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Yorodumi- EMDB-10212: Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10212 | ||||||||||||
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Title | Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus | ||||||||||||
Map data | Cryo-EM map of 50S-RsfS complex from Staphylococcus aureus | ||||||||||||
Sample |
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Keywords | Stress / S.aureus / RsfS / Hibernation / RIBOSOME | ||||||||||||
Function / homology | Function and homology information negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding ...negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) / Staphylococcus aureus (strain NCTC 8325) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | ||||||||||||
Authors | Khusainov I / Pellegrino S / Yusupova G / Yusupov M / Fatkhullin B | ||||||||||||
Funding support | France, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach. Authors: Iskander Khusainov / Bulat Fatkhullin / Simone Pellegrino / Aydar Bikmullin / Wen-Ti Liu / Azat Gabdulkhakov / Amr Al Shebel / Alexander Golubev / Denis Zeyer / Natalie Trachtmann / Georg A ...Authors: Iskander Khusainov / Bulat Fatkhullin / Simone Pellegrino / Aydar Bikmullin / Wen-Ti Liu / Azat Gabdulkhakov / Amr Al Shebel / Alexander Golubev / Denis Zeyer / Natalie Trachtmann / Georg A Sprenger / Shamil Validov / Konstantin Usachev / Gulnara Yusupova / Marat Yusupov / Abstract: For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced ...For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced proteins to the ribosome to prevent unnecessary translation. One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 protein onto the large ribosomal subunit and prevents its association with the small subunit. Here we describe the binding mode of Staphylococcus aureus RsfS to the large ribosomal subunit and present a 3.2 Å resolution cryo-EM reconstruction of the 50S-RsfS complex together with the crystal structure of uL14-RsfS complex solved at 2.3 Å resolution. The understanding of the detailed landscape of RsfS-uL14 interactions within the ribosome shed light on the mechanism of ribosome shutdown in the human pathogen S. aureus and might deliver a novel target for pharmacological drug development and treatment of bacterial infections. | ||||||||||||
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_10212.map.gz | 23.7 MB | EMDB map data format | |
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Header (meta data) | emd-10212-v30.xml emd-10212.xml | 46.6 KB 46.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10212_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_10212.png | 271.4 KB | ||
Filedesc metadata | emd-10212.cif.gz | 10.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10212 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10212 | HTTPS FTP |
-Related structure data
Related structure data | 6sj6MC 6sj5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_10212.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of 50S-RsfS complex from Staphylococcus aureus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.858 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 : 50S ribosomal subunit complex with stress induced ribosome silenc...
+Supramolecule #1: 50S ribosomal subunit complex with stress induced ribosome silenc...
+Supramolecule #3: Ribosomal silencing factor RsfS
+Supramolecule #2: 50S ribosomal subunit
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L13
+Macromolecule #7: 50S ribosomal protein L14
+Macromolecule #8: 50S ribosomal protein L15
+Macromolecule #9: 50S ribosomal protein L16
+Macromolecule #10: 50S ribosomal protein L17
+Macromolecule #11: 50S ribosomal protein L18
+Macromolecule #12: 50S ribosomal protein L19
+Macromolecule #13: 50S ribosomal protein L20
+Macromolecule #14: 50S ribosomal protein L21
+Macromolecule #15: 50S ribosomal protein L22
+Macromolecule #16: 50S ribosomal protein L23
+Macromolecule #17: 50S ribosomal protein L24
+Macromolecule #18: 50S ribosomal protein L25
+Macromolecule #19: 50S ribosomal protein L27
+Macromolecule #20: 50S ribosomal protein L28
+Macromolecule #21: 50S ribosomal protein L29
+Macromolecule #22: 50S ribosomal protein L30
+Macromolecule #23: 50S ribosomal protein L32
+Macromolecule #24: 50S ribosomal protein L34
+Macromolecule #25: 50S ribosomal protein L35
+Macromolecule #26: Ribosomal silencing factor RsfS
+Macromolecule #27: MAGNESIUM ION
+Macromolecule #28: POTASSIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 2 / Number real images: 1856 / Average exposure time: 43.0 sec. / Average electron dose: 24.6 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: 1.2 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |