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- EMDB-51307: CryoEM structure of the human INO80 core-nucleosome complex state N-6 -

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Basic information

Entry
Database: EMDB / ID: EMD-51307
TitleCryoEM structure of the human INO80 core-nucleosome complex state N-6
Map data
Sample
  • Complex: CryoEM structure of the human INO80 core-nucleosome complex state N-6
    • Complex: Histone Octamer
      • Protein or peptide: x 4 types
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: x 2 types
    • Protein or peptide: x 6 types
  • Ligand: x 2 types
KeywordsHomo sapiens / ATP-dependent chromatin remodeller / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / RPAP3/R2TP/prefoldin-like complex / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / R2TP complex / dynein axonemal particle / Swr1 complex / establishment of protein localization to chromatin ...positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / telomerase RNA localization to Cajal body / RPAP3/R2TP/prefoldin-like complex / positive regulation of telomere maintenance in response to DNA damage / regulation of DNA strand elongation / R2TP complex / dynein axonemal particle / Swr1 complex / establishment of protein localization to chromatin / Ino80 complex / regulation of double-strand break repair / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / UV-damage excision repair / ChAHP complex assembly / NuA4 histone acetyltransferase complex / regulation of chromosome organization / mitotic sister chromatid segregation / TFIID-class transcription factor complex binding / regulation of DNA replication / MLL1 complex / Telomere Extension By Telomerase / FXIIa activates plasma kallikrein-kinin system / protein folding chaperone complex / ATP-dependent activity, acting on DNA / Interaction of NuRD complexes with transcription factors / NuRD complex assembly / alpha-tubulin binding / CHD6, CHD7, CHD8, CHD9 subfamily / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / positive regulation of double-strand break repair via homologous recombination / CHD1 and CHD2 subfamily / enzyme regulator activity / negative regulation of megakaryocyte differentiation / regulation of G1/S transition of mitotic cell cycle / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / regulation of embryonic development / telomere organization / Interleukin-7 signaling / telomere maintenance / Deposition of new CENPA-containing nucleosomes at the centromere / TBP-class protein binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of DNA repair / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / : / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / cellular response to ionizing radiation / DNA helicase activity / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / cellular response to estradiol stimulus / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Transcriptional regulation by small RNAs / negative regulation of canonical Wnt signaling pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / epigenetic regulation of gene expression / chromatin DNA binding / double-strand break repair via homologous recombination / euchromatin / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / ADP binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / fibrillar center / beta-catenin binding / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Activation of anterior HOX genes in hindbrain development during early embryogenesis
Similarity search - Function
DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / HIT zinc finger ...DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / HIT zinc finger / Zinc finger, HIT-type / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin, conserved site / Actins signature 2. / Actin / Actin family / Actin / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H4 / Histone H3.1 / Histone H2B type 2-E / INO80 complex subunit C / INO80 complex subunit B / Actin-related protein 5 / Chromatin-remodeling ATPase INO80 / RuvB-like 2 / RuvB-like 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsSharma M / Aggarwal P / Hopfner KP
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)833613 INO3DEuropean Union
German Research Foundation (DFG)HO 2489/9-1 Germany
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex.
Authors: Priyanka Aggarwal / Manmohan Sharma / Stephan Woike / Franziska Kunert / Annika Brem / Manuela Moldt / Karl-Peter Hopfner /
Abstract: The ATP-dependent INO80 chromatin remodeller slides and repositions nucleosomes to shape and maintain chromatin around gene regulatory elements and replication origins. Recent work uncovered ...The ATP-dependent INO80 chromatin remodeller slides and repositions nucleosomes to shape and maintain chromatin around gene regulatory elements and replication origins. Recent work uncovered capabilities of yeast and fungal INO80 to bind and slide hexasomes, but whether this is a universal feature is unknown. Here, we show that human INO80 also slides hexasomes as efficiently as H2A and H2A.Z nucleosomes. By determining a variety of structures of human INO80 bound to canonical and H2A.Z nucleosomes as well as hexasomes, we reveal a predominantly topological sensing of nucleosomal species with at least three positions depending on entry DNA unwrapping. INO80 spin-rotates around the nucleosomal core particle as a function of entry DNA unwrapping. Different degrees of unwrapped entry DNA lead to two different nucleosomal and one hexasomal locations of INO80, determined by binding of the Snf2 ATPase to entry point of extranucleosomal DNA at the nucleosome/hexasome core. Acidic patch binding by the INO80 subunit IES2 can differentiate between (sub)nucleosomal species, is important for nucleosome but not hexasome sliding, and may sense unwrapped exit DNA. These findings provide structural and mechanistic insights into how human INO80 remodels diverse chromatin substrates in a topology driven manner.
History
DepositionAug 7, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51307.png

Downloads & links

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Map

FileDownload / File: emd_51307.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 419.6 Å		1.05 Å/pix.
x 400 pix.
= 419.6 Å		1.05 Å/pix.
x 400 pix.
= 419.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.049 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.4913188 - 3.0415597
Average (Standard dev.)0.002400801 (±0.0790682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51307_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_51307_half_map_2.map
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Sample components

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Entire : CryoEM structure of the human INO80 core-nucleosome complex state N-6

EntireName: CryoEM structure of the human INO80 core-nucleosome complex state N-6
Components
  • Complex: CryoEM structure of the human INO80 core-nucleosome complex state N-6
    • Complex: Histone Octamer
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 2-E
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: Nucleosomal DNA Strand 1
      • DNA: Nucleosomal DNA Strand 2
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: INO80 complex subunit C
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • Protein or peptide: INO80 complex subunit B
    • Protein or peptide: Actin-related protein 5
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: CryoEM structure of the human INO80 core-nucleosome complex state N-6

SupramoleculeName: CryoEM structure of the human INO80 core-nucleosome complex state N-6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histone Octamer

SupramoleculeName: Histone Octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #6-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Synthetic deoxyribonucleic acid

SupramoleculeName: Synthetic deoxyribonucleic acid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.296914 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLAG PPGTGKTALA LAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA IGLRIKETKE VYEGEVTELT PCETENPMGG YGKTISHVII G LKTAKGTK QLKLDPSIFE SLQKERVEAG DVIYIEANSG AVKRQGRCDT YATEFDLEAE EYVPLPKGDV HKKKEIIQDV TL HDLDVAN ARPQGGQDIL SMMGQLMKPK KTEITDKLRG EINKVVNKYI DQGIAELVPG VLFVDEVHML DIECFTYLHR ALE SSIAPI VIFASNRGNC VIRGTEDITS PHGIPLDLLD RVMIIRTMLY TPQEMKQIIK IRAQTEGINI SEEALNHLGE IGTK TTLRY SVQLLTPANL LAKINGKDSI EKEHVEEISE LFYDAKSSAK ILADQQDKYM K

UniProtKB: RuvB-like 1

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.222465 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIAG RAVLIAGQPG TGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL TQAFRRSIGV RIKEETEIIE GEVVEIQIDR PATGTGSKVG K LTLKTTEM ETIYDLGTKM IESLTKDKVQ AGDVITIDKA TGKISKLGRS FTRARDYDAM GSQTKFVQCP DGELQKRKEV VH TVSLHEI DVINSRTQGF LALFSGDTGE IKSEVREQIN AKVAEWREEG KAEIIPGVLF IDEVHMLDIE SFSFLNRALE SDM APVLIM ATNRGITRIR GTSYQSPHGI PIDLLDRLLI VSTTPYSEKD TKQILRIRCE EEDVEMSEDA YTVLTRIGLE TSLR YAIQL ITAASLVCRK RKGTEVQVDD IKRVYSLFLD ESRSTQYMKE YQDAFLFNEL KGETMDTS

UniProtKB: RuvB-like 2

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Macromolecule #3: INO80 complex subunit C

MacromoleculeName: INO80 complex subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.721623 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAQIPIVAT TSTPGIVRNS KKRPASPSHN GSSGGGYGAS KKKKASASSF AQGISMEAMS ENKMVPSEFS TGPVEKAAKP LPFKDPNFV HSGHGGAVAG KKNRTWKYLK QILASERALP WQLNDPNYFS IDAPPSFKPA KKYSDVSGLL ANYTDPQSKL R FSTIEEFS ...String:
MAAQIPIVAT TSTPGIVRNS KKRPASPSHN GSSGGGYGAS KKKKASASSF AQGISMEAMS ENKMVPSEFS TGPVEKAAKP LPFKDPNFV HSGHGGAVAG KKNRTWKYLK QILASERALP WQLNDPNYFS IDAPPSFKPA KKYSDVSGLL ANYTDPQSKL R FSTIEEFS YIRRLPSDVV TGYLALRKAT SIVP

UniProtKB: INO80 complex subunit C

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Macromolecule #6: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #7: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #8: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #9: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.820045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 2-E

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Macromolecule #10: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 177.032812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASELGARDD GGCTELAKPL YLQYLERALR LDHFLRQTSA IFNRNISSDD SEDGLDDSNP LLPQSGDPLI QVKEEPPNSL LGETSGAGS SGMLNTYSLN GVLQSESKCD KGNLYNFSKL KKSRKWLKSI LLSDESSEAD SQSEDDDEEE LNLSREELHN M LRLHKYKK ...String:
MASELGARDD GGCTELAKPL YLQYLERALR LDHFLRQTSA IFNRNISSDD SEDGLDDSNP LLPQSGDPLI QVKEEPPNSL LGETSGAGS SGMLNTYSLN GVLQSESKCD KGNLYNFSKL KKSRKWLKSI LLSDESSEAD SQSEDDDEEE LNLSREELHN M LRLHKYKK LHQNKYSKDK ELQQYQYYSA GLLSTYDPFY EQQRHLLGPK KKKFKEEKKL KAKLKKVKKK RRRDEELSSE ES PRRHHHQ TKVFAKFSHD APPPGTKKKH LSIEQLNARR RKVWLSIVKK ELPKANKQKA SARNLFLTNS RKLAHQCMKE VRR AALQAQ KNCKETLPRA RRLTKEMLLY WKKYEKVEKE HRKRAEKEAL EQRKLDEEMR EAKRQQRKLN FLITQTELYA HFMS RKRDM GHDGIQEEIL RKLEDSSTQR QIDIGGGVVV NITQEDYDSN HFKAQALKNA ENAYHIHQAR TRSFDEDAKE SRAAA LRAA NKSGTGFGES YSLANPSIRA GEDIPQPTIF NGKLKGYQLK GMNWLANLYE QGINGILADE MGLGKTVQSI ALLAHL AER ENIWGPFLII SPASTLNNWH QEFTRFVPKF KVLPYWGNPH DRKVIRRFWS QKTLYTQDAP FHVVITSYQL VVQDVKY FQ RVKWQYMVLD EAQALKSSSS VRWKILLQFQ CRNRLLLTGT PIQNTMAELW ALLHFIMPTL FDSHEEFNEW FSKDIESH A ENKSAIDENQ LSRLHMILKP FMLRRIKKDV ENELSDKIEI LMYCQLTSRQ KLLYQALKNK ISIEDLLQSS MGSTQQAQN TTSSLMNLVM QFRKVCNHPE LFERQETWSP FHISLKPYHI SKFIYRHGQI RVFNHSRDRW LRVLSPFAPD YIQRSLFHRK GINEESCFS FLRFIDISPA EMANLMLQGL LARWLALFLS LKASYRLHQL RSWGAPEGES HQRYLRNKDF LLGVNFPLSF P NLCSCPLL KSLVFSSHCK AVSGYSDQVV HQRRSATSSL RRCLLTELPS FLCVASPRVT AVPLDSYCND RSAEYERRVL KE GGSLAAK QCLLNGAPEL AADWLNRRSQ FFPEPAGGLW SIRPQNGWSF IRIPGKESLI TDSGKLYALD VLLTRLKSQG HRV LIYSQM TRMIDLLEEY MVYRKHTYMR LDGSSKISER RDMVADFQNR NDIFVFLLST RAGGLGINLT AADTVIFYDS DWNP TVDQQ AMDRAHRLGQ TKQVTVYRLI CKGTIEERIL QRAKEKSEIQ RMVISGGNFK PDTLKPKEVV SLLLDDEELE KKLRL RQEE KRQQEETNRV KERKRKREKY AEKKKKEDEL DGKRRKEGVN LVIPFVPSAD NSNLSADGDD SFISVDSAMP SPFSEI SIS SELHTGSIPL DESSSDMLVI VDDPASSAPQ SRATNSPASI TGSVSDTVNG ISIQEMPAAG RGHSARSRGR PKGSGST AK GAGKGRSRKS TAGSAAAMAG AKAGAAAASA AAYAAYGYNV SKGISASSPL QTSLVRPAGL ADFGPSSASS PLSSPLSK G NNVPGNPKNL HMTSSLAPDS LVRKQGKGTN PSGGR

UniProtKB: Chromatin-remodeling ATPase INO80

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Macromolecule #11: INO80 complex subunit B

MacromoleculeName: INO80 complex subunit B / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.704172 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSKLWRRGST SGAMEAPEPG EALELSLAGA HGHGVHKKKH KKHKKKHKKK HHQEEDAGPT QPSPAKPQLK LKIKLGGQVL GTKSVPTFT VIPEGPRSPS PLMVVDNEEE PMEGVPLEQY RAWLDEDSNL SPSPLRDLSG GLGGQEEEEE QRWLDALEKG E LDDNGDLK ...String:
MSKLWRRGST SGAMEAPEPG EALELSLAGA HGHGVHKKKH KKHKKKHKKK HHQEEDAGPT QPSPAKPQLK LKIKLGGQVL GTKSVPTFT VIPEGPRSPS PLMVVDNEEE PMEGVPLEQY RAWLDEDSNL SPSPLRDLSG GLGGQEEEEE QRWLDALEKG E LDDNGDLK KEINERLLTA RQRALLQKAR SQPSPMLPLP VAEGCPPPAL TEEMLLKREE RARKRRLQAA RRAEEHKNQT IE RLTKTAA TSGRGGRGGA RGERRGGRAA APAPMVRYCS GAQGSTLSFP PGVPAPTAVS QRPSPSGPPP RCSVPGCPHP RRY ACSRTG QALCSLQCYR INLQMRLGGP EGPGSPLLAT

UniProtKB: INO80 complex subunit B

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Macromolecule #12: Actin-related protein 5

MacromoleculeName: Actin-related protein 5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.372336 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAANVFPFRD ARAAPDPVLE AGPVAHGPLP VPLVLDNGSF QVRAGWACPG QDPGPEPRLQ FRAVCARGRG GARGASGPQV GNALGSLEP LRWMLRSPFD RNVPVNLELQ ELLLDYSFQH LGVSSQGCVD HPIVLTEAVC NPLYSRQMMS ELLFECYGIP K VAYGIDSL ...String:
MAANVFPFRD ARAAPDPVLE AGPVAHGPLP VPLVLDNGSF QVRAGWACPG QDPGPEPRLQ FRAVCARGRG GARGASGPQV GNALGSLEP LRWMLRSPFD RNVPVNLELQ ELLLDYSFQH LGVSSQGCVD HPIVLTEAVC NPLYSRQMMS ELLFECYGIP K VAYGIDSL FSFYHNKPKN SMCSGLIISS GYQCTHVLPI LEGRLDAKNC KRINLGGSQA AGYLQRLLQL KYPGHLAAIT LS RMEEILH EHSYIAEDYV EELHKWRCPD YYENNVHKMQ LPFSSKLLGS TLTSEEKQER RQQQLRRLQE LNARRREEKL QLD QERLDR LLYVQELLED GQMDQFHKAL IELNMDSPEE LQSYIQKLSI AVEQAKQKIL QAEVNLEVDV VDSKPETPDL EQLE PSLED VESMNDFDPL FSEETPGVEK PVTTVQPVFN LAAYHQLFVG TERIRAPEII FQPSLIGEEQ AGIAETLQYI LDRYP KDIQ EMLVQNVFLT GGNTMYPGMK ARMEKELLEM RPFRSSFQVQ LASNPVLDAW YGARDWALNH LDDNEVWITR KEYEEK GGE YLKEHCASNI YVPIRLPKQA SRSSDAQASS KGSAAGGGGA GEQA

UniProtKB: Actin-related protein 5

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Macromolecule #4: Nucleosomal DNA Strand 1

MacromoleculeName: Nucleosomal DNA Strand 1 / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.121051 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #5: Nucleosomal DNA Strand 2

MacromoleculeName: Nucleosomal DNA Strand 2 / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.715758 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
30.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
50.0 mMNaClSodium Chloride
0.5 mMDTTDithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Details: Negative Polarity
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.029 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionDetails: Minimum particle diameter (A) = 120 Maximum particle diameter (A) = 240
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zi4

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82269
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: MAXIMUM LIKELIHOOD WITH PHASES
Output model

PDB-9gev:
CryoEM structure of the human INO80 core-nucleosome complex state N-6

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