7ZI4: Human INO80 complex

Cryo-EM structure of the human INO80 complex bound to a WT nucleosome. Determined by electron microscopy at 3.2 Å resolution. Released 19 Apr 2023.

Method
Electron microscopy
Resolution
3.2 Å
Organisms
Homo sapiens, synthetic construct
Chains
20
Atoms
42,294
Mol. weight
820.3 kDa
Ligands
ADP, BEF, ZN
Released
19 Apr 2023

Explore 7ZI4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZI4 contains 227 α-helices and 216 β-strands across 18 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: 24 helices, 25 β-strands

ElementResiduesLengthSheet
α-helix13-142
β-strand1511
β-strand2612
β-strand3212
β-strand35-3623
β-strand39-4023
α-helix43-5816
β-strand6114
β-strand65-6955
α-helix76-8611
β-strand93-9755
α-helix98-1003
α-helix108-11811
β-strand120-140216
β-strand157-16376
β-strand166-17276
α-helix174-1829
β-strand189-19466
β-strand200-20676
α-helix207-2093
β-strand21517
β-strand220-22126
α-helix222-2243
β-strand229-23686
β-strand23916
α-helix240-2489
α-helix260-2623
α-helix265-2662
α-helix270-2723
α-helix273-28816
β-strand292-29656
β-strand298-30255
α-helix304-3063
α-helix309-31911
β-strand326-33165
β-strand33318
β-strand336-33729
α-helix3381
β-strand345-34629
α-helix347-3493
α-helix352-3576
β-strand359-36245
α-helix368-38215
α-helix388-40013
α-helix404-41916
α-helix427-43610
β-strand438110
α-helix440-44910
α-helix451-4533
Chain B: 18 helices, 23 β-strands
ElementResiduesLengthSheet
α-helix16-183
β-strand22111
α-helix38-403
β-strand42-43212
β-strand46-47212
α-helix50-6516
β-strand6811
β-strand71-76610
α-helix83-9412
β-strand100-104510
α-helix115-1239
β-strand128-147207
β-strand159-16467
β-strand169-17467
α-helix176-1849
β-strand191-19667
β-strand202-20767
β-strand22417
β-strand233-243117
α-helix244-2507
α-helix259-2624
α-helix270-28617
β-strand290-29237
β-strand295-299510
α-helix306-31510
β-strand323-328610
β-strand333-334213
α-helix3351
β-strand341-342213
α-helix343-3453
α-helix348-3536
β-strand354-358510
α-helix364-37815
β-strand382114
α-helix385-39612
α-helix400-41516
β-strand421114
α-helix424-4329
β-strand434115
α-helix436-4449
β-strand451116
Chain C: 20 helices, 26 β-strands
ElementResiduesLengthSheet
β-strand3-5317
α-helix10-145
β-strand15118
β-strand26119
β-strand32119
β-strand35-36220
β-strand39-40220
α-helix43-5816
β-strand61111
β-strand65-69515
α-helix76-8712
β-strand93-97515
α-helix108-11912
β-strand120-1422321
β-strand154-162921
β-strand167-172621
α-helix174-1829
β-strand189-194621
β-strand200-206721
β-strand220-221221
α-helix222-2243
β-strand229-2391121
α-helix240-2489
α-helix256-2616
α-helix273-28816
β-strand293-296421
β-strand298-302515
α-helix304-3063
α-helix309-31911
β-strand326-331615
β-strand333116
β-strand335-337322
α-helix3381
β-strand345-347322
α-helix352-3554
β-strand358-362515
α-helix365-3673
α-helix368-38215
β-strand386123
α-helix388-40013
α-helix403-4086
α-helix410-41910
β-strand425123
α-helix427-43610
β-strand438124
α-helix442-4498
Chain D: 19 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand22125
β-strand33126
β-strand39126
β-strand42-43227
β-strand46-47227
α-helix50-6516
β-strand68118
β-strand72-76524
α-helix83-9412
β-strand100-104524
α-helix115-12410
β-strand128-1502328
β-strand158-164728
β-strand169-174628
α-helix178-1858
β-strand191-196628
β-strand202-207628
α-helix210-2123
β-strand224128
β-strand233-2431128
α-helix244-2529
α-helix259-2624
α-helix270-28617
β-strand290-292328
β-strand295-299524
α-helix301-3033
α-helix306-31510
β-strand323-328624
β-strand333-334229
α-helix3351
β-strand341-342229
α-helix343-3453
α-helix348-3514
β-strand354-358524
α-helix364-37815
β-strand382130
α-helix384-39613
α-helix399-41517
β-strand421130
α-helix423-43210
β-strand434131
α-helix436-4438
α-helix444-4463
Chain E: 25 helices, 28 β-strands
ElementResiduesLengthSheet
α-helix13-142
β-strand15132
β-strand26133
α-helix311
β-strand32133
α-helix331
β-strand35-36234
β-strand39-40234
α-helix43-5816
β-strand61125
β-strand65-69531
α-helix76-8712
β-strand93-97531
α-helix108-11811
β-strand120-1392035
α-helix1411
β-strand142-143228
β-strand152-154328
β-strand157-162635
β-strand167-172635
α-helix175-1806
β-strand189-194635
β-strand200-205635
β-strand206136
α-helix219-2202
β-strand221136
α-helix222-2243
β-strand229-236835
β-strand239135
α-helix240-2489
α-helix256-2638
α-helix265-2662
α-helix273-28816
β-strand292-296535
β-strand298-302531
α-helix304-3063
α-helix309-31911
β-strand326-331631
β-strand335-337337
α-helix3381
β-strand345-347337
α-helix352-3554
β-strand358-362531
α-helix368-38215
β-strand386138
α-helix388-40114
α-helix403-4086
α-helix410-42011
β-strand425138
α-helix427-43610
β-strand438139
α-helix440-44910
α-helix451-4533
Chain F: 19 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand2214
β-strand42-43240
β-strand46-47240
α-helix50-6516
β-strand68132
β-strand71-76639
α-helix83-9412
β-strand100-104539
α-helix105-1084
α-helix115-12410
β-strand128-1472041
β-strand159-164641
β-strand169-172441
α-helix176-18510
β-strand191-195541
β-strand202-207641
α-helix209-2113
β-strand21716
β-strand224141
α-helix226-2283
β-strand233-2431141
α-helix244-2529
α-helix257-2626
α-helix270-28617
β-strand289-292441
β-strand295-299539
α-helix301-3033
α-helix306-31510
β-strand323-328639
β-strand332-334342
α-helix3351
β-strand341-343342
α-helix348-3514
β-strand356-358339
α-helix364-37714
α-helix384-39613
α-helix399-41517
α-helix423-43210
β-strand43415
α-helix436-44510
β-strand45118
Chain G: 39 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix520-53516
α-helix549-55911
β-strand570-573443
α-helix579-58911
β-strand595143
α-helix602-61211
β-strand626-629443
α-helix631-6366
α-helix638-6425
β-strand648-650343
α-helix654-6563
α-helix663-6697
β-strand676-677243
α-helix688-69811
α-helix706-7116
α-helix730-73910
β-strand759-765717
α-helix769-77911
α-helix810-8178
β-strand831-833344
α-helix835-8373
β-strand838-839245
α-helix842-8476
α-helix850-8534
α-helix855-8639
α-helix869-8779
α-helix890-8934
α-helix898-9069
α-helix909-93224
α-helix959-9646
α-helix966-9716
β-strand980-984546
β-strand986-989428
β-strand996-998328
β-strand1002-1005446
α-helix1006-10072
α-helix1008-10103
β-strand1017-1019344
α-helix1020-10223
β-strand1024-1025245
α-helix1029-103810
α-helix1044-10529
α-helix1055-10639
α-helix1064-10663
α-helix1070-10734
α-helix1090-10923
α-helix1095-10995
α-helix1101-111616
β-strand1120-1124517
α-helix1127-113913
β-strand1145-1146217
α-helix1153-116311
β-strand1171-1175517
α-helix1176-11805
β-strand1190-1193417
α-helix1203-12108
β-strand1220-1226717
α-helix1231-124818
Chain H: 15 helices, 20 β-strands
ElementResiduesLengthSheet
β-strand33-36451
β-strand41-46651
β-strand58-62551
β-strand65152
β-strand66-67253
β-strand74-75253
β-strand95152
β-strand98-99254
β-strand102-103254
α-helix107-11913
β-strand132151
α-helix144-15613
β-strand160-161251
α-helix166-1749
β-strand183-188655
β-strand193-198655
β-strand203155
β-strand209-211355
α-helix215-22915
α-helix239-24810
α-helix256-2627
α-helix266-2694
β-strand274156
β-strand444156
α-helix447-4504
α-helix452-4543
α-helix458-4603
α-helix468-4769
α-helix481-4888
β-strand491-495555
α-helix503-51412
β-strand523-525355
α-helix532-54211
β-strand552-553251
α-helix556-5594

10 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RuvB-like 1A, C, Eprotein456Homo sapiensQ9Y265 (AlphaFold model)
RuvB-like 2B, D, Fprotein463Homo sapiensQ9Y230 (AlphaFold model)
Chromatin-remodeling ATPase INO80Gprotein1556Homo sapiensQ9ULG1 (AlphaFold model)
Histone H4J, Nprotein103Homo sapiensP62805 (AlphaFold model)
INO80 complex subunit BRprotein356Homo sapiensQ9C086
Actin-related protein 5Hprotein607Homo sapiensQ9H9F9
INO80 complex subunit CQprotein192Homo sapiensQ6PI98
Histone H3.1I, Mprotein136Homo sapiensP68431
Histone H2A type 1-B/EK, Oprotein130Homo sapiensP04908
Histone H2B type 1-JL, Pprotein126Homo sapiensP06899
DNA (158-mer)XDNA158synthetic construct
DNA (158-mer)YDNA158synthetic construct
Sequence of entity 1 (A, C, E), FASTA
>7ZI4_1 RuvB-like 1 (chains A, C, E)
MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKK
MAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAI
GLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESL
QKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL
HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLF
VDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMI
IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN
GKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK
Sequence of entity 2 (B, D, F), FASTA
>7ZI4_2 RuvB-like 2 (chains B, D, F)
MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVL
EMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT
QAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIE
SLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH
TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDE
VHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTT
PYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTE
VQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS
Sequence of entity 3 (G), FASTA
>7ZI4_3 Chromatin-remodeling ATPase INO80 (chains G)
MASELGARDDGGCTELAKPLYLQYLERALRLDHFLRQTSAIFNRNISSDDSEDGLDDSNP
LLPQSGDPLIQVKEEPPNSLLGETSGAGSSGMLNTYSLNGVLQSESKCDKGNLYNFSKLK
KSRKWLKSILLSDESSEADSQSEDDDEEELNLSREELHNMLRLHKYKKLHQNKYSKDKEL
QQYQYYSAGLLSTYDPFYEQQRHLLGPKKKKFKEEKKLKAKLKKVKKKRRRDEELSSEES
PRRHHHQTKVFAKFSHDAPPPGTKKKHLSIEQLNARRRKVWLSIVKKELPKANKQKASAR
NLFLTNSRKLAHQCMKEVRRAALQAQKNCKETLPRARRLTKEMLLYWKKYEKVEKEHRKR
AEKEALEQRKLDEEMREAKRQQRKLNFLITQTELYAHFMSRKRDMGHDGIQEEILRKLED
SSTQRQIDIGGGVVVNITQEDYDSNHFKAQALKNAENAYHIHQARTRSFDEDAKESRAAA
LRAANKSGTGFGESYSLANPSIRAGEDIPQPTIFNGKLKGYQLKGMNWLANLYEQGINGI
LADEMGLGKTVQSIALLAHLAERENIWGPFLIISPASTLNNWHQEFTRFVPKFKVLPYWG
NPHDRKVIRRFWSQKTLYTQDAPFHVVITSYQLVVQDVKYFQRVKWQYMVLDEAQALKSS
SSVRWKILLQFQCRNRLLLTGTPIQNTMAELWALLHFIMPTLFDSHEEFNEWFSKDIESH
AENKSAIDENQLSRLHMILKPFMLRRIKKDVENELSDKIEILMYCQLTSRQKLLYQALKN
KISIEDLLQSSMGSTQQAQNTTSSLMNLVMQFRKVCNHPELFERQETWSPFHISLKPYHI
SKFIYRHGQIRVFNHSRDRWLRVLSPFAPDYIQRSLFHRKGINEESCFSFLRFIDISPAE
MANLMLQGLLARWLALFLSLKASYRLHQLRSWGAPEGESHQRYLRNKDFLLGVNFPLSFP
NLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAV
PLDSYCNDRSAEYERRVLKEGGSLAAKQCLLNGAPELAADWLNRRSQFFPEPAGGLWSIR
PQNGWSFIRIPGKESLITDSGKLYALDVLLTRLKSQGHRVLIYSQMTRMIDLLEEYMVYR
KHTYMRLDGSSKISERRDMVADFQNRNDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNP
TVDQQAMDRAHRLGQTKQVTVYRLICKGTIEERILQRAKEKSEIQRMVISGGNFKPDTLK
PKEVVSLLLDDEELEKKLRLRQEEKRQQEETNRVKERKRKREKYAEKKKKEDELDGKRRK
EGVNLVIPFVPSADNSNLSADGDDSFISVDSAMPSPFSEISISSELHTGSIPLDESSSDM
LVIVDDPASSAPQSRATNSPASITGSVSDTVNGISIQEMPAAGRGHSARSRGRPKGSGST
AKGAGKGRSRKSTAGSAAAMAGAKAGAAAASAAAYAAYGYNVSKGISASSPLQTSLVRPA
GLADFGPSSASSPLSSPLSKGNNVPGNPKNLHMTSSLAPDSLVRKQGKGTNPSGGR
Sequence of entity 4 (J, N), FASTA
>7ZI4_4 Histone H4 (chains J, N)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 5 (R), FASTA
>7ZI4_5 INO80 complex subunit B (chains R)
MSKLWRRGSTSGAMEAPEPGEALELSLAGAHGHGVHKKKHKKHKKKHKKKHHQEEDAGPT
QPSPAKPQLKLKIKLGGQVLGTKSVPTFTVIPEGPRSPSPLMVVDNEEEPMEGVPLEQYR
AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQRWLDALEKGELDDNGDLKKEINERLLTARQ
RALLQKARSQPSPMLPLPVAEGCPPPALTEEMLLKREERARKRRLQAARRAEEHKNQTIE
RLTKTAATSGRGGRGGARGERRGGRAAAPAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRP
SPSGPPPRCSVPGCPHPRRYACSRTGQALCSLQCYRINLQMRLGGPEGPGSPLLAT
Sequence of entity 6 (H), FASTA
>7ZI4_6 Actin-related protein 5 (chains H)
MAANVFPFRDARAAPDPVLEAGPVAHGPLPVPLVLDNGSFQVRAGWACPGQDPGPEPRLQ
FRAVCARGRGGARGASGPQVGNALGSLEPLRWMLRSPFDRNVPVNLELQELLLDYSFQHL
GVSSQGCVDHPIVLTEAVCNPLYSRQMMSELLFECYGIPKVAYGIDSLFSFYHNKPKNSM
CSGLIISSGYQCTHVLPILEGRLDAKNCKRINLGGSQAAGYLQRLLQLKYPGHLAAITLS
RMEEILHEHSYIAEDYVEELHKWRCPDYYENNVHKMQLPFSSKLLGSTLTSEEKQERRQQ
QLRRLQELNARRREEKLQLDQERLDRLLYVQELLEDGQMDQFHKALIELNMDSPEELQSY
IQKLSIAVEQAKQKILQAEVNLEVDVVDSKPETPDLEQLEPSLEDVESMNDFDPLFSEET
PGVEKPVTTVQPVFNLAAYHQLFVGTERIRAPEIIFQPSLIGEEQAGIAETLQYILDRYP
KDIQEMLVQNVFLTGGNTMYPGMKARMEKELLEMRPFRSSFQVQLASNPVLDAWYGARDW
ALNHLDDNEVWITRKEYEEKGGEYLKEHCASNIYVPIRLPKQASRSSDAQASSKGSAAGG
GGAGEQA
Sequence of entity 7 (Q), FASTA
>7ZI4_7 INO80 complex subunit C (chains Q)
MAAQIPIVATTSTPGIVRNSKKRPASPSHNGSSGGGYGASKKKKASASSFAQGISMEAMS
ENKMVPSEFSTGPVEKAAKPLPFKDPNFVHSGHGGAVAGKKNRTWKNLKQILASERALPW
QLNDPNYFSIDAPPSFKPAKKYSDVSGLLANYTDPQSKLRFSTIEEFSYIRRLPSDVVTG
YLALRKATSIVP
Sequence of entity 8 (I, M), FASTA
>7ZI4_8 Histone H3.1 (chains I, M)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 9 (K, O), FASTA
>7ZI4_9 Histone H2A type 1-B/E (chains K, O)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 10 (L, P), FASTA
>7ZI4_10 Histone H2B type 1-J (chains L, P)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 11 (X), FASTA
>7ZI4_11 DNA (158-MER) (chains X)
CCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTAC
GCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTC
AGATATATACATCCTGTGCATGTACTCGGGATATTGAT
Sequence of entity 12 (Y), FASTA
>7ZI4_12 DNA (158-MER) (chains Y)
ATCAATATCCCGAGTACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGG
AGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCT
AGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGG

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P28
BEFBeryllium trifluoride ionBe F31
ZNZinc ionZn1

Primary citation

Cryo-EM structure of the human INO80 complex bound to a WT nucleosome. Vance, N.R., Ayala, R., Willhoft, O. et al. To be published.

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

Browse structure collections

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