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Yorodumi- EMDB-22026: Reprocessing of EMPIAR-10218 data (20S proteasome) with particles... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22026 | |||||||||
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Title | Reprocessing of EMPIAR-10218 data (20S proteasome) with particles picked by Kpicker | |||||||||
Map data | 20S proteasome | |||||||||
Sample |
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Function / homology | Function and homology information proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / endopeptidase activity / ubiquitin-dependent protein catabolic process / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | McSweeney DM / McSweeney SM / Liu Q | |||||||||
Citation | Journal: IUCrJ / Year: 2020 Title: A self-supervised workflow for particle picking in cryo-EM. Authors: Donal M McSweeney / Sean M McSweeney / Qun Liu / Abstract: High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an ...High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as , , , and . | |||||||||
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_22026.map.gz | 34.4 MB | EMDB map data format | |
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Header (meta data) | emd-22026-v30.xml emd-22026.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22026_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_22026.png | 242.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22026 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22026 | HTTPS FTP |
-Validation report
Summary document | emd_22026_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_22026_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_22026_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22026 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22026 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22026.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 20S proteasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6616 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 20S proteasome
Entire | Name: 20S proteasome |
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Components |
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-Supramolecule #1: 20S proteasome
Supramolecule | Name: 20S proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.59 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |