9CCD: DeltaNhp10 INO80

DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, INO80 core module. Determined by electron microscopy at 3.01 Å resolution. Released 16 Jul 2025.

Method: Electron microscopy
Resolution: 3.01 Å
Organism: Saccharomyces cerevisiae
Chains: 10
Atoms: 27,123
Mol. weight: 619.88 kDa
Ligands: ADP
Released: 16 Jul 2025

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

Secondary structure: helices and β-sheets

9CCD contains 169 α-helices and 193 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: 19 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1026-1027	2	1
β-strand	1030	1	2
β-strand	1071-1072	2	3
β-strand	1078	1	2
β-strand	1082-1084	3	4
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	5
α-helix	1139-1144	6
α-helix	1148-1153	6
α-helix	1170-1177	8
α-helix	1186-1190	5
α-helix	1193-1200	8
α-helix	1203-1205	3
β-strand	1214-1215	2	1
α-helix	1217-1219	3
β-strand	1220-1222	3	4
α-helix	1228-1237	10
α-helix	1240-1245	6
α-helix	1251-1258	8
α-helix	1265-1267	3
α-helix	1269-1270	2
α-helix	1275-1277	3
α-helix	1281-1283	3

Chain R: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	6
α-helix	18-22	5
α-helix	25-26	2
β-strand	40-44	5	7
β-strand	48-53	6	7
β-strand	61-64	4	7
β-strand	67	1	8
β-strand	82	1	8
α-helix	83-86	4
α-helix	90-94	5
β-strand	97	1	8
β-strand	100-101	2	9
β-strand	104-105	2	9
α-helix	109-121	13
β-strand	134-136	3	7
α-helix	144-157	14
β-strand	163-164	2	7
α-helix	168-176	9
β-strand	184-189	6	10
β-strand	194-200	7	10
β-strand	203-204	2	10
β-strand	210-212	3	10
α-helix	216-230	15
α-helix	237-238	2
α-helix	240-249	10
α-helix	257-262	6
α-helix	267-273	7
β-strand	275-278	4	6
α-helix	279-280	2
α-helix	590-596	7
α-helix	607-610	4
β-strand	611-614	4	6
α-helix	617-623	7
α-helix	638-648	11
β-strand	653	1	11
β-strand	656	1	11
α-helix	659-665	7
β-strand	668-671	4	10
α-helix	673-676	4
α-helix	680-691	12
β-strand	693	1	12
β-strand	700-701	2	10
α-helix	709-715	7
α-helix	716-720	5
α-helix	723-726	4
β-strand	729	1	7
α-helix	731-737	7
β-strand	753	1	13

Chain S: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	29-37	9
α-helix	55-57	3
α-helix	63-82	20
β-strand	96	1	13
β-strand	104	1	10
α-helix	105-108	4
α-helix	111-114	4
β-strand	115	1	14
β-strand	122	1	14
β-strand	125-126	2	15
β-strand	133-134	2	15
α-helix	137-139	3
α-helix	140-144	5
α-helix	147-148	2
α-helix	152-155	4

Chain T: 19 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	16
β-strand	35	1	17
β-strand	41	1	17
β-strand	44-45	2	18
β-strand	48-49	2	18
α-helix	52-66	15
β-strand	70	1	19
β-strand	74-79	6	20
α-helix	85-96	12
β-strand	102-106	5	20
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-151	23	12
β-strand	163-172	10	12
β-strand	175-181	7	12
α-helix	183-191	9
β-strand	198-203	6	12
β-strand	208-215	8	12
β-strand	224	1	21
β-strand	229-230	2	12
β-strand	238-248	11	12
α-helix	249-256	8
α-helix	274-277	4
α-helix	279-281	3
α-helix	282-296	15
β-strand	301-305	5	12
β-strand	307-311	5	20
α-helix	313-315	3
β-strand	317	1	22
α-helix	318-328	11
β-strand	335-340	6	20
β-strand	342	1	23
β-strand	344-346	3	24
α-helix	347	1
β-strand	348	1	22
β-strand	354-356	3	24
α-helix	361-364	4
β-strand	369-372	4	20
α-helix	377-390	14
β-strand	394-395	2	25
α-helix	397-409	13
α-helix	412-416	5
α-helix	419-428	10
β-strand	433-434	2	25
α-helix	436-445	10
β-strand	447	1	26
α-helix	449-457	9

Chain U: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	19
β-strand	31	1	27
β-strand	37	1	27
β-strand	40-41	2	28
β-strand	44-45	2	28
α-helix	48-63	16
β-strand	66	1	29
β-strand	70-74	5	30
α-helix	81-92	12
β-strand	98-102	5	30
α-helix	113-122	10
β-strand	125-147	23	5
β-strand	154-161	8	5
β-strand	166-171	6	5
α-helix	173-180	8
β-strand	188-193	6	5
β-strand	199-205	7	5
α-helix	206-208	3
β-strand	221-222	2	5
α-helix	223-225	3
β-strand	230-240	11	5
α-helix	241-247	7
α-helix	254-259	6
α-helix	268-283	16
β-strand	286-290	5	5
β-strand	292-296	5	30
α-helix	303-312	10
β-strand	320-325	6	30
β-strand	329-331	3	31
α-helix	332	1
β-strand	338-340	3	31
α-helix	345-349	5
β-strand	352-355	4	30
α-helix	361-374	14
β-strand	379	1	32
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	32
α-helix	420-429	10
β-strand	431	1	20
α-helix	433-442	10
α-helix	444-446	3
β-strand	448	1	23

Chain V: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	29
α-helix	35-36	2
β-strand	44-45	2	33
β-strand	48-49	2	33
α-helix	52-67	16
β-strand	70	1	34
β-strand	74-78	5	35
α-helix	85-96	12
β-strand	102-106	5	35
α-helix	107-110	4
α-helix	117-126	10
β-strand	129-151	23	36
α-helix	152	1
α-helix	155-156	2
β-strand	160	1	37
β-strand	163-172	10	36
β-strand	175-181	7	36
α-helix	185-191	7
β-strand	198-203	6	36
β-strand	207-214	8	36
α-helix	216-218	3
α-helix	232-233	2
β-strand	238-248	11	36
α-helix	249-257	9
α-helix	265-272	8
α-helix	282-297	16
β-strand	301-305	5	36
β-strand	307-311	5	35
α-helix	313-315	3
β-strand	317	1	38
α-helix	318-327	10
β-strand	335-340	6	35
β-strand	342	1	39
β-strand	344-346	3	40
α-helix	347	1
β-strand	348	1	38
β-strand	354-356	3	40
α-helix	361-364	4
β-strand	368-371	4	35
α-helix	377-390	14
β-strand	395	1	41
α-helix	397-409	13
α-helix	412-417	6
α-helix	420-428	9
β-strand	434	1	41
α-helix	436-445	10
β-strand	447	1	30
α-helix	449-457	9

Chain W: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	20	1	34
β-strand	31	1	42
β-strand	37	1	42
β-strand	40-41	2	43
β-strand	44-45	2	43
α-helix	48-63	16
β-strand	66	1	44
β-strand	70-74	5	45
α-helix	81-92	12
β-strand	98-102	5	45
α-helix	103-106	4
α-helix	113-122	10
β-strand	125-147	23	46
β-strand	154-161	8	46
β-strand	166-171	6	46
α-helix	173-180	8
β-strand	188-193	6	46
β-strand	198-204	7	46
α-helix	219-220	2
β-strand	221	1	46
β-strand	230-240	11	46
α-helix	241-247	7
α-helix	253-259	7
α-helix	267-283	17
β-strand	286-290	5	46
β-strand	292-296	5	45
α-helix	303-312	10
β-strand	320-325	6	45
β-strand	330-331	2	47
α-helix	332	1
β-strand	338-339	2	47
α-helix	340-342	3
α-helix	345-349	5
β-strand	351-355	5	45
α-helix	361-374	14
β-strand	379	1	48
α-helix	381-393	13
α-helix	396-412	17
β-strand	418	1	48
α-helix	420-429	10
β-strand	431	1	35
α-helix	433-441	9
β-strand	448	1	39

Chain X: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	44
β-strand	35	1	49
β-strand	41	1	49
β-strand	44-45	2	50
β-strand	48-49	2	50
α-helix	52-67	16
β-strand	74-78	5	51
α-helix	86-96	11
β-strand	102-106	5	51
α-helix	117-126	10
β-strand	129-151	23	3
β-strand	163-172	10	3
β-strand	175-181	7	3
α-helix	183-190	8
β-strand	198-203	6	3
β-strand	209-215	7	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	238-248	11	3
α-helix	249-257	9
α-helix	265-272	8
α-helix	274-275	2
α-helix	282-297	16
β-strand	302-305	4	3
β-strand	307-311	5	51
α-helix	313-315	3
β-strand	317	1	52
α-helix	318-327	10
β-strand	335-340	6	51
β-strand	342	1	53
β-strand	344-346	3	54
α-helix	347	1
β-strand	348	1	52
β-strand	354-356	3	54
α-helix	361-364	4
β-strand	369-371	3	51
α-helix	377-390	14
α-helix	397-409	13
α-helix	412-416	5
α-helix	419-427	9
α-helix	436-445	10
β-strand	447	1	45
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

>9CCD_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

>9CCD_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

>9CCD_3 Chromatin-remodeling complex subunit IES6 (chains S)
MSGSRGNSSNSSVSNNSNNNNNNDGGDERLLFLRSVGERNEIGFPSRFKSAHYKKPTRRH
KSARQLISDENKRINALLTKANKAAESSTAARRLVPKATYFSVEAPPSIRPAKKYCDVTG
LKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLRGANFVLK

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

>9CCD_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

>9CCD_5 RuvB-like protein 2 (chains U, W, Y)
MSIQTSDPNETSDLKSLSLIAAHSHITGLGLDENLQPRPTSEGMVGQLQARRAAGVILKM
VQNGTIAGRAVLVAGPPSTGKTALAMGVSQSLGKDVPFTAIAGSEIFSLELSKTEALTQA
FRKSIGIKIKEETELIEGEVVEIQIDRSITGGHKQGKLTIKTTDMETIYELGNKMIDGLT
KEKVLAGDVISIDKASGKITKLGRSFARSRDYDAMGADTRFVQCPEGELQKRKTVVHTVS
LHEIDVINSRTQGFLALFTGDTGEIRSEVRDQINTKVAEWKEEGKAEIVPGVLFIDEVHM
LDIECFSFINRALEDEFAPIVMMATNRGVSKTRGTNYKSPHGLPLDLLDRSIIITTKSYN
EQEIKTILSIRAQEEEVELSSDALDLLTKTGVETSLRYSSNLISVAQQIAMKRKNNTVEV
EDVKRAYLLFLDSARSVKYVQENESQYIDDQGNVQISIAK

Sequence of entity 6 (Z), FASTA

>9CCD_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
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
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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