CryoEM structure of the human INO80 core-nucleosome complex state N-7

2026-05-27 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Sequence discrepancy STRUCTURE_SUMMARY atom_site citation citation_author em_admin em_software entity entity_poly entity_poly_seq pdbx_contact_author pdbx_poly_seq_scheme pdbx_unobs_or_zero_occ_atoms struct_conf struct_ref_seq_dif _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly_seq.mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_mon_id _struct_conf.beg_auth_comp_id _struct_conf.beg_label_comp_id STRUCTURE_SUMMARY citation citation_author em_admin em_software entity entity_poly struct_ref_seq_dif _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can PDBe PDBe 2024-08-08 2025-08-20 2025-08-20 2026-05-27 European Research Council (ERC) 833613 INO3D European Union German Research Foundation (DFG) HO 2489/9-1 Germany CryoEM structure of the human INO80 core-nucleosome complex state N-7 Sharma M Aggarwal P Hopfner KP Homo sapiens, ATP-dependent chromatin remodeller, DNA BINDING PROTEIN Aggarwal P Sharma M Woike S Kunert F Brem A Moldt M Hopfner KP Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Res. UK 54 2026 41775336 doi:10.1093/nar/gkag138 1362-4962 0389 NARHAD 9gfb FULLOVERLAP EMDB EMD-51312 associated EM volume

CryoEM structure of the human INO80 core-nucleosome complex stage 1

CryoEM structure of the human INO80 core-nucleosome complex state N-7 CryoEM structure of the human INO80 core-nucleosome complex state N-7 0 1 2 3 4 5 6 7 8 9 10 11 12 Homo sapiens Histone Octamer 1 9 10 11 12 Homo sapiens Synthetic deoxyribonucleic acid 1 7 8 Homo sapiens RuvB-like 1 Homo sapiens 0.050296914 3 Trichoplusia ni LEVO MKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALA LAIAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIG LKTAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTL HDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALE SSIAPIVIFASNRGNCVIRGTEDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTK TTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK Q9Y265 3.6.4.12 RuvB-like 2 Homo sapiens 0.051222464999999995 3 Trichoplusia ni LEVO MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPG TGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGK LTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVH TVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEVHMLDIESFSFLNRALESDM APVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLR YAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNELKGETMDTS Q9Y230 3.6.4.12 Chromatin-remodeling ATPase INO80 Homo sapiens 0.17703281199999998 1 Trichoplusia ni 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.- INO80 complex subunit B Homo sapiens 0.038704171999999995 1 Trichoplusia ni LEVO MSKLWRRGSTSGAMEAPEPGEALELSLAGAHGHGVHKKKHKKHKKKHKKKHHQEEDAGPTQPSPAKPQLKLKIKLGGQVL GTKSVPTFTVIPEGPRSPSPLMVVDNEEEPMEGVPLEQYRAWLDEDSNLSPSPLRDLSGGLGGQEEEEEQRWLDALEKGE LDDNGDLKKEINERLLTARQRALLQKARSQPSPMLPLPVAEGCPPPALTEEMLLKREERARKRRLQAARRAEEHKNQTIE RLTKTAATSGRGGRGGARGERRGGRAAAPAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRPSPSGPPPRCSVPGCPHPRRY ACSRTGQALCSLQCYRINLQMRLGGPEGPGSPLLAT Q9C086 INO80 complex subunit C Homo sapiens 0.020721622999999998 1 Trichoplusia ni LEVO MAAQIPIVATTSTPGIVRNSKKRPASPSHNGSSGGGYGASKKKKASASSFAQGISMEAMSENKMVPSEFSTGPVEKAAKP LPFKDPNFVHSGHGGAVAGKKNRTWKYLKQILASERALPWQLNDPNYFSIDAPPSFKPAKKYSDVSGLLANYTDPQSKLR FSTIEEFSYIRRLPSDVVTGYLALRKATSIVP Q6PI98 Actin-related protein 5 Homo sapiens 0.06837233599999999 1 Trichoplusia ni LEVO MAANVFPFRDARAAPDPVLEAGPVAHGPLPVPLVLDNGSFQVRAGWACPGQDPGPEPRLQFRAVCARGRGGARGASGPQV GNALGSLEPLRWMLRSPFDRNVPVNLELQELLLDYSFQHLGVSSQGCVDHPIVLTEAVCNPLYSRQMMSELLFECYGIPK VAYGIDSLFSFYHNKPKNSMCSGLIISSGYQCTHVLPILEGRLDAKNCKRINLGGSQAAGYLQRLLQLKYPGHLAAITLS RMEEILHEHSYIAEDYVEELHKWRCPDYYENNVHKMQLPFSSKLLGSTLTSEEKQERRQQQLRRLQELNARRREEKLQLD QERLDRLLYVQELLEDGQMDQFHKALIELNMDSPEELQSYIQKLSIAVEQAKQKILQAEVNLEVDVVDSKPETPDLEQLE PSLEDVESMNDFDPLFSEETPGVEKPVTTVQPVFNLAAYHQLFVGTERIRAPEIIFQPSLIGEEQAGIAETLQYILDRYP KDIQEMLVQNVFLTGGNTMYPGMKARMEKELLEMRPFRSSFQVQLASNPVLDAWYGARDWALNHLDDNEVWITRKEYEEK GGEYLKEHCASNIYVPIRLPKQASRSSDAQASSKGSAAGGGGAGEQA Q9H9F9 Nucleosomal DNA strand 1 synthetic construct 0.047121051 1 (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) DNA Nucleosomal DNA strand 2 synthetic construct 0.046715757999999996 1 (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) DNA Histone H3.1 Homo sapiens 0.015437166999999998 2 Escherichia coli LEVO MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK TDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA P68431 Histone H4 Homo sapiens 0.011263230999999999 2 Escherichia coli LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62805 Histone H2A type 1-B/E Homo sapiens 0.014034354999999998 2 Escherichia coli LEVO SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK P04908 Histone H2B type 2-E Homo sapiens 0.013820045 2 Escherichia coli LEVO PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK Q16778 ADENOSINE-5'-TRIPHOSPHATE 0.000507181 1 ATP ADENOSINE-5'-DIPHOSPHATE 0.000427201 6 ADP ZINC ION 6.5409e-05 1 ZN singleParticle particle 8.0 30.0 HEPES 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid 50.0 NaCl Sodium Chloride 0.5 DTT Dithiothreitol Quantifoil R2/1 COPPER 200 GLOW DISCHARGE 7

Negative Polarity

ETHANE 95 283 LEICA EM GP TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.1 2.9 GATAN K2 SUMMIT (4k x 4k) 1.029 1

Minimum particle diameter (A) = 120 Maximum particle diameter (A) = 240

cryoSPARC 4.5.3 Patch CTF Estimation PHASE FLIPPING AND AMPLITUDE CORRECTION 7ZI4 3.55 FSC 0.143 CUT-OFF cryoSPARC 4.5.3 64537 MAXIMUM LIKELIHOOD RELION 4.0 MAXIMUM LIKELIHOOD RELION 4.0 emd_51312.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.6 419.6 419.6 90.0 90.0 90.0 X Y Z -1.3067902 2.7173262 0.0025178941 0.07215231 1.049 1.049 1.049 0.28 AUTHOR ::::EMDATABANK.org::::EMD-51312:::: FLEXIBLE FIT MAXIMUM LIKELIHOOD WITH PHASES RECIPROCAL emd_51312_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.6 419.6 419.6 90.0 90.0 90.0 X Y Z -0.6340454 1.6598411 0.0028331715 0.07736519 1.049 1.049 1.049 AUTHOR ::::EMDATABANK.org::::EMD-51312:::: emd_51312_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.6 419.6 419.6 90.0 90.0 90.0 X Y Z -0.62538886 1.7231718 0.0028130687 0.07768181 1.049 1.049 1.049 AUTHOR ::::EMDATABANK.org::::EMD-51312::::