	1228-1237	10
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	1275-1276	2
β-strand	1287	1	4
α-helix	1291-1296	6
α-helix	1299-1314	16
β-strand	1318-1322	5	3
α-helix	1325-1338	14
β-strand	1342-1344	3	3
α-helix	1354-1363	10
β-strand	1369-1373	5	3
α-helix	1374-1377	4
β-strand	1388-1391	4	3
α-helix	1398-1402	5
α-helix	1405-1407	3
β-strand	1418-1424	7	3
α-helix	1428-1445	18

Chain R: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	11
α-helix	18-20	3
α-helix	25-26	2
α-helix	31-33	3
β-strand	40-44	5	12
β-strand	48-53	6	12
β-strand	61-64	4	12
β-strand	67	1	13
β-strand	82	1	13
α-helix	83-86	4
α-helix	90-94	5
β-strand	97	1	13
β-strand	100-101	2	14
β-strand	104-105	2	14
α-helix	109-120	12
α-helix	133	1
β-strand	134-136	3	12
α-helix	144-156	13
β-strand	162-164	3	12
α-helix	168-176	9
β-strand	184-189	6	15
β-strand	194-200	7	15
β-strand	203-204	2	15
β-strand	210-212	3	15
α-helix	216-230	15
α-helix	240-249	10
α-helix	257-260	4
α-helix	267-270	4
β-strand	277-278	2	11
α-helix	590-596	7
α-helix	608-610	3
β-strand	611-612	2	11
α-helix	617-620	4
α-helix	622-625	4
α-helix	638-646	9
β-strand	653	1	16
β-strand	656	1	16
α-helix	659-665	7
β-strand	668-671	4	15
α-helix	673-675	3
α-helix	680-691	12
β-strand	693	1	17
β-strand	700-702	3	15
α-helix	709-715	7
α-helix	722-726	5
β-strand	729-730	2	12
α-helix	731-737	7
β-strand	753	1	18

Chain S: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	31-37	7
α-helix	63-82	20
β-strand	96	1	18
β-strand	104	1	15
α-helix	105-108	4
α-helix	111-114	4
β-strand	115	1	19
β-strand	122	1	19
β-strand	125-126	2	20
β-strand	133-134	2	20
α-helix	137-139	3
α-helix	140-144	5
α-helix	151-155	5

Chain T: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	21
β-strand	35	1	22
α-helix	40	1
β-strand	41	1	22
α-helix	42	1
β-strand	44-45	2	23
β-strand	48-49	2	23
α-helix	52-67	16
β-strand	70	1	24
β-strand	74-79	6	25
α-helix	85-96	12
β-strand	102-106	5	25
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-151	23	17
β-strand	163-172	10	17
β-strand	175-181	7	17
α-helix	183-191	9
β-strand	198-203	6	17
β-strand	209-214	6	17
α-helix	216-218	3
β-strand	224	1	26
β-strand	229	1	17
α-helix	231-233	3
β-strand	238-248	11	17
α-helix	249-256	8
α-helix	274-277	4
α-helix	282-297	16
β-strand	301-305	5	17
β-strand	307-311	5	25
α-helix	313-315	3
α-helix	318-327	10
β-strand	335-340	6	25
β-strand	342	1	27
β-strand	344-346	3	28
α-helix	347	1
β-strand	354-356	3	28
α-helix	361-364	4
β-strand	367-372	6	25
α-helix	373-375	3
α-helix	377-390	14
β-strand	395	1	29
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-428	10
β-strand	434	1	29
α-helix	436-445	10
β-strand	447	1	30
α-helix	449-457	9

Chain U: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	24
β-strand	31	1	31
β-strand	37	1	31
β-strand	40-41	2	32
β-strand	44-45	2	32
α-helix	48-63	16
β-strand	66	1	33
β-strand	70-74	5	34
α-helix	81-92	12
β-strand	98-102	5	34
α-helix	103-106	4
α-helix	113-122	10
β-strand	125-143	19	9
β-strand	156-161	6	9
β-strand	166-171	6	9
α-helix	173-180	8
β-strand	188-193	6	9
β-strand	199-205	7	9
β-strand	221-222	2	9
α-helix	223-225	3
β-strand	230-240	11	9
α-helix	241-248	8
α-helix	254-259	6
α-helix	267-283	17
β-strand	287-290	4	9
β-strand	292-296	5	34
β-strand	302	1	35
α-helix	303-312	10
β-strand	320-325	6	34
β-strand	329-331	3	36
α-helix	332	1
β-strand	333	1	35
β-strand	338-340	3	36
α-helix	345-349	5
β-strand	352-355	4	34
α-helix	357-359	3
α-helix	361-374	14
β-strand	379	1	37
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	37
α-helix	420-429	10
β-strand	431	1	25
α-helix	433-442	10
α-helix	444-446	3
β-strand	448	1	27

Chain V: 22 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	33
β-strand	35	1	38
α-helix	36	1
β-strand	41	1	38
β-strand	44-45	2	39
β-strand	48-49	2	39
α-helix	52-67	16
β-strand	70	1	40
β-strand	74-78	5	41
α-helix	85-96	12
β-strand	102-106	5	41
α-helix	117-126	10
β-strand	129-151	23	42
α-helix	152	1
α-helix	155-156	2
β-strand	162-172	11	42
β-strand	175-181	7	42
α-helix	185-192	8
β-strand	198-203	6	42
β-strand	207	1	42
β-strand	211-215	5	42
α-helix	216-218	3
β-strand	224	1	9
β-strand	229-230	2	42
α-helix	231-234	4
β-strand	238-248	11	42
α-helix	249-257	9
α-helix	265-272	8
α-helix	282-297	16
β-strand	301-305	5	42
β-strand	307-311	5	41
α-helix	313-315	3
β-strand	317	1	43
α-helix	318-327	10
β-strand	335-340	6	41
β-strand	342	1	44
β-strand	344-346	3	45
α-helix	347	1
β-strand	348	1	43
β-strand	354-356	3	45
α-helix	361-364	4
β-strand	367-371	5	41
α-helix	377-390	14
β-strand	394-395	2	46
α-helix	397-409	13
α-helix	412-417	6
α-helix	419-428	10
β-strand	433-434	2	46
α-helix	436-445	10
β-strand	447	1	34
α-helix	449-458	10

Chain W: 18 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	40
β-strand	31	1	47
α-helix	36	1
β-strand	37	1	47
α-helix	38	1
β-strand	40-41	2	48
β-strand	44-45	2	48
α-helix	48-63	16
β-strand	66	1	49
β-strand	70-74	5	50
α-helix	81-92	12
β-strand	98-101	4	50
α-helix	113-122	10
β-strand	125-147	23	42
β-strand	154-161	8	42
β-strand	166-171	6	42
α-helix	173-180	8
β-strand	188-193	6	42
β-strand	198-204	7	42
β-strand	221	1	42
α-helix	223-225	3
β-strand	230-240	11	42
α-helix	241-249	9
α-helix	253-259	7
α-helix	267-283	17
β-strand	286-290	5	42
β-strand	292-296	5	50
β-strand	302	1	51
α-helix	303-312	10
β-strand	320-325	6	50
β-strand	329-331	3	52
α-helix	332	1
β-strand	333	1	51
β-strand	338-340	3	52
α-helix	345-349	5
β-strand	351-355	5	50
α-helix	361-374	14
β-strand	379	1	53
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	53
α-helix	420-429	10
β-strand	431	1	41
α-helix	433-442	10
β-strand	448	1	44

Chain X: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	49
β-strand	35	1	54
β-strand	41	1	54
β-strand	44-45	2	55
β-strand	48-49	2	55
α-helix	52-67	16
β-strand	74-78	5	56
α-helix	85-96	12
β-strand	102-106	5	56
α-helix	107-110	4
α-helix	117-127	11
β-strand	129-151	23	7
β-strand	163-172	10	7
β-strand	175-181	7	7
α-helix	183-191	9
β-strand	198-203	6	7
β-strand	209-215	7	7
β-strand	223	1	42
α-helix	227-228	2
β-strand	229-230	2	7
α-helix	232-234	3
β-strand	238-248	11	7
α-helix	249-257	9
β-strand	261	1	10
α-helix	265-272	8
α-helix	274-275	2
α-helix	282-298	17
β-strand	301-305	5	7
β-strand	307-311	5	56
α-helix	313-315	3
β-strand	317	1	57
α-helix	318-327	10
β-strand	335-340	6	56
β-strand	342	1	58
β-strand	344-346	3	59
α-helix	347	1
β-strand	348	1	57
β-strand	354-356	3	59
α-helix	361-364	4
β-strand	369-371	3	56
α-helix	377-390	14
β-strand	394-395	2	60
α-helix	397-409	13
α-helix	412-416	5
α-helix	419-428	10
β-strand	433-434	2	60
α-helix	436-445	10
β-strand	447	1	50
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

>9CAT_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

>9CAT_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

>9CAT_3 Chromatin-remodeling complex subunit IES6 (chains S)
MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRH
KSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTG
LKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK

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

>9CAT_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

>9CAT_5 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK

Sequence of entity 6 (Z), FASTA

>9CAT_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:

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
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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