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Yorodumi- EMDB-8274: YphC and YsxC GTPases assist the maturation of the central protub... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8274 | |||||||||
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Title | YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase-associated region, and functional core of the 50S ribosomal subunit | |||||||||
Map data | 50S ribosomal subunit assembly intermediate obtained upon depletion of YsxC protein in Bacillus subtilis | |||||||||
Sample |
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Keywords | Ribosome assembly / 50S subunit / YsxC protein / RIBOSOME | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | Ni X / Davis JH / Jain N / Razi A / Benlekbir S / McArthur AG / Rubinstein JR / Britton RA / Williamson JR / Ortega J | |||||||||
Funding support | Canada, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2016 Title: YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit. Authors: Xiaodan Ni / Joseph H Davis / Nikhil Jain / Aida Razi / Samir Benlekbir / Andrew G McArthur / John L Rubinstein / Robert A Britton / James R Williamson / Joaquin Ortega / Abstract: YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we ...YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45SYphC and 44.5SYsxC particles. Quantitative mass spectrometry analysis and the 5-6 Å resolution cryo-EM maps of the 45SYphC and 44.5SYsxC particles revealed that the two GTPases participate in the maturation of the central protuberance, GTPase associated region and key RNA helices in the A, P and E functional sites of the 50S subunit. We observed that YphC and YsxC bind specifically to the two immature particles, suggesting that they represent either on-pathway intermediates or that their structure has not significantly diverged from that of the actual substrate. These results describe the nature of these immature particles, a widely used tool to study the assembly process of the ribosome. They also provide the first insights into the function of YphC and YsxC in 50S subunit assembly and are consistent with this process occurring through multiple parallel pathways, as it has been described for the 30S subunit. | |||||||||
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_8274.map.gz | 9 MB | EMDB map data format | |
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Header (meta data) | emd-8274-v30.xml emd-8274.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8274_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_8274.png | 49 KB | ||
Filedesc metadata | emd-8274.cif.gz | 3.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8274 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8274 | HTTPS FTP |
-Validation report
Summary document | emd_8274_validation.pdf.gz | 531.4 KB | Display | EMDB validaton report |
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Full document | emd_8274_full_validation.pdf.gz | 531 KB | Display | |
Data in XML | emd_8274_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_8274_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8274 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8274 | 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_8274.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 50S ribosomal subunit assembly intermediate obtained upon depletion of YsxC protein in Bacillus subtilis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Assembly intermediate of the 50S subunit, Class I
Entire | Name: Assembly intermediate of the 50S subunit, Class I |
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Components |
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-Supramolecule #1: Assembly intermediate of the 50S subunit, Class I
Supramolecule | Name: Assembly intermediate of the 50S subunit, Class I / type: complex / ID: 1 / Parent: 0 / Details: Obtained upon depletion of YsxC protein |
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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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Grid | Model: C-flats CFT-222C / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III Details: Plunged into liquid ethane (FEI VITROBOT MARK III). |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.5 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |