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Yorodumi- EMDB-44093: Cryo-EM structure of native SWR1, free complex (composite structure) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44093 | ||||||||||||
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Title | Cryo-EM structure of native SWR1, free complex (composite structure) | ||||||||||||
Map data | Composite cryo-EM structure of free native SWR1 complex | ||||||||||||
Sample |
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Keywords | Chromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z / GENE REGULATION | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Louder RK / Park G / Wu C | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Cell(Cambridge,Mass.) / Year: 2024 Title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler Authors: Louder RK / Park G / Ye Z / Cha JS / Gardner AM / Lei Q / Ranjan A / Hollmuller E / Stengel F / Pugh BF / Wu C | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44093.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-44093-v30.xml emd-44093.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_44093.png | 123.4 KB | ||
Filedesc metadata | emd-44093.cif.gz | 4.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44093 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44093 | HTTPS FTP |
-Validation report
Summary document | emd_44093_validation.pdf.gz | 344.1 KB | Display | EMDB validaton report |
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Full document | emd_44093_full_validation.pdf.gz | 343.7 KB | Display | |
Data in XML | emd_44093_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_44093_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44093 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44093 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_44093.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite cryo-EM structure of free native SWR1 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Native SWR1 complex
Entire | Name: Native SWR1 complex |
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Components |
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-Supramolecule #1: Native SWR1 complex
Supramolecule | Name: Native SWR1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 / Details: Endogenously purified yeast SWR1 complex |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 |
Molecular weight | Theoretical: 1.19 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.6 Component:
Details: 25 mM HEPES, 0.2 mM EDTA, 1 mM MgCl2, 100 mM KOAc, 1 mM DTT, 0.25 mM TCEP, 1% glycerol buffer | |||||||||||||||||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot time and blot force of 5.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Software | Name: SerialEM (ver. 3.7.6) |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3691 / Average exposure time: 4.0 sec. / Average electron dose: 54.0 e/Å2 Details: Each micrograph was fractionated into 64 frames within a 4 second exposure. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.7 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 | Chain - Source name: Other / Chain - Initial model type: experimental model Details: Model built from other cryo-EM structures in this study |
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Software | Name: UCSF ChimeraX (ver. 1.6) |
Refinement | Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |