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Yorodumi- EMDB-16180: 20S Proteasome subtomogram average from Singleshot acquisition on... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16180 | |||||||||
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Title | 20S Proteasome subtomogram average from Singleshot acquisition on mixed Riobsome-Proteasome sample | |||||||||
Map data | Multishot tomography Riboprot 20S bin1 tomoman-stopgap | |||||||||
Sample |
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Keywords | 20s Proteasome / PROTEIN BINDING | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Khavnekar S / Plitzko JM / Erdmann PSE | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: J Struct Biol / Year: 2023 Title: Multishot tomography for high-resolution in situ subtomogram averaging. Authors: S Khavnekar / W Wan / P Majumder / W Wietrzynski / P S Erdmann / J M Plitzko / Abstract: Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can ...Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16180.map.gz | 48.9 MB | EMDB map data format | |
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Header (meta data) | emd-16180-v30.xml emd-16180.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_16180.png | 54.3 KB | ||
Masks | emd_16180_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-16180.cif.gz | 3.9 KB | ||
Others | emd_16180_half_map_1.map.gz emd_16180_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16180 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16180 | HTTPS FTP |
-Validation report
Summary document | emd_16180_validation.pdf.gz | 1.4 MB | Display | EMDB validaton report |
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Full document | emd_16180_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | emd_16180_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_16180_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16180 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16180 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16180.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Multishot tomography Riboprot 20S bin1 tomoman-stopgap | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16180_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Multishot tomography Riboprot 20S bin1 tomoman-stopgap
File | emd_16180_half_map_1.map | ||||||||||||
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Annotation | Multishot tomography Riboprot 20S bin1 tomoman-stopgap | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Multishot tomography Riboprot 20S bin1 tomoman-stopgap
File | emd_16180_half_map_2.map | ||||||||||||
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Annotation | Multishot tomography Riboprot 20S bin1 tomoman-stopgap | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T. acidophilum 20S Proteasome
Entire | Name: T. acidophilum 20S Proteasome |
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Components |
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-Supramolecule #1: T. acidophilum 20S Proteasome
Supramolecule | Name: T. acidophilum 20S Proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 750 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP / Number subtomograms used: 5000 |
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Extraction | Number tomograms: 25 / Number images used: 5000 / Software - Name: STOPGAP (ver. 0.7) |
Final 3D classification | Software - Name: STOPGAP |
Final angle assignment | Type: OTHER / Software - Name: STOPGAP |