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Yorodumi- PDB-7zi4: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome -
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-Basic information
Entry | Database: PDB / ID: 7zi4 | ||||||
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Title | Cryo-EM structure of the human INO80 complex bound to a WT nucleosome | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / chromatin remodeler / transcription / replication / DNA repair | ||||||
Function / homology | Function and homology information positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / 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 / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body ...positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / 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 / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / Ino80 complex / UV-damage excision repair / Telomere Extension By Telomerase / protein folding chaperone complex / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / mitotic sister chromatid segregation / protein localization to CENP-A containing chromatin / TFIID-class transcription factor complex binding / regulation of embryonic development / CENP-A containing nucleosome / MLL1 complex / positive regulation of double-strand break repair via homologous recombination / negative regulation of tumor necrosis factor-mediated signaling pathway / alpha-tubulin binding / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / positive regulation of DNA repair / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / Packaging Of Telomere Ends / ATP-dependent activity, acting on DNA / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / cellular response to estradiol stimulus / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / TBP-class protein binding / DNA helicase activity / telomere maintenance / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to ionizing radiation / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / DNA Damage Recognition in GG-NER / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / euchromatin / heterochromatin formation / chromatin DNA binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / ADP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Vance, N.R. / Ayala, R. / Willhoft, O. / Tvardovskiy, A. / McCormack, E.A. / Bartke, T. / Zhang, X. / Wigley, D.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Authors: Vance, N.R. / Ayala, R. / Willhoft, O. / Tvardovskiy, A. / McCormack, E.A. / Bartke, T. / Zhang, X. / Wigley, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zi4.cif.gz | 989.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zi4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7zi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zi4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7zi4_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7zi4_validation.xml.gz | 135 KB | Display | |
Data in CIF | 7zi4_validation.cif.gz | 208.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/7zi4 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/7zi4 | HTTPS FTP |
-Related structure data
Related structure data | 14737MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 8 types, 16 molecules ACEBDFGNJHIMKOLP
#1: Protein | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y265, DNA helicase #2: Protein | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y230, DNA helicase #3: Protein | | 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: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9ULG1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #4: Protein | Mass: 11394.426 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 #6: Protein | | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H9F9 #8: Protein | 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 #9: Protein | Mass: 14165.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908 #10: Protein | Mass: 13935.239 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899 |
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-INO80 complex subunit ... , 2 types, 2 molecules RQ
#5: Protein | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9C086 |
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#7: Protein | 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PI98 |
-DNA chain , 2 types, 2 molecules XY
#11: DNA chain | Mass: 48569.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#12: DNA chain | Mass: 48975.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 10 molecules
#13: Chemical | ChemComp-ADP / #14: Chemical | ChemComp-BEF / | #15: Chemical | ChemComp-ZN / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of human INO80core bound to a WT nucleosome / Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.0 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: 4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 88000 X / Calibrated magnification: 88000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77.15 K / Temperature (min): 77.15 K |
Image recording | Average exposure time: 5.1 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 9760 |
Image scans | Sampling size: 5 µm / Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3647005 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156300 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6HTS Accession code: 6HTS / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
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