+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3607 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SWR1 chromatin remodelling complex | |||||||||
Map data | SWR1 chromatin remodelling complex | |||||||||
Sample |
| |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 21.0 Å | |||||||||
Authors | Chaban Y / Lin C-L / Wigley DB | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2017 Title: Functional characterization and architecture of recombinant yeast SWR1 histone exchange complex. Authors: Chia-Liang Lin / Yuriy Chaban / David M Rees / Elizabeth A McCormack / Lorraine Ocloo / Dale B Wigley / Abstract: We have prepared recombinant fourteen subunit yeast SWR1 complex from insect cells using a modified MultiBac system. The 1.07 MDa recombinant protein complex has histone-exchange activity. Full ...We have prepared recombinant fourteen subunit yeast SWR1 complex from insect cells using a modified MultiBac system. The 1.07 MDa recombinant protein complex has histone-exchange activity. Full exchange activity is realized with a single SWR1 complex bound to a nucleosome. We also prepared mutant complexes that lack a variety of subunits or combinations of subunits and these start to reveal roles for some of these subunits as well as indicating interactions between them in the full complex. Complexes containing a series of N-terminally and C-terminally truncated Swr1 subunits reveal further details about interactions between subunits as well as their binding sites on the Swr1 subunit. Finally, we present electron microscopy studies revealing the dynamic nature of the complex and a 21 Å resolution reconstruction of the intact complex provides details not apparent in previously reported structures, including a large central cavity of sufficient size to accommodate a nucleosome. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3607.map.gz | 1008.7 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3607-v30.xml emd-3607.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | emd_3607.png | 80.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3607 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3607 | HTTPS FTP |
-Validation report
Summary document | emd_3607_validation.pdf.gz | 192.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3607_full_validation.pdf.gz | 191.6 KB | Display | |
Data in XML | emd_3607_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3607 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3607 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3607.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | SWR1 chromatin remodelling complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : SWR1 chromatin remodelling complex
Entire | Name: SWR1 chromatin remodelling complex |
---|---|
Components |
|
-Supramolecule #1: SWR1 chromatin remodelling complex
Supramolecule | Name: SWR1 chromatin remodelling complex / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
---|---|
Staining | Type: NEGATIVE / Material: Uranyl Acetate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: Initial 3D model was obtained from 2D class averages using angular reconstitution technique. |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 6000 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |