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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 / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex ...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 / establishment of protein localization to chromatin / R2TP complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / Ino80 complex / regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / UV-damage excision repair / box C/D snoRNP assembly / protein folding chaperone complex / NuA4 histone acetyltransferase complex / regulation of chromosome organization / regulation of G1/S transition of mitotic cell cycle / TFIID-class transcription factor complex binding / regulation of DNA replication / mitotic sister chromatid segregation / MLL1 complex / regulation of embryonic development / Telomere Extension By Telomerase / alpha-tubulin binding / ATP-dependent activity, acting on DNA / positive regulation of double-strand break repair via homologous recombination / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / spindle assembly / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / cellular response to ionizing radiation / telomere maintenance / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / DNA helicase activity / Assembly of the ORC complex at the origin of replication / positive regulation of DNA repair / TBP-class protein binding / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / epigenetic regulation of gene expression / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / double-strand break repair via homologous recombination / DNA Damage Recognition in GG-NER / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to estradiol stimulus / chromatin DNA binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / negative regulation of canonical Wnt signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / ADP binding / Metalloprotease DUBs / beta-catenin binding / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / fibrillar center / Transcriptional regulation of granulopoiesis / UCH proteinases / HCMV Early Events
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 H2B signature. / Histone H2A conserved site / Histone H2A 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. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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: To Be Published
Title: CryoEM structure of the human INO80 core-nucleosome complex state N-7
Authors: Sharma, M. / Aggarwal, P. / Hopfner, K.P.
History
DepositionAug 8, 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
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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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)815,42228
Polymers812,28620
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: 20672.553 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
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
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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