Cryo-EM structure of the human INO80 complex bound to a WT nucleosome

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update _pdbx_entry_details.has_protein_modification PDBe PDBe 2022-04-07 2023-04-19 2023-04-19 2026-09-02 Wellcome Trust 209327/Z/17/Z United Kingdom Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Vance NR Ayala R Willhoft O Tvardovskiy A McCormack EA Bartke T Zhang X Wigley DB chromatin remodeler, transcription, replication, DNA repair, DNA BINDING PROTEIN Vance NR Ayala R Willhoft O Tvardovskiy A McCormack EA Bartke T Zhang X Wigley DB Cryo-EM structure of the human INO80 complex bound to a WT nucleosome To Be Published 0353 7zi4 FULLOVERLAP PDB 6HTS unspecified PDB 6FML unspecified EMDB EMD-14737 associated EM volume

Complex of human INO80core bound to a WT nucleosome Complex of human INO80core bound to a WT nucleosome 0 1 2 3 4 5 6 7 8 9 10 11 12 Homo sapiens 1.0 RuvB-like 1 Homo sapiens 0.050296914 3 Spodoptera frugiperda LEVO MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALA LAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIG LKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALE SSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTK TTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK Q9Y265 3.6.4.12 RuvB-like 2 Homo sapiens 0.051222464999999995 3 Spodoptera frugiperda LEVO MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPG TGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGK LTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDM APVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLR YAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS Q9Y230 3.6.4.12 Chromatin-remodeling ATPase INO80 Homo sapiens 0.17703281199999998 1 Spodoptera frugiperda LEVO MASELGARDDGGCTELAKPLYLQYLERALRLDHFLRQTSAIFNRNISSDDSEDGLDDSNPLLPQSGDPLIQVKEEPPNSL LGETSGAGSSGMLNTYSLNGVLQSESKCDKGNLYNFSKLKKSRKWLKSILLSDESSEADSQSEDDDEEELNLSREELHNM LRLHKYKKLHQNKYSKDKELQQYQYYSAGLLSTYDPFYEQQRHLLGPKKKKFKEEKKLKAKLKKVKKKRRRDEELSSEES PRRHHHQTKVFAKFSHDAPPPGTKKKHLSIEQLNARRRKVWLSIVKKELPKANKQKASARNLFLTNSRKLAHQCMKEVRR AALQAQKNCKETLPRARRLTKEMLLYWKKYEKVEKEHRKRAEKEALEQRKLDEEMREAKRQQRKLNFLITQTELYAHFMS RKRDMGHDGIQEEILRKLEDSSTQRQIDIGGGVVVNITQEDYDSNHFKAQALKNAENAYHIHQARTRSFDEDAKESRAAA LRAANKSGTGFGESYSLANPSIRAGEDIPQPTIFNGKLKGYQLKGMNWLANLYEQGINGILADEMGLGKTVQSIALLAHL AERENIWGPFLIISPASTLNNWHQEFTRFVPKFKVLPYWGNPHDRKVIRRFWSQKTLYTQDAPFHVVITSYQLVVQDVKY FQRVKWQYMVLDEAQALKSSSSVRWKILLQFQCRNRLLLTGTPIQNTMAELWALLHFIMPTLFDSHEEFNEWFSKDIESH AENKSAIDENQLSRLHMILKPFMLRRIKKDVENELSDKIEILMYCQLTSRQKLLYQALKNKISIEDLLQSSMGSTQQAQN TTSSLMNLVMQFRKVCNHPELFERQETWSPFHISLKPYHISKFIYRHGQIRVFNHSRDRWLRVLSPFAPDYIQRSLFHRK GINEESCFSFLRFIDISPAEMANLMLQGLLARWLALFLSLKASYRLHQLRSWGAPEGESHQRYLRNKDFLLGVNFPLSFP