9GE5: Human INO80-Hexasome complex

CryoEM structure of the human INO80-Hexasome complex. Determined by electron microscopy at 3.35 Å resolution. Released 20 Aug 2025.

Method: Electron microscopy
Resolution: 3.35 Å
Organisms: Homo sapiens, synthetic construct
Chains: 18
Atoms: 40,014
Mol. weight: 608.55 kDa
Ligands: ATP, ADP, ZN
Released: 20 Aug 2025

Explore 9GE5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GE5 contains 261 α-helices and 223 β-strands across 16 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 A: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
β-strand	26	1	2
α-helix	31	1
β-strand	32	1	2
α-helix	33	1
β-strand	35-36	2	3
β-strand	39-40	2	3
α-helix	43-57	15
β-strand	61	1	4
β-strand	65-69	5	5
α-helix	76-87	12
β-strand	93-97	5	5
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-140	21	6
β-strand	157-163	7	6
β-strand	166-172	7	6
α-helix	174-182	9
β-strand	189-194	6	6
β-strand	199-206	8	6
α-helix	207-209	3
β-strand	215	1	7
β-strand	220-221	2	6
α-helix	222-224	3
β-strand	229-239	11	6
α-helix	240-246	7
α-helix	250-251	2
α-helix	260-262	3
α-helix	273-288	16
β-strand	292-296	5	6
β-strand	298-302	5	5
α-helix	304-306	3
α-helix	309-318	10
α-helix	324-325	2
β-strand	326-331	6	5
β-strand	333	1	8
β-strand	337	1	9
α-helix	338	1
β-strand	345	1	9
α-helix	347-349	3
α-helix	352-355	4
β-strand	359-362	4	5
α-helix	364-367	4
α-helix	368-382	15
β-strand	386	1	10
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	10
α-helix	427-436	10
β-strand	438	1	11
α-helix	440-448	9
α-helix	451-453	3

Chain B: 28 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
α-helix	10-14	5
β-strand	15	1	13
β-strand	26	1	14
α-helix	31	1
β-strand	32	1	14
α-helix	33	1
β-strand	35-36	2	15
β-strand	39-40	2	15
α-helix	43-57	15
β-strand	61	1	16
β-strand	65-69	5	17
α-helix	76-87	12
β-strand	93-97	5	17
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-143	24	18
β-strand	153-163	11	18
β-strand	166-172	7	18
α-helix	174-182	9
β-strand	189-194	6	18
β-strand	199-205	7	18
β-strand	206	1	19
α-helix	207-209	3
β-strand	215	1	20
β-strand	221	1	19
α-helix	222-225	4
β-strand	229-239	11	18
α-helix	240-248	9
α-helix	256-261	6
α-helix	273-288	16
β-strand	292-296	5	18
β-strand	298-302	5	17
α-helix	304-306	3
α-helix	309-320	12
α-helix	324-325	2
β-strand	326-331	6	17
β-strand	333	1	21
α-helix	336	1
β-strand	337	1	22
α-helix	338	1
β-strand	345	1	22
α-helix	347-349	3
α-helix	352-355	4
β-strand	359-362	4	17
α-helix	364-367	4
α-helix	368-382	15
β-strand	386	1	23
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	23
α-helix	427-436	10
β-strand	437-438	2	24
α-helix	440-449	10
α-helix	451-453	3

Chain C: 29 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	25
β-strand	26	1	26
α-helix	31	1
β-strand	32	1	26
α-helix	33	1
β-strand	35-36	2	27
β-strand	39-40	2	27
α-helix	43-57	15
β-strand	61	1	28
β-strand	65-69	5	29
α-helix	78-87	10
β-strand	93-97	5	29
α-helix	98-101	4
α-helix	108-118	11
β-strand	120-142	23	20
α-helix	146-147	2
β-strand	152-163	12	20
β-strand	166-172	7	20
α-helix	175-179	5
β-strand	189-194	6	20
β-strand	200-205	6	20
β-strand	206	1	30
α-helix	207-209	3
β-strand	221	1	30
α-helix	222-224	3
β-strand	229-239	11	20
α-helix	240-248	9
α-helix	256-263	8
α-helix	265-266	2
α-helix	273-288	16
β-strand	292-296	5	20
β-strand	298-302	5	29
α-helix	304-306	3
α-helix	309-318	10
α-helix	324-325	2
β-strand	326-331	6	29
β-strand	333	1	31
α-helix	336	1
β-strand	337	1	32
α-helix	338	1
β-strand	345	1	32
α-helix	347-349	3
α-helix	352-355	4
β-strand	359-362	4	29
α-helix	364-367	4
α-helix	368-382	15
β-strand	386	1	33
α-helix	388-400	13
α-helix	403-408	6
α-helix	410-419	10
β-strand	425	1	33
α-helix	427-436	10
β-strand	438	1	34
α-helix	440-449	10
α-helix	451-453	3

Chain D: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	16
β-strand	42-43	2	35
β-strand	46-47	2	35
α-helix	50-65	16
β-strand	68	1	1
β-strand	71-76	6	11
α-helix	83-94	12
β-strand	100-104	5	11
α-helix	105-107	3
α-helix	115-125	11
β-strand	127-147	21	7
β-strand	159-164	6	7
β-strand	169-174	6	7
α-helix	175	1
α-helix	176-184	9
β-strand	191-196	6	7
β-strand	202-208	7	7
α-helix	209-211	3
β-strand	224-225	2	7
α-helix	226-229	4
β-strand	233-243	11	7
α-helix	244-252	9
α-helix	257-262	6
α-helix	270-286	17
β-strand	290-293	4	7
β-strand	295-299	5	11
α-helix	301-303	3
α-helix	306-315	10
α-helix	321-322	2
β-strand	323-328	6	11
β-strand	333-334	2	36
α-helix	335	1
β-strand	341-342	2	36
α-helix	343-345	3
α-helix	348-351	4
β-strand	355-358	4	11
α-helix	361-363	3
α-helix	364-378	15
β-strand	382	1	37
α-helix	384-396	13
α-helix	400-415	16
β-strand	421	1	37
α-helix	423-432	10
β-strand	434	1	17
α-helix	436-443	8
β-strand	451	1	21

Chain E: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	28
β-strand	33	1	38
α-helix	38	1
β-strand	39	1	38
α-helix	40	1
β-strand	42-43	2	39
β-strand	46-47	2	39
α-helix	50-65	16
β-strand	68	1	13
β-strand	72-76	5	24
α-helix	83-94	12
β-strand	100-104	5	24
α-helix	105-108	4
α-helix	115-124	10
β-strand	127-149	23	20
β-strand	158-164	7	20
β-strand	169-174	6	20
α-helix	175	1
α-helix	176-184	9
β-strand	191-196	6	20
β-strand	201	1	20
β-strand	204-207	4	20
α-helix	211-213	3
α-helix	226-228	3
β-strand	233-243	11	20
α-helix	244-252	9
α-helix	259-262	4
α-helix	270-285	16
β-strand	290-293	4	20
β-strand	295-299	5	24
α-helix	301-303	3
α-helix	306-315	10
α-helix	321-322	2
β-strand	323-328	6	24
β-strand	333-334	2	40
α-helix	335	1
β-strand	341-342	2	40
α-helix	343-345	3
α-helix	348-351	4
β-strand	355-358	4	24
α-helix	364-377	14
β-strand	382	1	41
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	41
α-helix	423-432	10
β-strand	434	1	29
α-helix	436-442	7
β-strand	451	1	31

Chain F: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	4
β-strand	33	1	42
α-helix	38	1
β-strand	39	1	42
α-helix	40	1
β-strand	42-43	2	43
β-strand	46-47	2	43
α-helix	50-65	16
β-strand	68	1	25
β-strand	72-76	5	34
α-helix	83-94	12
β-strand	100-104	5	34
α-helix	105-108	4
α-helix	115-124	10
β-strand	127-148	22	44
β-strand	158-165	8	44
β-strand	168-172	5	44
α-helix	176-185	10
β-strand	191-196	6	44
β-strand	201-208	8	44
α-helix	209-211	3
β-strand	217	1	6
β-strand	224-225	2	44
α-helix	226-228	3
β-strand	233-243	11	44
α-helix	244-250	7
α-helix	258-262	5
α-helix	270-285	16
β-strand	289-293	5	44
β-strand	295-299	5	34
α-helix	301-303	3
α-helix	306-315	10
β-strand	323-328	6	34
β-strand	333-334	2	45
α-helix	335	1
β-strand	341-342	2	45
α-helix	343-345	3
α-helix	348-351	4
β-strand	355-358	4	34
α-helix	361-363	3
α-helix	364-378	15
β-strand	382	1	46
α-helix	384-396	13
α-helix	399-415	17
β-strand	421	1	46
α-helix	423-432	10
β-strand	434	1	5
α-helix	436-444	9
α-helix	447-449	3
β-strand	451	1	8

Chain G: 48 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	520-535	16
β-strand	539-540	2	47
α-helix	543-544	2
α-helix	551-558	8
α-helix	564-567	4
β-strand	570-574	5	47
α-helix	576-578	3
α-helix	581-584	4
α-helix	585-587	3
β-strand	595-597	3	47
α-helix	602-605	4
α-helix	606-608	3
α-helix	609-612	4
β-strand	626-630	5	47
α-helix	631-641	11
β-strand	648-652	5	47
α-helix	654-657	4
α-helix	663-668	6
β-strand	675-679	5	47
α-helix	688-690	3
α-helix	692-698	7
α-helix	706-709	4
α-helix	730-739	10
β-strand	743	1	47
α-helix	749-752	4
α-helix	755-758	4
β-strand	759-765	7	12
α-helix	766-768	3
α-helix	771-779	9
α-helix	809-817	9
α-helix	819-821	3
β-strand	831-833	3	48
α-helix	839	1
β-strand	840	1	49
α-helix	841	1
α-helix	842-847	6
α-helix	850-853	4
α-helix	855-863	9
α-helix	869-876	8
α-helix	889-892	4
α-helix	898-906	9
α-helix	909-931	23
β-strand	944	1	44
α-helix	959-964	6
α-helix	968-971	4
β-strand	980-989	10	20
β-strand	996-1005	10	20
α-helix	1006-1007	2
β-strand	1017-1019	3	48
α-helix	1020-1022	3
β-strand	1026	1	49
α-helix	1029-1040	12
α-helix	1044-1052	9
α-helix	1055-1061	7
α-helix	1064-1066	3
α-helix	1070-1073	4
α-helix	1076-1078	3
α-helix	1095-1099	5
α-helix	1101-1116	16
β-strand	1120-1124	5	12
α-helix	1127-1139	13
β-strand	1146	1	12
α-helix	1155-1163	9
β-strand	1171-1175	5	12
β-strand	1190-1193	4	12
α-helix	1202-1207	6
β-strand	1220-1226	7	12
α-helix	1232-1247	16

Chain H: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	210-234	25
β-strand	273-278	6	20
β-strand	281-286	6	20
β-strand	288	1	50
β-strand	290	1	50
β-strand	297	1	20
α-helix	306-307	2
β-strand	308	1	51
α-helix	316	1
β-strand	317	1	51
α-helix	318	1
β-strand	320-322	3	44
β-strand	328-329	2	44
α-helix	332-339	8

8 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
RuvB-like 1	A, B, C	protein	453	Homo sapiens	Q9Y265 (AlphaFold model)
RuvB-like 2	D, E, F	protein	439	Homo sapiens	Q9Y230 (AlphaFold model)
Chromatin-remodeling ATPase INO80	G	protein	733	Homo sapiens	Q9ULG1 (AlphaFold model)
INO80 complex subunit B	H	protein	135	Homo sapiens	Q9C086 (AlphaFold model)
INO80 complex subunit C	I	protein	107	Homo sapiens	Q6PI98
Actin-related protein 5	J	protein	576	Homo sapiens	Q9H9F9
Hexasomal DNA Strand 1	K	DNA	113	synthetic construct
Hexasomal DNA strand 2	L	DNA	113	synthetic construct
Histone H3.1	M, Q	protein	94	Homo sapiens	P68431
Histone H4	N	protein	81	Homo sapiens	P62805
Histone H4	R	protein	78	Homo sapiens	P62805
Histone H2A type 1-B/E	S	protein	108	Homo sapiens	P04908

1 more molecules are not listed.

Sequence of entity 1 (A, B, C), FASTA

>9GE5_1 RuvB-like 1 (chains A, B, C)
KIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKM
AGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIG
LRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQ
KERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLH
DLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFV
DEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMII
RTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKING
KDSIEKEHVEEISELFYDAKSSAKILADQQDKY

Sequence of entity 2 (D, E, F), FASTA

>9GE5_2 RuvB-like 2 (chains D, E, F)
DVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVL
IAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEE
TEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVIT
IDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVSLHEIDVINSRT
QGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNR
ALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIR
CEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFL
DESRSTQYMKEYQDAFLFN

Sequence of entity 3 (G), FASTA

>9GE5_3 Chromatin-remodeling ATPase INO80 (chains G)
LKGYQLKGMNWLANLYEQGINGILADEMGLGKTVQSIALLAHLAERENIWGPFLIISPAS
TLNNWHQEFTRFVPKFKVLPYWGNPHDRKVIRRFWSQKTLYTQDAPFHVVITSYQLVVQD
VKYFQRVKWQYMVLDEAQALKSSSSVRWKILLQFQCRNRLLLTGTPIQNTMAELWALLHF
IMPTLFDSHEEFNEWFSKDIESHAENKSAIDENQLSRLHMILKPFMLRRIKKDVENELSD
KIEILMYCQLTSRQKLLYQALKNKISIEDLLQSSMGSTQQAQNTTSSLMNLVMQFRKVCN
HPELFERQETWSPFHISLKPYHISKFIYRHGQIRVFNHSRDRWLRVLSPFAPDYIQRSLF
HRKGINEESCFSFLRFIDISPAEMANLMLQGLLARWLALFLSLKASYRLHQLRSWGAPEG
ESHQRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSS
LRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNGAPEL
AADWLNRRSQFFPEPAGGLWSIRPQNGWSFIRIPGKESLITDSGKLYALDVLLTRLKSQG
HRVLIYSQMTRMIDLLEEYMVYRKHTYMRLDGSSKISERRDMVADFQNRNDIFVFLLSTR
AGGLGINLTAADTVIFYDSDWNPTVDQQAMDRAHRLGQTKQVTVYRLICKGTIEERILQR
AKEKSEIQRMVIS

Sequence of entity 4 (H), FASTA

>9GE5_4 INO80 complex subunit B (chains H)
LTEEMLLKREERARKRRLQAARRAEEHKNQTIERLTKTAATSGRGGRGGARGERRGGRAA
APAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRPSPSGPPPRCSVPGCPHPRRYACSRTGQ
ALCSLQCYRINLQMR

Sequence of entity 5 (I), FASTA

>9GE5_5 INO80 complex subunit C (chains I)
KDPNFVHSGHGGAVAGKKNRTWKYLKQILASERALPWQLNDPNYFSIDAPPSFKPAKKYS
DVSGLLANYTDPQSKLRFSTIEEFSYIRRLPSDVVTGYLALRKATSI

Sequence of entity 6 (J), FASTA

>9GE5_6 Actin-related protein 5 (chains J)
PFRDARAAPDPVLEAGPVAHGPLPVPLVLDNGSFQVRAGWACPGQDPGPEPRLQFRAVCA
RGRGGARGASGPQVGNALGSLEPLRWMLRSPFDRNVPVNLELQELLLDYSFQHLGVSSQG
CVDHPIVLTEAVCNPLYSRQMMSELLFECYGIPKVAYGIDSLFSFYHNKPKNSMCSGLII
SSGYQCTHVLPILEGRLDAKNCKRINLGGSQAAGYLQRLLQLKYPGHLAAITLSRMEEIL
HEHSYIAEDYVEELHKWRCPDYYENNVHKMQLPFSSKLLGSTLTSEEKQERRQQQLRRLQ
ELNARRREEKLQLDQERLDRLLYVQELLEDGQMDQFHKALIELNMDSPEELQSYIQKLSI
AVEQAKQKILQAEVNLEVDVVDSKPETPDLEQLEPSLEDVESMNDFDPLFSEETPGVEKP
VTTVQPVFNLAAYHQLFVGTERIRAPEIIFQPSLIGEEQAGIAETLQYILDRYPKDIQEM
LVQNVFLTGGNTMYPGMKARMEKELLEMRPFRSSFQVQLASNPVLDAWYGARDWALNHLD
DNEVWITRKEYEEKGGEYLKEHCASNIYVPIRLPKQ

Sequence of entity 7 (K), FASTA

>9GE5_7 Hexasomal DNA Strand 1 (chains K)
ATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGA
CAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCG

Sequence of entity 8 (L), FASTA

>9GE5_8 Hexasomal DNA strand 2 (chains L)
CGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCG
CGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATAT

Sequence of entity 9 (M, Q), FASTA

>9GE5_9 Histone H3.1 (chains M, Q)
RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLV
GLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 10 (N), FASTA

>9GE5_10 Histone H4 (chains N)
LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTV
TAMDVVYALKRQGRTLYGFGG

Sequence of entity 11 (R), FASTA

>9GE5_11 Histone H4 (chains R)
NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAM
DVVYALKRQGRTLYGFGG

Sequence of entity 12 (S), FASTA

>9GE5_12 Histone H2A type 1-B/E (chains S)
RAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	7
ZN	Zinc ion	Zn	1

Primary citation

Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Aggarwal, P., Sharma, M., Woike, S. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag138 · PubMed

Other PDB entries of the same protein (UniProt Q9Y265 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2C9O 2.2 Å, 3D Structure of the human RuvB-like helicase RuvBL1
8QR1 2.4 Å, Cryo-EM structure of the human Tip60 complex
9EMA 2.4 Å, RUVBL1/2 in complex with ATP and CB-6644 inhibitor
6K0R 2.5 Å, Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin
9C57 2.75 Å, Reconstituted P400 Subcomplex of the human TIP60 complex
2XSZ 3.0 Å, The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II
9CAE 3.07 Å, Cryo-EM structure of the reconstituted RuvBL lobe of the human TIP60 complex (composite…
7ZI4 3.2 Å, Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
8X15 3.2 Å, Structure of nucleosome-bound SRCAP-C in the apo state
8X19 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state
8X1C 3.2 Å, Structure of nucleosome-bound SRCAP-C in the ADP-bound state
8XVT 3.2 Å, The core subcomplex of human NuA4/TIP60 complex

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