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

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Entry
Database: PDB / ID: 9ge4
TitleCryoEM structure of the human INO80 core- H2A.Z nucleosome complex
Components
  • (Histone H2A.Z) x 2
  • (Nucleosome DNA strand ...) x 2
  • Histone H2B type 2-E
  • Histone H3.1
  • Histone H4
KeywordsDNA / Homo sapiens / Nucleosome
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
DNA / DNA (> 10) / DNA (> 100) / Histone H2A.Z / Histone H4 / Histone H3.1 / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsAggarwal, P. / Sharma, M. / 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 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Nucleosome DNA strand 1 (152-MER)
L: Nucleosome DNA strand 2 (152-MER)
M: Histone H3.1
N: Histone H4
O: Histone H2A.Z
P: Histone H2B type 2-E
Q: Histone H3.1
R: Histone H4
S: Histone H2A.Z
T: Histone H2B type 2-E


Theoretical massNumber of molelcules
Total (without water)201,77910
Polymers201,77910
Non-polymers00
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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Nucleosome DNA strand ... , 2 types, 2 molecules KL

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


Mass: 47121.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain Nucleosome DNA strand 2 (152-MER)


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

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Protein , 5 types, 8 molecules MQNROPTS

#3: 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
#4: 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
#5: Protein Histone H2A.Z / H2A/z


Mass: 13450.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AZ1, H2AFZ, H2AZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S5
#6: 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
#7: Protein Histone H2A.Z / H2A/z


Mass: 13450.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AZ1, H2AFZ, H2AZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S5

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Details

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
1Human INO80 remodeller with H2A.Z containing nucleosomesCOMPLEXall0RECOMBINANT
2Histone OctamerCOMPLEX#3-#71RECOMBINANT
3Synthetic deoxyribonucleic acidCOMPLEX#1-#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
33NO
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
21Trichoplusia ni (cabbage looper)7111
32Escherichia coli (E. coli)562
43synthetic 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: FEI TITAN 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 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selectionBlob Picker
4cryoSPARC4.5.3CTF correctionPatch CTF Estimation
7Coot0.9.8.93model fitting
8ISOLDE1.8model fitting
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
14REFMAC5.8.0425model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12419217
Details: Minimum particle diameter (A) = 120 Maximum particle diameter (A) = 240
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94892 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: MAXIMUM LIKELIHOOD WITH PHASES
RefinementResolution: 3.52→3.52 Å / Cor.coef. Fo:Fc: 0.934 / SU B: 23.588 / SU ML: 0.332 / ESU R: 0.542
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.29669 --
obs0.29669 95668 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 134.964 Å2
Refinement stepCycle: 1 / Total: 12125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01112961
ELECTRON MICROSCOPYr_bond_other_d00.0169473
ELECTRON MICROSCOPYr_angle_refined_deg1.9751.82618805
ELECTRON MICROSCOPYr_angle_other_deg0.6641.69921972
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.515740
ELECTRON MICROSCOPYr_dihedral_angle_2_deg8.407576
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.5101141
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0920.22142
ELECTRON MICROSCOPYr_gen_planes_refined0.0160.0210719
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022507
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it16.8417.8122984
ELECTRON MICROSCOPYr_mcbond_other16.8417.8122984
ELECTRON MICROSCOPYr_mcangle_it26.31513.9773716
ELECTRON MICROSCOPYr_mcangle_other26.31213.9793717
ELECTRON MICROSCOPYr_scbond_it23.46815.5939977
ELECTRON MICROSCOPYr_scbond_other23.46715.5939978
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other37.91628.07515090
ELECTRON MICROSCOPYr_long_range_B_refined50.065160.4848314
ELECTRON MICROSCOPYr_long_range_B_other50.065160.4848313
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.32 7003 -
obs--100 %

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