NLCSCPLLKSLVFSSHCKAVSGYSDQVVHQRRSATSSLRRCLLTELPSFLCVASPRVTAVPLDSYCNDRSAEYERRVLKE GGSLAAKQCLLNGAPELAADWLNRRSQFFPEPAGGLWSIRPQNGWSFIRIPGKESLITDSGKLYALDVLLTRLKSQGHRV LIYSQMTRMIDLLEEYMVYRKHTYMRLDGSSKISERRDMVADFQNRNDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNP TVDQQAMDRAHRLGQTKQVTVYRLICKGTIEERILQRAKEKSEIQRMVISGGNFKPDTLKPKEVVSLLLDDEELEKKLRL RQEEKRQQEETNRVKERKRKREKYAEKKKKEDELDGKRRKEGVNLVIPFVPSADNSNLSADGDDSFISVDSAMPSPFSEI SISSELHTGSIPLDESSSDMLVIVDDPASSAPQSRATNSPASITGSVSDTVNGISIQEMPAAGRGHSARSRGRPKGSGST AKGAGKGRSRKSTAGSAAAMAGAKAGAAAASAAAYAAYGYNVSKGISASSPLQTSLVRPAGLADFGPSSASSPLSSPLSK GNNVPGNPKNLHMTSSLAPDSLVRKQGKGTNPSGGR Q9ULG1 3.6.4.- Histone H4 Homo sapiens 0.011394426 2 Escherichia coli LEVO MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK TVTAMDVVYALKRQGRTLYGFGG P62805 INO80 complex subunit B Homo sapiens 0.038704171999999995 1 Spodoptera frugiperda LEVO MSKLWRRGSTSGAMEAPEPGEALELSLAGAHGHGVHKKKHKKHKKKHKKKHHQEEDAGPTQPSPAKPQLKLKIKLGGQVL GTKSVPTFTVIPEGPRSPSPLMVVDNEEEPMEGVPLEQYRAWLDEDSNLSPSPLRDLSGGLGGQEEEEEQRWLDALEKGE LDDNGDLKKEINERLLTARQRALLQKARSQPSPMLPLPVAEGCPPPALTEEMLLKREERARKRRLQAARRAEEHKNQTIE RLTKTAATSGRGGRGGARGERRGGRAAAPAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRPSPSGPPPRCSVPGCPHPRRY ACSRTGQALCSLQCYRINLQMRLGGPEGPGSPLLAT Q9C086 Actin-related protein 5 Homo sapiens 0.06837233599999999 1 Spodoptera frugiperda LEVO MAANVFPFRDARAAPDPVLEAGPVAHGPLPVPLVLDNGSFQVRAGWACPGQDPGPEPRLQFRAVCARGRGGARGASGPQV GNALGSLEPLRWMLRSPFDRNVPVNLELQELLLDYSFQHLGVSSQGCVDHPIVLTEAVCNPLYSRQMMSELLFECYGIPK VAYGIDSLFSFYHNKPKNSMCSGLIISSGYQCTHVLPILEGRLDAKNCKRINLGGSQAAGYLQRLLQLKYPGHLAAITLS RMEEILHEHSYIAEDYVEELHKWRCPDYYENNVHKMQLPFSSKLLGSTLTSEEKQERRQQQLRRLQELNARRREEKLQLD QERLDRLLYVQELLEDGQMDQFHKALIELNMDSPEELQSYIQKLSIAVEQAKQKILQAEVNLEVDVVDSKPETPDLEQLE PSLEDVESMNDFDPLFSEETPGVEKPVTTVQPVFNLAAYHQLFVGTERIRAPEIIFQPSLIGEEQAGIAETLQYILDRYP KDIQEMLVQNVFLTGGNTMYPGMKARMEKELLEMRPFRSSFQVQLASNPVLDAWYGARDWALNHLDDNEVWITRKEYEEK GGEYLKEHCASNIYVPIRLPKQASRSSDAQASSKGSAAGGGGAGEQA Q9H9F9 INO80 complex subunit C Homo sapiens 0.020672553 1 Spodoptera frugiperda LEVO MAAQIPIVATTSTPGIVRNSKKRPASPSHNGSSGGGYGASKKKKASASSFAQGISMEAMSENKMVPSEFSTGPVEKAAKP LPFKDPNFVHSGHGGAVAGKKNRTWKNLKQILASERALPWQLNDPNYFSIDAPPSFKPAKKYSDVSGLLANYTDPQSKLR FSTIEEFSYIRRLPSDVVTGYLALRKATSIVP Q6PI98 Histone H3.1 Homo sapiens 0.015437166999999998 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P68431 Histone H2A type 1-B/E Homo sapiens 0.014165550999999998 2 Escherichia coli LEVO MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII PRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P04908 Histone H2B type 1-J Homo sapiens 0.013935238999999999 2 Escherichia coli LEVO MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK P06899 DNA (158-MER) synthetic construct 0.048569934 1 (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA) (DT)(DG)(DT)(DA)(DC)(DT)(DC)(DG)(DG)(DG)(DA)(DT)(DA)(DT)(DT)(DG)(DA)(DT) DNA DNA (158-MER) synthetic construct 0.04897523 1 (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC)(DC)(DG)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DG) (DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT) (DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG) DNA ADENOSINE-5'-DIPHOSPHATE 0.000427201 8 ADP BERYLLIUM TRIFLUORIDE ION 6.600700000000001e-05 1 BEF ZINC ION 6.5409e-05 1 ZN singleParticle particle 0.25 8.0 25.0 HEPES 50.0 NaCl 1.0 TCEP 3.0 ADP 3.0 BeCl2 15.0 NaF 5.0 MgCl2 Quantifoil R2/2 COPPER 300 ETHANE 100 277.15 FEI VITROBOT MARK IV

4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.5 0.5 3.0 3.0 88000.0 88000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.15 77.15 GATAN K3 (6k x 4k) 5760 4092 2 9760 5.1 50.0 1 3647005 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION 6HTS 1 3.2 FSC 0.143 CUT-OFF RELION 4 156300 MAXIMUM LIKELIHOOD RELION 4 MAXIMUM LIKELIHOOD RELION 4 2 148566.0 RELION 4 emd_14737.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 368 368 368 0 0 0 368 368 368 404.80002 404.80002 404.80002 90.0 90.0 90.0 Z Y X -26.213028000000001 51.823680000000003 0.0031996632 1.1331027 1.1 1.1 1.1 4.5 AUTHOR ::::EMDATABANK.org::::EMD-14737:::: 6HTS PDB experimental model REAL emd_14737_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 368 368 368 0 0 0 368 368 368 404.80002 404.80002 404.80002 90.0 90.0 90.0 X Y Z -0.014072412 0.045159962 0.00007159632 0.0015675212 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-14737:::: emd_14737_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 368 368 368 0 0 0 368 368 368 404.80002 404.80002 404.80002 90.0 90.0 90.0 X Y Z -0.011266669 0.039712954 0.000041487372 0.0014877437 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-14737:::: emd_14737_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 368 368 368 0 0 0 368 368 368 404.80002 404.80002 404.80002 90.0 90.0 90.0 X Y Z -0.014693186 0.053176682 0.000077309225 0.0017834501 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-14737:::: emd_14737_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 368 368 368 0 0 0 368 368 368 404.80002 404.80002 404.80002 90.0 90.0 90.0 X Y Z -0.028002543 0.07455315 0.000076131575 0.0030361272 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-14737:::: emd_14737_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 368 368 368 0 0 0 368 368 368 404.80002 404.80002 404.80002 90.0 90.0 90.0 X Y Z -0.025953151 0.07099639 0.00007827896 0.0030399987 1.1 1.1 1.1 AUTHOR ::::EMDATABANK.org::::EMD-14737::::