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Yorodumi- EMDB-46065: Cryo-EM structure of native SWR1 bound to DNA in the absence of n... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-46065 | ||||||||||||
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Title | Cryo-EM structure of native SWR1 bound to DNA in the absence of nucleotide (composite structure) | ||||||||||||
Map data | |||||||||||||
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: 5.8 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_46065.map.gz | 4.7 MB | EMDB map data format | |
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Header (meta data) | emd-46065-v30.xml emd-46065.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_46065.png | 141.9 KB | ||
Filedesc metadata | emd-46065.cif.gz | 4.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-46065 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-46065 | HTTPS FTP |
-Validation report
Summary document | emd_46065_validation.pdf.gz | 346.1 KB | Display | EMDB validaton report |
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Full document | emd_46065_full_validation.pdf.gz | 345.6 KB | Display | |
Data in XML | emd_46065_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_46065_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-46065 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-46065 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_46065.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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 bound to DNA.
Entire | Name: Native SWR1 bound to DNA. |
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Components |
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-Supramolecule #1: Native SWR1 bound to DNA.
Supramolecule | Name: Native SWR1 bound to DNA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 Details: Endogenously purified yeast SWR1 complex bound to 54bp DNA. |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 |
Molecular weight | Theoretical: 1.19 MDa |
-Supramolecule #2: Native SWR1 complex
Supramolecule | Name: Native SWR1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6 / Details: Endogenously purified yeast SWR1 complex |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.08 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.6 Component:
Details: 80 nM SWR1, 160 nM DNA, 0.01% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 5% glycerol | |||||||||||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS | |||||||||||||||||||||||||||
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 10.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6294 / 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: 3.6 µm / Nominal defocus min: 2.0 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
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15003 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |