[English] 日本語
Yorodumi- EMDB-43864: Structure of Circularly Permuted 50S Ribosomal Subunit Assembly I... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43864 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Circularly Permuted 50S Ribosomal Subunit Assembly Intermediate - CP78 Class B | ||||||||||||
Map data | Class B CP78 50S Ribosomal Intermediate | ||||||||||||
Sample |
| ||||||||||||
Keywords | 50S subunit / assembly intermediate / RNA-protein complex / ribosome | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | ||||||||||||
Authors | Dong X / Sheng K / Williamson JR | ||||||||||||
Funding support | United States, 3 items
| ||||||||||||
Citation | Journal: To Be Published Title: Assembly of Bacterial Ribosome with Circularly Permuted rRNA Authors: Dong X / Sheng K / Williamson JR / Gebert L / Aiyer S / Lyumkis D | ||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_43864.map.gz | 91.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-43864-v30.xml emd-43864.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43864_fsc.xml | 12.3 KB | Display | FSC data file |
Images | emd_43864.png | 88.1 KB | ||
Filedesc metadata | emd-43864.cif.gz | 4.5 KB | ||
Others | emd_43864_half_map_1.map.gz emd_43864_half_map_2.map.gz | 173.8 MB 173.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43864 | HTTPS FTP |
-Validation report
Summary document | emd_43864_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_43864_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_43864_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_43864_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43864 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_43864.map.gz / Format: CCP4 / Size: 187 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Class B CP78 50S Ribosomal Intermediate | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Class B CP78 50S Ribosomal Intermediate - Half Map 2
File | emd_43864_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Class B CP78 50S Ribosomal Intermediate - Half Map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Class B CP78 50S Ribosomal Intermediate - Half Map 1
File | emd_43864_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Class B CP78 50S Ribosomal Intermediate - Half Map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : CP78 iSAT 50S ribosomal subunit assembly intermediate
Entire | Name: CP78 iSAT 50S ribosomal subunit assembly intermediate |
---|---|
Components |
|
-Supramolecule #1: CP78 iSAT 50S ribosomal subunit assembly intermediate
Supramolecule | Name: CP78 iSAT 50S ribosomal subunit assembly intermediate / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: Most of the sucrose was removed by spin concentration. | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 3 microliter of the sample was added.. | ||||||||||||||||||
Details | The in vitro assembled large ribosomal subunit was purified by sucrose gradient and was spin-concentrated in a 100 kDa MW-cutoff filter. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Details | In order to account for highly preferred orientation of the specimen, data were acquired using tilts ranging at -20 degrees. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2015 / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |