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Yorodumi- EMDB-17006: CryoEM Structure INO80core Hexasome complex composite map state1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17006 | |||||||||||||||
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Title | CryoEM Structure INO80core Hexasome complex composite map state1 | |||||||||||||||
Map data | ctINO80 hexasome complex composite map | |||||||||||||||
Sample |
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Keywords | ATP-dependent chromatin remodeler / DNA BINDING PROTEIN | |||||||||||||||
Function / homology | Function and homology information DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex ...DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / 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 / DNA helicase activity / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / mitotic spindle / PKMTs methylate histone lysines / kinetochore / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm Similarity search - Function | |||||||||||||||
Biological species | Thermochaetoides thermophila (fungus) / Homo sapiens (human) / Synthetic construct (others) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Zhang M / Jungblut A / Hoffmann T / Eustermann S | |||||||||||||||
Funding support | Germany, European Union, 4 items
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Citation | Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: Features and development of Coot. Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan / Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17006.map.gz | 28.3 MB | EMDB map data format | |
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Header (meta data) | emd-17006-v30.xml emd-17006.xml | 44 KB 44 KB | Display Display | EMDB header |
Images | emd_17006.png | 168 KB | ||
Others | emd_17006_additional_1.map.gz | 140.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17006 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17006 | HTTPS FTP |
-Validation report
Summary document | emd_17006_validation.pdf.gz | 439.9 KB | Display | EMDB validaton report |
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Full document | emd_17006_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | emd_17006_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_17006_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17006 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17006 | HTTPS FTP |
-Related structure data
Related structure data | 8oo7MC 8oo9C 8ooaC 8oocC 8oofC 8ookC 8oopC 8oorC 8oosC 8ootC C: citing same article (ref.) M: atomic model generated by this map |
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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_17006.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | ctINO80 hexasome complex composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: ctINO80 hexasome complex overall refinement (used as a...
File | emd_17006_additional_1.map | ||||||||||||
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Annotation | ctINO80 hexasome complex overall refinement (used as a reference map to generate composite map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : INO80 core module in complex with hexasome
+Supramolecule #1: INO80 core module in complex with hexasome
+Supramolecule #2: Chromatin remodeler INO80
+Supramolecule #3: Histones
+Supramolecule #4: DNA
+Macromolecule #1: RuvB-like protein 1
+Macromolecule #2: RuvB-like protein 2
+Macromolecule #3: Chromatin-remodeling ATPase Ino80
+Macromolecule #4: Ino eighty subunit 2
+Macromolecule #5: Chromatin-remodeling complex subunit IES6
+Macromolecule #6: Actin-related protein 5
+Macromolecule #9: Histone H3.1
+Macromolecule #10: Histone H4
+Macromolecule #11: Histone H2A
+Macromolecule #12: Histone H2B
+Macromolecule #7: DNA Strand 1
+Macromolecule #8: DNA Strand 2
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: TETRAFLUOROALUMINATE ION
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.88 mg/mL |
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Buffer | pH: 7.5 Details: 30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Details: FISHIONE Instruments, Nanoclean 10% O2 90% Argon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV Details: wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807). |
Details | 11-subunit ctINO80 reconstituted with hexasome |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 15384 / Average electron dose: 50.36 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: OTHER | ||||||||||
Output model | PDB-8oo7: |