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Yorodumi- EMDB-17007: CryoEM Structure INO80core Hexasome complex ATPase-DNA refinement... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17007 | |||||||||||||||
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Title | CryoEM Structure INO80core Hexasome complex ATPase-DNA refinement state1 | |||||||||||||||
Map data | ctINO80-hexasome ATPase-DNA focused refinement sharpened map | |||||||||||||||
Sample |
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Keywords | ATP-dependent chromatin remodeler / DNA BINDING PROTEIN | |||||||||||||||
Biological species | Thermochaetoides thermophila (fungus) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_17007.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-17007-v30.xml emd-17007.xml | 28.8 KB 28.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17007_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_17007.png | 53.9 KB | ||
Filedesc metadata | emd-17007.cif.gz | 8.4 KB | ||
Others | emd_17007_additional_1.map.gz emd_17007_half_map_1.map.gz emd_17007_half_map_2.map.gz | 140.4 MB 140.6 MB 140.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17007 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17007 | HTTPS FTP |
-Validation report
Summary document | emd_17007_validation.pdf.gz | 715.7 KB | Display | EMDB validaton report |
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Full document | emd_17007_full_validation.pdf.gz | 715.3 KB | Display | |
Data in XML | emd_17007_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_17007_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17007 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17007 | HTTPS FTP |
-Related structure data
Related structure data | 8oo9MC 8oo7C 8ooaC 8oocC 8oofC 8ookC 8oopC 8oorC 8oosC 8ootC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17007.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | ctINO80-hexasome ATPase-DNA focused refinement sharpened map | ||||||||||||||||||||
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: unsharpened map ctINO80-hexasome ATPase-DNA focused refinement
File | emd_17007_additional_1.map | ||||||||||||
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Annotation | unsharpened map ctINO80-hexasome ATPase-DNA focused refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1 ctINO80-hexasome ATPase-DNA focused refinement
File | emd_17007_half_map_1.map | ||||||||||||
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Annotation | half map 1 ctINO80-hexasome ATPase-DNA focused refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2 ctINO80-hexasome ATPase-DNA focused refinement
File | emd_17007_half_map_2.map | ||||||||||||
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Annotation | half map 2 ctINO80-hexasome ATPase-DNA focused refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : INO80 core module in complex with hexasome
Entire | Name: INO80 core module in complex with hexasome |
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Components |
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-Supramolecule #1: INO80 core module in complex with hexasome
Supramolecule | Name: INO80 core module in complex with hexasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct ...Details: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct INO80 + hexasome has an overall weight of 1.1MDa Ino80, Ies2, Ies6, Ies4,Arp6, Rvb1, Rvb2, Arp8, Arp4, Actin, Taf14 Hexasome DNA, 2xH3, 2xH4, H2A, H2B |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 861 KDa |
-Macromolecule #1: Chromatin-remodeling ATPase INO80
Macromolecule | Name: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 1 / Details: Ino80 N-terminal truncation C-terminal 2xFlagTag / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermochaetoides thermophila (fungus) |
Molecular weight | Theoretical: 130.887656 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: LELKFQSKGY NQIYDQIWRD LARKDVSKVF RLATDSYATK ASNLKKTAIL ASKEAKRWQL RTNKGTKDLQ ARAKRVMRDM MGFWKRNER EERDLRKAAE RLELENARKE EADREAARQR RKLNFLISQT ELYSHFISKK IKTHEVERST DHPDVATDEK D KIPEPTLN ...String: LELKFQSKGY NQIYDQIWRD LARKDVSKVF RLATDSYATK ASNLKKTAIL ASKEAKRWQL RTNKGTKDLQ ARAKRVMRDM MGFWKRNER EERDLRKAAE RLELENARKE EADREAARQR RKLNFLISQT ELYSHFISKK IKTHEVERST DHPDVATDEK D KIPEPTLN INVPEPTGPI APKVTDFNSL DFDNEDESAL QAAAMANAQN AIAEAQKKAR EFNKDETKLD EDGEMNFQHP EL TEFEVAQ PKLLNCQLKE YQLKGLNWLV NLYEQGINGI LADEMGLGKT VQSISVMAYL AERYDIWGPF LVVAPASTLH NWQ QEVSKF VPDFKVLPYW GTAADRKVLR KFWDRKHTTY KKDSPFHVMI TSYQLVVSDV AYFQKMKWQY MILDEAQAIK SSQS SRWKC LLGFHCRNRL LLTGTPIQNN MQELWALLHF IMPSLFDSHD EFSEWFSKDI ESHAQSNTKL NEDQLKRLHM ILKPF MLRR VKKHVQKELG DKIEIDVFCE LSYRQRAMYQ SLRNQISIMD LIEKATVGDN EDSATLMNLV MQFRKVCNHP DLFERA DTS SPFFCGHFAE TGSFLREGTN VALGYSTRSL VEYRLPRLIW CDGGRLDKPG PGNLVAGFRS KYLNHMMNIW TPENIRS SL EGIENFTWLR FVDTSLQEAY RASHTDVFAR AVDLASKQNR LGHMQIVYDE PEDKKWTPVH ALFQICEREN PKAVAEIT T EGVLRDLMNI ARVKYRELGL CRLEKAARPR ASAPPIEVVC DSRSAVIERE NIMFHPAMRK ALFGPTPSEI KEASFGPRP VTLYPPRALL PAPDHDKQRF TNITVPSMAR FVTDSGKLAK LDELLRELKE GGHRVLLYFQ MTRMIDLMEE YLTYRNYKYC RLDGSTKLE DRRDTVADFQ TRPEIFIFLL STRAGGLGIN LTTADTVIFY DSDWNPTIDS QAMDRAHRLG QTKQVTVYRL I TRGTIEER IRKRALQKEE VQRVVITGTG SVDFSGRRPP ENRNRDIAMW LADDEQAEMI ERREKELIES GEYDKIMQQR RK GGKRKRG AANGDTVPSL EDMYHEGEGH FDDNKGSGAA TPVDADSLGR GGKRKKAGGS KKAKTTKQRL AIADGEIDID YKD DDDKGT DYKDDDDK |
-Macromolecule #2: DNA strand 1
Macromolecule | Name: DNA strand 1 / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 69.527195 KDa |
Sequence | String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DC)(DA)(DA)(DG)(DC)(DT) ...String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DC)(DA)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG) (DC)(DG)(DA)(DC)(DC)(DT)(DT)(DG)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG) (DT) (DC)(DG)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DT) (DT)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC) (DC)(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DG)(DT)(DA)(DC)(DC)(DG) |
-Macromolecule #3: DNA strand 2
Macromolecule | Name: DNA strand 2 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 70.043562 KDa |
Sequence | String: (DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT) (DA)(DT)(DC)(DC)(DG)(DA) ...String: (DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG)(DG) (DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA)(DG) (DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC) (DT) (DA)(DT)(DC)(DC)(DG)(DA)(DC)(DT) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC)(DA) (DA)(DG) (DG)(DT)(DC)(DG)(DC)(DT)(DG) (DT)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT) (DG)(DC)(DA) (DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG)(DG)(DG)(DA)(DG) (DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG)(DT)(DT)(DA)(DA)(DA) (DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG) (DA) (DG)(DC)(DT)(DT)(DG)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC)(DC)(DA)(DG) |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ChemComp-ALF: |
-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: 10% Oxygene 90% Argone |
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 |