+Open data
-Basic information
Entry | Database: PDB / ID: 6sj6 | ||||||||||||
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Title | Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus | ||||||||||||
Components |
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Keywords | RIBOSOME / Stress / S.aureus / RsfS / Hibernation | ||||||||||||
Function / homology | Function and homology information negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å | ||||||||||||
Authors | Khusainov, I. / Pellegrino, S. / Yusupova, G. / Yusupov, M. / Fatkhullin, B. | ||||||||||||
Funding support | France, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6sj6.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6sj6.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6sj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sj6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6sj6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6sj6_validation.xml.gz | 121.2 KB | Display | |
Data in CIF | 6sj6_validation.cif.gz | 205 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/6sj6 ftp://data.pdbj.org/pub/pdb/validation_reports/sj/6sj6 | HTTPS FTP |
-Related structure data
Related structure data | 10212MC 6sj5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 946696.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: GenBank: 1613890206 |
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#2: RNA chain | Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: GenBank: 1569642733 |
+50S ribosomal protein ... , 23 types, 23 molecules DEFMNOPQRSTUVWXYZ012467
-Protein , 1 types, 1 molecules 9
#26: Protein | Mass: 13497.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria) Strain: NCTC 8325 / Gene: rsfS, SAOUHSC_01695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G298 |
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-Non-polymers , 2 types, 59 molecules
#27: Chemical | ChemComp-MG / #28: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 1.35 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 43 sec. / Electron dose: 24.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 1856 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 172729 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83885 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5LI0 Accession code: 5LI0 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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