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Yorodumi- EMDB-14737: Cryo-EM structure of the human INO80 complex bound to a WT nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14737 | |||||||||
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Title | Cryo-EM structure of the human INO80 complex bound to a WT nucleosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | chromatin remodeler / transcription / replication / DNA repair / DNA BINDING PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Vance NR / Ayala R / Willhoft O / Tvardovskiy A / McCormack EA / Bartke T / Zhang X / Wigley DB | |||||||||
Funding support | United Kingdom, 1 items
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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 NR / Ayala R / Willhoft O / Tvardovskiy A / McCormack EA / Bartke T / Zhang X / Wigley DB | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14737.map.gz | 144 MB | EMDB map data format | |
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Header (meta data) | emd-14737-v30.xml emd-14737.xml | 41.4 KB 41.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14737_fsc.xml | 13 KB | Display | FSC data file |
Images | emd_14737.png | 81.6 KB | ||
Filedesc metadata | emd-14737.cif.gz | 10.1 KB | ||
Others | emd_14737_additional_1.map.gz emd_14737_additional_2.map.gz emd_14737_additional_3.map.gz emd_14737_half_map_1.map.gz emd_14737_half_map_2.map.gz | 150.1 MB 149.2 MB 149.7 MB 150.4 MB 150.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14737 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14737 | HTTPS FTP |
-Validation report
Summary document | emd_14737_validation.pdf.gz | 789.9 KB | Display | EMDB validaton report |
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Full document | emd_14737_full_validation.pdf.gz | 789.5 KB | Display | |
Data in XML | emd_14737_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_14737_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14737 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14737 | HTTPS FTP |
-Related structure data
Related structure data | 7zi4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14737.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #3
File | emd_14737_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_14737_additional_2.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_14737_additional_3.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_14737_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14737_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of human INO80core bound to a WT nucleosome
+Supramolecule #1: Complex of human INO80core bound to a WT nucleosome
+Macromolecule #1: RuvB-like 1
+Macromolecule #2: RuvB-like 2
+Macromolecule #3: Chromatin-remodeling ATPase INO80
+Macromolecule #4: Histone H4
+Macromolecule #5: INO80 complex subunit B
+Macromolecule #6: Actin-related protein 5
+Macromolecule #7: INO80 complex subunit C
+Macromolecule #8: Histone H3.1
+Macromolecule #9: Histone H2A type 1-B/E
+Macromolecule #10: Histone H2B type 1-J
+Macromolecule #11: DNA (158-MER)
+Macromolecule #12: DNA (158-MER)
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #15: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL | ||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 | ||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV 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
Microscope | TFS KRIOS |
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Temperature | Min: 77.15 K / Max: 77.15 K |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 9760 / Average exposure time: 5.1 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 88000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 88000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |