[English] 日本語
![](img/lk-miru.gif)
- EMDB-17032: CryoEM Structure INO80 hexasome complex Arp8 module bound to DNA -
+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM Structure INO80 hexasome complex Arp8 module bound to DNA | |||||||||||||||
![]() | ctINO80 hexasome complex Arp8 Module unsharpened map | |||||||||||||||
![]() |
| |||||||||||||||
![]() | ATP-dependent chromatin remodeler / DNA BINDING PROTEIN | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Zhang M / Jungblut A / Hoffmann T / Eustermann S | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 40.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 35.7 KB | ||
Others | ![]() ![]() | 40.8 MB 40.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | ctINO80 hexasome complex Arp8 Module unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: ctINO80 hexasome complex Arp8 Module half map
File | emd_17032_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | ctINO80 hexasome complex Arp8 Module half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: ctINO80 hexasome complex Arp8 Module half map
File | emd_17032_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | ctINO80 hexasome complex Arp8 Module half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : INO80 core module in complex with hexasome
Entire | Name: INO80 core module in complex with hexasome |
---|---|
Components |
|
-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-#12 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: ![]() |
Molecular weight | Theoretical: 861 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.88 mg/mL |
---|---|
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% 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 |
---|---|
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: ![]() |
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 |