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Yorodumi- EMDB-9194: T20S proteasome using Topaz at threshold t-3 (EMPIAR-10025 reproc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9194 | ||||||||||||||||||||||||
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Title | T20S proteasome using Topaz at threshold t-3 (EMPIAR-10025 reprocessing) | ||||||||||||||||||||||||
Map data | Cryosparc v0 sharpened map for Topaz t-3 threshold | ||||||||||||||||||||||||
Sample |
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Biological species | Thermoplasma acidophilum (acidophilic) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||||||||||||||||||||
Authors | Bepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger B | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Res Comput Mol Biol / Year: 2018 Title: Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Authors: Tristan Bepler / Andrew Morin / Alex J Noble / Julia Brasch / Lawrence Shapiro / Bonnie Berger / | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9194.map.gz | 229.6 MB | EMDB map data format | |
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Header (meta data) | emd-9194-v30.xml emd-9194.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_9194.png | 173.5 KB | ||
Masks | emd_9194_msk_1.map | 244.1 MB | Mask map | |
Others | emd_9194_additional.map.gz emd_9194_additional_1.map.gz emd_9194_half_map_1.map.gz emd_9194_half_map_2.map.gz | 119.9 MB 119.9 MB 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9194 | HTTPS FTP |
-Validation report
Summary document | emd_9194_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_9194_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_9194_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9194 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9194 | HTTPS FTP |
-Related structure data
Related structure data | 9201C 9202C 9206C 9207C 9208C 9209C 9210C 9211C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9194.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryosparc v0 sharpened map for Topaz t-3 threshold | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6575 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_9194_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryosparc v0 unsharpened map for Topaz t-3 threshold
File | emd_9194_additional.map | ||||||||||||
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Annotation | Cryosparc v0 unsharpened map for Topaz t-3 threshold | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cryosparc v0 unsharpened map for Topaz t-3 threshold
File | emd_9194_additional_1.map | ||||||||||||
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Annotation | Cryosparc v0 unsharpened map for Topaz t-3 threshold | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc v0 halfmap A for Topaz t-3 threshold
File | emd_9194_half_map_1.map | ||||||||||||
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Annotation | Cryosparc v0 halfmap A for Topaz t-3 threshold | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryosparc v0 halfmap B for Topaz t-3 threshold
File | emd_9194_half_map_2.map | ||||||||||||
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Annotation | Cryosparc v0 halfmap B for Topaz t-3 threshold | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T20S proteasome
Entire | Name: T20S proteasome |
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Components |
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-Supramolecule #1: T20S proteasome
Supramolecule | Name: T20S proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Recombinant expression | Organism: Thermoplasma acidophilum (acidophilic) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.21 mg/mL |
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Buffer | pH: 7.8 / Details: 20 mM Tris, 150 mM NaCl |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 Details: Blot for 2.5 seconds before plunging. Vitrification carried out at room temperature.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |