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- EMDB-17007: CryoEM Structure INO80core Hexasome complex ATPase-DNA refinement... -

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Basic information

Entry
Database: EMDB / ID: EMD-17007
TitleCryoEM Structure INO80core Hexasome complex ATPase-DNA refinement state1
Map datactINO80-hexasome ATPase-DNA focused refinement sharpened map
Sample
  • Complex: INO80 core module in complex with hexasome
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • DNA: DNA strand 1DNA
    • DNA: DNA strand 2DNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION
KeywordsATP-dependent chromatin remodeler / DNA BINDING PROTEIN
Biological speciesThermochaetoides thermophila (fungus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang M / Jungblut A / Hoffmann T / Eustermann S
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND847543 Germany
European Research Council (ERC)833613European Union
German Research Foundation (DFG)CRC136 Germany
German Research Foundation (DFG)CRC1064 Germany
CitationJournal: 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
DepositionApr 4, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17007.png

Downloads & links

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Map

FileDownload / File: emd_17007.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationctINO80-hexasome ATPase-DNA focused refinement sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.14418435 - 1.2388167
Average (Standard dev.)0.00069278065 (±0.013745803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map ctINO80-hexasome ATPase-DNA focused refinement

Fileemd_17007_additional_1.map
Annotationunsharpened map ctINO80-hexasome ATPase-DNA focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 ctINO80-hexasome ATPase-DNA focused refinement

Fileemd_17007_half_map_1.map
Annotationhalf map 1 ctINO80-hexasome ATPase-DNA focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 ctINO80-hexasome ATPase-DNA focused refinement

Fileemd_17007_half_map_2.map
Annotationhalf map 2 ctINO80-hexasome ATPase-DNA focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : INO80 core module in complex with hexasome

EntireName: INO80 core module in complex with hexasome
Components
  • Complex: INO80 core module in complex with hexasome
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • DNA: DNA strand 1DNA
    • DNA: DNA strand 2DNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION

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Supramolecule #1: INO80 core module in complex with hexasome

SupramoleculeName: 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
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 861 KDa

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Macromolecule #1: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 1 / Details: Ino80 N-terminal truncation C-terminal 2xFlagTag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 130.887656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: DNA strand 1

MacromoleculeName: DNA strand 1 / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.527195 KDa
SequenceString: (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)

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Macromolecule #3: DNA strand 2

MacromoleculeName: DNA strand 2 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 70.043562 KDa
SequenceString: (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)

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.88 mg/mL
BufferpH: 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
GridModel: 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
VitrificationCryogen 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).
Details11-subunit ctINO80 reconstituted with hexasome

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 15384 / Average electron dose: 50.36 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2137460
Details: Particles were initially picked by WARP to generate an initial model, which was subsequently used for the 3D template picking
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Details: de novo 3D model was generated by using gradient-driven algorithm implemented in RELION 4.0
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 72400
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3i62

source_name: PDB, initial_model_type: experimental model

8av6

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: OTHER
Output model

PDB-8oo9:
CryoEM Structure INO80core Hexasome complex ATPase-DNA refinement state1

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