[English] 日本語
Yorodumi- EMDB-16162: E.coli 70S ribosome subtomogram average from singleshot acquisiti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16162 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E.coli 70S ribosome subtomogram average from singleshot acquisition on mixed Ribosome-Proteasome sample | |||||||||
Map data | Multishot Tomography Riboprot Singleshot Ribo bin2 tomoman-stopgap | |||||||||
Sample |
| |||||||||
Keywords | 70s / RIBOSOME | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.8 Å | |||||||||
Authors | Khavnekar S / Plitzko JM / Erdmann PSE | |||||||||
Funding support | Germany, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_16162.map.gz | 25 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-16162-v30.xml emd-16162.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_16162.png | 46.9 KB | ||
Masks | emd_16162_msk_1.map | 27 MB | Mask map | |
Filedesc metadata | emd-16162.cif.gz | 3.8 KB | ||
Others | emd_16162_half_map_1.map.gz emd_16162_half_map_2.map.gz | 24.9 MB 24.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16162 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16162 | HTTPS FTP |
-Validation report
Summary document | emd_16162_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_16162_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_16162_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_16162_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16162 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16162 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_16162.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Multishot Tomography Riboprot Singleshot Ribo bin2 tomoman-stopgap | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_16162_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Multishot Tomography Riboprot Singleshot Ribo bin2 tomoman-stopgap
File | emd_16162_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Multishot Tomography Riboprot Singleshot Ribo bin2 tomoman-stopgap | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Multishot Tomography Riboprot Singleshot Ribo bin2 tomoman-stopgap
File | emd_16162_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Multishot Tomography Riboprot Singleshot Ribo bin2 tomoman-stopgap | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : 70S
Entire | Name: 70S |
---|---|
Components |
|
-Supramolecule #1: 70S
Supramolecule | Name: 70S / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP / Number subtomograms used: 7000 |
---|---|
Extraction | Number tomograms: 25 / Number images used: 7000 / Software - Name: STOPGAP (ver. 0.7) |
Final 3D classification | Software - Name: STOPGAP |
Final angle assignment | Type: OTHER / Software - Name: STOPGAP |