+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24977 | |||||||||
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Title | The 45SRbgA particles incubated at 37C for 15 min Class1 | |||||||||
Map data | Refine map | |||||||||
Sample |
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Function / homology | Function and homology information large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome ...large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Ortega J / Seffouh A | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: RbgA ensures the correct timing in the maturation of the 50S subunits functional sites. Authors: Amal Seffouh / Chirstian Trahan / Tanzila Wasi / Nikhil Jain / Kaustuv Basu / Robert A Britton / Marlene Oeffinger / Joaquin Ortega / Abstract: RbgA is an essential protein for the assembly of the 50S subunit in Bacillus subtilis. Depletion of RbgA leads to the accumulation of the 45S intermediate. A strain expressing a RbgA variant with ...RbgA is an essential protein for the assembly of the 50S subunit in Bacillus subtilis. Depletion of RbgA leads to the accumulation of the 45S intermediate. A strain expressing a RbgA variant with reduced GTPase activity generates spontaneous suppressor mutations in uL6. Each suppressor strain accumulates a unique 44S intermediate. We reasoned that characterizing the structure of these mutant 44S intermediates may explain why RbgA is required to catalyze the folding of the 50S functional sites. We found that in the 44S particles, rRNA helices H42 and H97, near the binding site of uL6, adopt a flexible conformation and allow the central protuberance and functional sites in the mutant 44S particles to mature in any order. Instead, the wild-type 45S particles exhibit a stable H42-H97 interaction and their functional sites always mature last. The dependence on RbgA was also less pronounced in the 44S particles. We concluded that the binding of uL6 pauses the maturation of the functional sites, but the central protuberance continues to fold. RbgA exclusively binds intermediates with a formed central protuberance and licenses the folding of the functional sites. Through this mechanism, RbgA ensures that the functional sites of the 50S mature last. | |||||||||
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_24977.map.gz | 229.2 MB | EMDB map data format | |
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Header (meta data) | emd-24977-v30.xml emd-24977.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24977_fsc.xml | 15.1 KB | Display | FSC data file |
Images | emd_24977.png | 87.7 KB | ||
Others | emd_24977_additional_1.map.gz | 29.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24977 | HTTPS FTP |
-Validation report
Summary document | emd_24977_validation.pdf.gz | 491.3 KB | Display | EMDB validaton report |
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Full document | emd_24977_full_validation.pdf.gz | 490.9 KB | Display | |
Data in XML | emd_24977_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | emd_24977_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24977 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24977 | HTTPS FTP |
-Related 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_24977.map.gz / Format: CCP4 / Size: 290.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Refine map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Postprocess
File | emd_24977_additional_1.map | ||||||||||||
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Annotation | Postprocess | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The 45SRbgA particles incubated at 37C for 15 min Class1
Entire | Name: The 45SRbgA particles incubated at 37C for 15 min Class1 |
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Components |
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-Supramolecule #1: The 45SRbgA particles incubated at 37C for 15 min Class1
Supramolecule | Name: The 45SRbgA particles incubated at 37C for 15 min Class1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bacillus subtilis (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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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 |