6HTS: Human INO80 complex

Cryo-EM structure of the human INO80 complex bound to nucleosome. Determined by electron microscopy at 4.8 Å resolution. Released 7 Nov 2018.

Method
Electron microscopy
Resolution
4.8 Å
Organisms
Homo sapiens, synthetic construct
Chains
19
Atoms
38,744
Mol. weight
811.32 kDa
Ligands
ZN, ADP
Released
7 Nov 2018

Explore 6HTS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HTS contains 239 α-helices and 208 β-strands across 17 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, 27 β-strands

ElementResiduesLengthSheet
α-helix13-142
β-strand1511
β-strand2612
α-helix311
β-strand3212
α-helix331
β-strand35-3623
β-strand39-4023
α-helix43-5816
β-strand6114
β-strand65-6955
α-helix76-8712
β-strand93-9755
α-helix108-11912
β-strand121-134146
β-strand138-14036
β-strand157-16376
β-strand166-17276
α-helix174-1829
β-strand189-19466
β-strand200-20676
α-helix207-2115
β-strand21517
β-strand220-22126
α-helix222-2254
β-strand229-239116
α-helix240-2489
α-helix260-2623
α-helix265-2662
α-helix270-2723
α-helix273-28917
β-strand292-29546
β-strand298-30255
α-helix304-3063
α-helix309-32012
α-helix324-3252
β-strand326-33165
β-strand33318
β-strand336-33729
α-helix3381
β-strand345-34629
α-helix347-3493
α-helix352-3576
β-strand359-36245
α-helix365-3673
α-helix368-38215
β-strand386110
α-helix388-40013
α-helix403-4086
α-helix410-42011
β-strand425110
α-helix427-43610
β-strand438111
α-helix440-45011
Chain B: 18 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand22112
β-strand42-43213
β-strand46-47213
α-helix50-6516
β-strand6811
β-strand72-77611
α-helix83-9412
β-strand100-104511
α-helix115-12612
β-strand128-148217
β-strand158-16477
β-strand169-17467
α-helix176-1849
β-strand191-19667
β-strand202-20767
α-helix226-2283
β-strand233-243117
α-helix244-2529
α-helix256-2627
α-helix270-28617
β-strand290-29237
β-strand295-299511
β-strand305114
α-helix306-31712
β-strand323-328611
β-strand333-334215
α-helix3351
β-strand336114
β-strand341-342215
α-helix343-3453
α-helix348-3514
β-strand355-359511
α-helix360-3634
α-helix364-37815
α-helix384-39613
α-helix399-41618
α-helix423-43210
β-strand434116
α-helix436-44510
β-strand451117
Chain C: 26 helices, 28 β-strands
ElementResiduesLengthSheet
α-helix13-142
β-strand15118
β-strand26119
α-helix311
β-strand32119
α-helix331
β-strand35-36220
β-strand39-40220
α-helix43-5816
β-strand61112
β-strand65-69516
α-helix76-8712
β-strand93-97516
α-helix108-11912
β-strand121-1402021
β-strand143122
β-strand153122
β-strand157-162621
β-strand167-172621
α-helix174-1829
β-strand189-194621
β-strand200-206721
α-helix207-2115
β-strand215123
β-strand220-221221
α-helix222-2243
β-strand229-2391121
α-helix240-2489
α-helix256-2638
α-helix270-2723
α-helix273-28917
β-strand292-295421
β-strand298-302516
α-helix304-3063
α-helix309-32012
α-helix324-3252
β-strand326-331616
β-strand333117
β-strand336-337224
α-helix3381
β-strand345-346224
α-helix347-3493
α-helix352-3576
β-strand359-362416
α-helix365-3673
α-helix368-38114
β-strand386125
α-helix388-40013
α-helix403-4086
α-helix410-42011
β-strand425125
α-helix427-43610
β-strand438126
α-helix440-44910
Chain D: 22 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand22127
β-strand33128
α-helix381
β-strand39128
α-helix401
β-strand42-43229
β-strand46-47229
α-helix50-6516
β-strand68118
β-strand72-77626
α-helix83-9311
β-strand100-104526
α-helix115-12612
β-strand128-1492223
β-strand158-164723
β-strand169-174623
α-helix176-1849
β-strand191-196623
β-strand202-207623
α-helix226-2283
β-strand233-2431123
α-helix244-2529
α-helix257-2626
α-helix270-28617
β-strand289-292423
β-strand295-299526
α-helix301-3033
α-helix306-31510
α-helix321-3233
β-strand324-328526
β-strand333-334230
α-helix3351
β-strand341-342230
α-helix343-3453
α-helix348-3536
β-strand355-359526
α-helix360-3623
α-helix364-37714
α-helix386-39611
α-helix399-41517
α-helix423-43210
β-strand434131
α-helix436-44510
β-strand451132
Chain E: 28 helices, 29 β-strands
ElementResiduesLengthSheet
α-helix13-142
β-strand15133
β-strand26134
α-helix311
β-strand32134
α-helix331
β-strand35-36235
β-strand39-40235
α-helix43-5816
β-strand61127
β-strand65-69531
α-helix76-8712
β-strand93-97531
α-helix98-1014
α-helix108-11912
β-strand121-1331336
β-strand134137
β-strand137-139337
β-strand152-154323
β-strand157-162637
β-strand167-172637
α-helix175-1828
β-strand189-194636
β-strand200-206736
α-helix207-2115
β-strand215138
β-strand220-221236
α-helix222-2254
β-strand229-2391136
α-helix240-2489
α-helix256-2638
α-helix265-2662
α-helix270-2723
α-helix273-28917
β-strand292-295436
β-strand298-302531
α-helix304-3063
α-helix309-31911
α-helix324-3252
β-strand326-331631
β-strand333132
β-strand336-337239
α-helix3381
β-strand345-346239
α-helix347-3493
α-helix352-3576
β-strand359-362431
α-helix365-3673
α-helix368-38215
β-strand386140
α-helix388-40013
α-helix403-4086
α-helix410-42011
β-strand425140
α-helix427-43610
β-strand438141
α-helix440-44910
Chain F: 18 helices, 21 β-strands
ElementResiduesLengthSheet
β-strand2214
β-strand42-43242
β-strand46-47242
α-helix50-6516
β-strand68133
β-strand72-76541
α-helix83-9412
β-strand100-104541
α-helix115-12511
β-strand128-1482138
β-strand158-164738
β-strand169-174638
α-helix176-1849
β-strand191-195538
β-strand202-207638
α-helix209-2124
β-strand224138
α-helix226-2283
β-strand233-2431138
α-helix244-2529
α-helix256-2627
α-helix270-28617
β-strand290-292338
β-strand295-299541
α-helix306-31712
β-strand323-327541
β-strand332143
α-helix334-3352
β-strand343143
α-helix348-3514
β-strand354-358541
α-helix361-3633
α-helix364-37815
α-helix386-39611
α-helix399-41517
α-helix423-43210
β-strand43415
α-helix436-44510
β-strand45118
Chain G: 35 helices, 24 β-strands
ElementResiduesLengthSheet
α-helix520-53415
β-strand539-541344
α-helix545-5473
α-helix549-5579
β-strand570-573444
α-helix579-58911
β-strand595144
β-strand598144
α-helix602-61211
β-strand626-629444
α-helix631-6366
α-helix638-6414
β-strand648-652544
α-helix654-6574
α-helix663-6708
β-strand675-679544
α-helix688-69811
α-helix728-73912
β-strand743-744244
α-helix756-7572
β-strand760-765645
α-helix769-77810
α-helix810-8156
β-strand828146
β-strand831-833347
α-helix835-8373
β-strand838-839248
α-helix842-8465
α-helix855-8639
α-helix869-8779
α-helix889-8935
α-helix898-90710
α-helix909-93022
α-helix936-9372
α-helix938-9414
α-helix959-9646
α-helix966-9716
β-strand989-990249
β-strand996-997249
β-strand1017-1019347
α-helix1020-10223
β-strand1024-1025248
α-helix1030-103910
α-helix1044-10518
α-helix1055-106410
β-strand1089146
α-helix1101-111616
β-strand1120-1123445
α-helix1127-113812
β-strand1143150
β-strand1146145
α-helix1153-11619
β-strand1169150
β-strand1171-1174445
α-helix1176-11794
β-strand1190-1193445
α-helix1202-12087
β-strand1220-1226745
α-helix1231-124717
Chain H: 20 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand33-37551
β-strand41-45551
β-strand59-62451
β-strand98-99252
β-strand102-103252
α-helix106-12015
β-strand132-135451
α-helix142-15110
α-helix152-1565
β-strand161-164451
α-helix166-1749
β-strand183-188653
β-strand193-199753
β-strand202-203253
β-strand209-211353
α-helix215-22915
α-helix231-2366
α-helix239-24911
α-helix256-2638
β-strand271154
β-strand444154
α-helix447-4504
α-helix452-4543
α-helix458-4603
α-helix468-47811
α-helix483-4897
β-strand491-494453
α-helix496-4994
α-helix503-51412
α-helix520-5212
β-strand524153
α-helix532-54211
α-helix544-5507
β-strand552151
α-helix554-5607
α-helix563-5664

9 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 INO80Gprotein1290Homo sapiensQ9ULG1 (AlphaFold model)
Actin-related protein 5Hprotein607Homo sapiensQ9H9F9 (AlphaFold model)
Histone H3.1I, Mprotein136Homo sapiensP68431
Histone H4J, Nprotein103Homo sapiensP62805
Histone H2A type 1-B/EK, Oprotein130Homo sapiensP04908
Histone H2B type 1-JL, Pprotein126Homo sapiensP06899
INO80 complex subunit BRprotein356Homo sapiensQ9C086
DNA (150-mer)XDNA228synthetic construct
DNA (150-mer)YDNA228synthetic construct
Sequence of entity 1 (A, C, E), FASTA
>6HTS_1 RuvB-like 1 (chains A, C, E)
MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKK
MAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAI
GLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESL
QKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL
HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLF
VDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMI
IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKIN
GKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK
Sequence of entity 2 (B, D, F), FASTA
>6HTS_2 RuvB-like 2 (chains B, D, F)
MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVL
EMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALT
QAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIE
SLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH
TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDE
VHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTT
PYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTE
VQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS
Sequence of entity 3 (G), FASTA
>6HTS_3 Chromatin-remodeling ATPase INO80 (chains G)
HLSIEQLNARRRKVWLSIVKKELPKANKQKASARNLFLTNSRKLAHQCMKEVRRAALQAQ
KNCKETLPRARRLTKEMLLYWKKYEKVEKEHRKRAEKEALEQRKLDEEMREAKRQQRKLN
FLITQTELYAHFMSRKRDMGHDGIQEEILRKLEDSSTQRQIDIGGGVVVNITQEDYDSNH
FKAQALKNAENAYHIHQARTRSFDEDAKESRAAALRAANKSGTGFGESYSLANPSIRAGE
DIPQPTIFNGKLKGYQLKGMNWLANLYEQGINGILADEMGLGKTVQSIALLAHLAERENI
WGPFLIISPASTLNNWHQEFTRFVPKFKVLPYWGNPHDRKVIRRFWSQKTLYTQDAPFHV
VITSYQLVVQDVKYFQRVKWQYMVLDEAQALKSSSSVRWKILLQFQCRNRLLLTGTPIQN
TMAELWALLHFIMPTLFDSHEEFNEWFSKDIESHAENKSAIDENQLSRLHMILKPFMLRR
IKKDVENELSDKIEILMYCQLTSRQKLLYQALKNKISIEDLLQSSMGSTQQAQNTTSSLM
NLVMQFRKVCNHPELFERQETWSPFHISLKPYHISKFIYRHGQIRVFNHSRDRWLRVLSP
FAPDYIQRSLFHRKGINEESCFSFLRFIDISPAEMANLMLQGLLARWLALFLSLKASYRL
HQLRSWGAPEGESHQRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQ
VVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAA
KQCLLNGAPELAADWLNRRSQFFPEPAGGLWSIRPQNGWSFIRIPGKESLITDSGKLYAL
DVLLTRLKSQGHRVLIYSQMTRMIDLLEEYMVYRKHTYMRLDGSSKISERRDMVADFQNR
NDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTVDQQAMDRAHRLGQTKQVTVYRLIC
KGTIEERILQRAKEKSEIQRMVISGGNFKPDTLKPKEVVSLLLDDEELEKKLRLRQEEKR
QQEETNRVKERKRKREKYAEKKKKEDELDGKRRKEGVNLVIPFVPSADNSNLSADGDDSF
ISVDSAMPSPFSEISISSELHTGSIPLDESSSDMLVIVDDPASSAPQSRATNSPASITGS
VSDTVNGISIQEMPAAGRGHSARSRGRPKGSGSTAKGAGKGRSRKSTAGSAAAMAGAKAG
AAAASAAAYAAYGYNVSKGISASSPLQTSLVRPAGLADFGPSSASSPLSSPLSKGNNVPG
NPKNLHMTSSLAPDSLVRKQGKGTNPSGGR
Sequence of entity 4 (H), FASTA
>6HTS_4 Actin-related protein 5 (chains H)
MAANVFPFRDARAAPDPVLEAGPVAHGPLPVPLVLDNGSFQVRAGWACPGQDPGPEPRLQ
FRAVCARGRGGARGASGPQVGNALGSLEPLRWMLRSPFDRNVPVNLELQELLLDYSFQHL
GVSSQGCVDHPIVLTEAVCNPLYSRQMMSELLFECYGIPKVAYGIDSLFSFYHNKPKNSM
CSGLIISSGYQCTHVLPILEGRLDAKNCKRINLGGSQAAGYLQRLLQLKYPGHLAAITLS
RMEEILHEHSYIAEDYVEELHKWRCPDYYENNVHKMQLPFSSKLLGSTLTSEEKQERRQQ
QLRRLQELNARRREEKLQLDQERLDRLLYVQELLEDGQMDQFHKALIELNMDSPEELQSY
IQKLSIAVEQAKQKILQAEVNLEVDVVDSKPETPDLEQLEPSLEDVESMNDFDPLFSEET
PGVEKPVTTVQPVFNLAAYHQLFVGTERIRAPEIIFQPSLIGEEQAGIAETLQYILDRYP
KDIQEMLVQNVFLTGGNTMYPGMKARMEKELLEMRPFRSSFQVQLASNPVLDAWYGARDW
ALNHLDDNEVWITRKEYEEKGGEYLKEHCASNIYVPIRLPKQASRSSDAQASSKGSAAGG
GGAGEQA
Sequence of entity 5 (I, M), FASTA
>6HTS_5 Histone H3.1 (chains I, M)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 6 (J, N), FASTA
>6HTS_6 Histone H4 (chains J, N)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (K, O), FASTA
>6HTS_7 Histone H2A type 1-B/E (chains K, O)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 8 (L, P), FASTA
>6HTS_8 Histone H2B type 1-J (chains L, P)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 9 (R), FASTA
>6HTS_9 INO80 complex subunit B (chains R)
MSKLWRRGSTSGAMEAPEPGEALELSLAGAHGHGVHKKKHKKHKKKHKKKHHQEEDAGPT
QPSPAKPQLKLKIKLGGQVLGTKSVPTFTVIPEGPRSPSPLMVVDNEEEPMEGVPLEQYR
AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQRWLDALEKGELDDNGDLKKEINERLLTARQ
RALLQKARSQPSPMLPLPVAEGCPPPALTEEMLLKREERARKRRLQAARRAEEHKNQTIE
RLTKTAATSGRGGRGGARGERRGGRAAAPAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRP
SPSGPPPRCSVPGCPHPRRYACSRTGQALCSLQCYRINLQMRLGGPEGPGSPLLAT
Sequence of entity 10 (X), FASTA
>6HTS_10 DNA (150-MER) (chains X)
GTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACCCCGAGTACATGCACAGGATG
TATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGG
GGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCT
CGGCACCGGGATTGTCCAGGGCGGCCGCGGATGCATTAATGCAGATTC
Sequence of entity 11 (Y), FASTA
>6HTS_11 DNA (150-MER) (chains Y)
GAATCTGCATTAATGCATCCGCGGCCGCCCTGGACAATCCCGGTGCCGAGGCCGCTCAAT
TGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAA
CCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCAT
GTACTCGGGGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGAC

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P26

Primary citation

Structure and regulation of the human INO80-nucleosome complex. Ayala, R., Willhoft, O., Aramayo, R.J. et al. Nature (2018) 556:391-395. DOI 10.1038/s41586-018-0021-6 · PubMed

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

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