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Yorodumi- EMDB-40309: E. coli 50S assembly intermediate from bL17-depletion strain, cla... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40309 | |||||||||
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Title | E. coli 50S assembly intermediate from bL17-depletion strain, class: rl17-B-b1 | |||||||||
Map data | rl17-B-b1 Class Particle stack from (doi: 10.1016/j.cell.2016.11.020.) was reanalyzed by CryoSPARC ab-initio subclassification. The map was aligned to 50S reference map and resampled on the same grid. | |||||||||
Sample |
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Keywords | Ribosome / 50S intermediate / RNP | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.45 Å | |||||||||
Authors | Sheng K / Williamson JR | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Assembly landscape for the bacterial large ribosomal subunit. Authors: Kai Sheng / Ning Li / Jessica N Rabuck-Gibbons / Xiyu Dong / Dmitry Lyumkis / James R Williamson / Abstract: Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic ...Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40309.map.gz | 13.4 MB | EMDB map data format | |
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Header (meta data) | emd-40309-v30.xml emd-40309.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40309_fsc.xml | 5.2 KB | Display | FSC data file |
Images | emd_40309.png | 90.9 KB | ||
Others | emd_40309_half_map_1.map.gz emd_40309_half_map_2.map.gz | 14.5 MB 14.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40309 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40309 | HTTPS FTP |
-Validation report
Summary document | emd_40309_validation.pdf.gz | 987.9 KB | Display | EMDB validaton report |
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Full document | emd_40309_full_validation.pdf.gz | 987.5 KB | Display | |
Data in XML | emd_40309_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_40309_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40309 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40309 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40309.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | rl17-B-b1 Class Particle stack from (doi: 10.1016/j.cell.2016.11.020.) was reanalyzed by CryoSPARC ab-initio subclassification. The map was aligned to 50S reference map and resampled on the same grid. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: raw reconstruction without alignment
File | emd_40309_half_map_1.map | ||||||||||||
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Annotation | raw reconstruction without alignment | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: raw reconstruction without alignment
File | emd_40309_half_map_2.map | ||||||||||||
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Annotation | raw reconstruction without alignment | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli 50S assembly intermediate from bL17-depletion strain, cla...
Entire | Name: E. coli 50S assembly intermediate from bL17-depletion strain, class: rl17-B-b1 |
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Components |
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-Supramolecule #1: E. coli 50S assembly intermediate from bL17-depletion strain, cla...
Supramolecule | Name: E. coli 50S assembly intermediate from bL17-depletion strain, class: rl17-B-b1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 33.0 e/Å2 Details: Data were collected with tilts ranging from 0 to 60 degrees in 10-degree increments. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |