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- PDB-9gfb: CryoEM structure of the human INO80 core-nucleosome complex state N-7 -

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Entry
Database: PDB / ID: 9gfb
TitleCryoEM structure of the human INO80 core-nucleosome complex state N-7
Components
  • (INO80 complex subunit ...) x 2
  • (Nucleosomal DNA strand ...) x 2
  • Actin-related protein 5
  • Chromatin-remodeling ATPase INO80
  • Histone H2A type 1-B/E
  • Histone H2B type 2-E
  • Histone H3.1
  • Histone H4
  • RuvB-like 1
  • RuvB-like 2
KeywordsDNA BINDING PROTEIN / Homo sapiens / ATP-dependent chromatin remodeller
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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / 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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / R2TP complex / dynein axonemal particle / RPAP3/R2TP/prefoldin-like complex / 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 / regulation of chromosome organization / NuA4 histone acetyltransferase complex / MLL1 complex / regulation of DNA replication / TFIID-class transcription factor complex binding / mitotic sister chromatid segregation / regulation of embryonic development / Telomere Extension By Telomerase / protein folding chaperone complex / ATP-dependent activity, acting on DNA / RNA polymerase II core promoter sequence-specific DNA binding / alpha-tubulin binding / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / spindle assembly / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Regulation of PD-L1(CD274) transcription / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Interleukin-7 signaling / epigenetic regulation of gene expression / telomere maintenance / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / TBP-class protein binding / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / DNA helicase activity / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / Dengue Virus-Host Interactions / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / cellular response to ionizing radiation / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / cellular response to estradiol stimulus / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / innate immune response in mucosa / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / negative regulation of canonical Wnt signaling pathway / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / euchromatin / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / chromatin DNA binding / ADP binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / double-strand break repair via homologous recombination / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / beta-catenin binding / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / fibrillar center / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / Transcriptional regulation of granulopoiesis / nuclear matrix / RMTs methylate histone arginines
Similarity search - Function
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 / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H4 / Histone H3.1 / Histone H2B type 2-E / INO80 complex subunit C ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA (> 100) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsSharma, M. / Aggarwal, P. / Hopfner, K.P.
Funding supportEuropean Union, Germany, 2items
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 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
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Revision 2.0May 27, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / citation ...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
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Description: Sequence discrepancy / Provider: author / Type: Coordinate replacement
Revision 1.1May 27, 2026Data content type: EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RuvB-like 1
B: RuvB-like 1
C: RuvB-like 1
D: RuvB-like 2
E: RuvB-like 2
F: RuvB-like 2
G: Chromatin-remodeling ATPase INO80
H: INO80 complex subunit B
I: INO80 complex subunit C
J: Actin-related protein 5
K: Nucleosomal DNA strand 1
L: Nucleosomal DNA strand 2
M: Histone H3.1
N: Histone H4
O: Histone H2A type 1-B/E
P: Histone H2B type 2-E
Q: Histone H3.1
R: Histone H4
S: Histone H2A type 1-B/E
T: Histone H2B type 2-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)815,47128
Polymers812,33520
Non-polymers3,1368
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 8 types, 16 molecules ABCDEFGJMQNROSPT

#1: Protein RuvB-like 1 / 49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa ...49 kDa TATA box-binding protein-interacting protein / 49 kDa TBP-interacting protein / 54 kDa erythrocyte cytosolic protein / ECP-54 / INO80 complex subunit H / Nuclear matrix protein 238 / NMP 238 / Pontin 52 / TIP49a / TIP60-associated protein 54-alpha / TAP54-alpha


Mass: 50296.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL1, INO80H, NMP238, TIP49, TIP49A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y265, DNA helicase
#2: Protein RuvB-like 2 / 48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa ...48 kDa TATA box-binding protein-interacting protein / 48 kDa TBP-interacting protein / 51 kDa erythrocyte cytosolic protein / ECP-51 / INO80 complex subunit J / Repressing pontin 52 / Reptin 52 / TIP49b / TIP60-associated protein 54-beta / TAP54-beta


Mass: 51222.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y230, DNA helicase
#3: Protein Chromatin-remodeling ATPase INO80 / hINO80 / DNA helicase-related INO80 complex homolog 1 / DNA helicase-related protein INO80 / INO80 ...hINO80 / DNA helicase-related INO80 complex homolog 1 / DNA helicase-related protein INO80 / INO80 complex subunit A


Mass: 177032.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INO80, INO80A, INOC1, KIAA1259 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9ULG1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#6: Protein Actin-related protein 5 / hARP5 / Sarcoma antigen NY-SAR-16


Mass: 68372.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR5, ARP5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H9F9
#9: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#10: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#11: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14034.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#12: Protein Histone H2B type 2-E / H2B-clustered histone 21 / Histone H2B-GL105 / Histone H2B.q / H2B/q


Mass: 13820.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC21, H2BFQ, HIST2H2BE / Production host: Escherichia coli (E. coli) / References: UniProt: Q16778

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INO80 complex subunit ... , 2 types, 2 molecules HI

#4: Protein INO80 complex subunit B / High mobility group AT-hook 1-like 4 / IES2 homolog / hIes2 / PAP-1-associated protein 1 / PAPA-1 / ...High mobility group AT-hook 1-like 4 / IES2 homolog / hIes2 / PAP-1-associated protein 1 / PAPA-1 / Zinc finger HIT domain-containing protein 4


Mass: 38704.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INO80B, HMGA1L4, PAPA1, ZNHIT4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9C086
#5: Protein INO80 complex subunit C / IES6 homolog / hIes6


Mass: 20721.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INO80C, C18orf37 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PI98

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Nucleosomal DNA strand ... , 2 types, 2 molecules KL

#7: DNA chain Nucleosomal DNA strand 1


Mass: 47121.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain Nucleosomal DNA strand 2


Mass: 46715.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#13: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#14: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#15: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1CryoEM structure of the human INO80 core-nucleosome complex state N-7COMPLEX#1-#120RECOMBINANT
2Histone OctamerCOMPLEX#9-#121RECOMBINANT
3Synthetic deoxyribonucleic acidCOMPLEX#7-#81RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Trichoplusia ni (cabbage looper)7111
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
130 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
250 mMSodium ChlorideNaCl1
30.5 mMDithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Negative Polarity / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm
Image recordingElectron dose: 1.029 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.5.3particle selectionBlob Picker
4cryoSPARC4.5.3CTF correctionPatch CTF Estimation
7Coot0.9.8.93model fitting
8ISOLDE1.8model fitting
10REFMAC5.8.0425model refinement
11RELION4initial Euler assignment
12RELION4final Euler assignment
14cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Minimum particle diameter (A) = 120 Maximum particle diameter (A) = 240
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64537 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: MAXIMUM LIKELIHOOD WITH PHASES

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