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- EMDB-51289: CryoEM structure of the human INO80 core- H2A.Z nucleosome complex -

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Entry
Database: EMDB / ID: EMD-51289
TitleCryoEM structure of the human INO80 core- H2A.Z nucleosome complex
Map data
Sample
  • Complex: Human INO80 remodeller with H2A.Z containing nucleosomes
    • Complex: Histone Octamer
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.Z
      • Protein or peptide: Histone H2B type 2-E
      • Protein or peptide: Histone H2A.Z
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: Nucleosome DNA strand 1 (152-MER)
      • DNA: Nucleosome DNA strand 2 (152-MER)
KeywordsHomo sapiens / Nucleosome / DNA
Function / homology
Function and homology information


nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine ...nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 / epigenetic regulation of gene expression / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / cellular response to estradiol stimulus / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / chromatin DNA binding / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / antibacterial humoral response / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / : / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
: / 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 ...: / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2A.Z / Histone H4 / Histone H3.1 / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsAggarwal P / Sharma M / 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-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51289.png

Downloads & links

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Map

FileDownload / File: emd_51289.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 440 pix.
= 414.92 Å		0.94 Å/pix.
x 440 pix.
= 414.92 Å		0.94 Å/pix.
x 440 pix.
= 414.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.943 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.56890786 - 1.0151318
Average (Standard dev.)0.00046128812 (±0.018709272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 414.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51289_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51289_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human INO80 remodeller with H2A.Z containing nucleosomes

EntireName: Human INO80 remodeller with H2A.Z containing nucleosomes
Components
  • Complex: Human INO80 remodeller with H2A.Z containing nucleosomes
    • Complex: Histone Octamer
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.Z
      • Protein or peptide: Histone H2B type 2-E
      • Protein or peptide: Histone H2A.Z
    • Complex: Synthetic deoxyribonucleic acid
      • DNA: Nucleosome DNA strand 1 (152-MER)
      • DNA: Nucleosome DNA strand 2 (152-MER)

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Supramolecule #1: Human INO80 remodeller with H2A.Z containing nucleosomes

SupramoleculeName: Human INO80 remodeller with H2A.Z containing nucleosomes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: #3-#7
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: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nucleosome DNA strand 1 (152-MER)

MacromoleculeName: Nucleosome DNA strand 1 (152-MER) / type: dna / ID: 1 / 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 #2: Nucleosome DNA strand 2 (152-MER)

MacromoleculeName: Nucleosome DNA strand 2 (152-MER) / type: dna / ID: 2 / 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 #3: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 3 / 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 #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / 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 #5: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.450601 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV IPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

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Macromolecule #6: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 6 / 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 #7: Histone H2A.Z

MacromoleculeName: Histone H2A.Z / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.450601 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGGKAGKDSG KAKTKAVSRS QRAGLQFPVG RIHRHLKSRT TSHGRVGATA AVYSAAILEY LTAEVLELAG NASKDLKVKR ITPRHLQLA IRGDEELDSL IKATIAGGGV LPHIHKSLIG KKGQQKTV

UniProtKB: Histone H2A.Z

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 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 selectionNumber selected: 12419217
Details: 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: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94892
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)

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Atomic model buiding 1

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

PDB-9ge4:
CryoEM structure of the human INO80 core- H2A.Z nucleosome complex

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