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Open data
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Basic information
Entry | Database: PDB / ID: 5li0 | ||||||
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Title | 70S ribosome from Staphylococcus aureus | ||||||
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![]() | RIBOSOME / pathogenic ribosome / bL31 B-type | ||||||
Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Khusainov, I. / Vicens, Q. / Bochler, A. / Grosse, F. / Myasnikov, A. / Menetret, J.F. / Chicher, J. / Marzi, S. / Romby, P. / Yusupova, G. ...Khusainov, I. / Vicens, Q. / Bochler, A. / Grosse, F. / Myasnikov, A. / Menetret, J.F. / Chicher, J. / Marzi, S. / Romby, P. / Yusupova, G. / Yusupov, M. / Hashem, Y. | ||||||
![]() | ![]() Title: Structure of the 70S ribosome from human pathogen Staphylococcus aureus. Authors: Iskander Khusainov / Quentin Vicens / Anthony Bochler / François Grosse / Alexander Myasnikov / Jean-François Ménétret / Johana Chicher / Stefano Marzi / Pascale Romby / Gulnara Yusupova ...Authors: Iskander Khusainov / Quentin Vicens / Anthony Bochler / François Grosse / Alexander Myasnikov / Jean-François Ménétret / Johana Chicher / Stefano Marzi / Pascale Romby / Gulnara Yusupova / Marat Yusupov / Yaser Hashem / ![]() ![]() Abstract: Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact ...Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance. Here, we present the first full 70S ribosome structure from Staphylococcus aureus, a Gram-positive pathogenic bacterium, solved by cryo-electron microscopy. Comparative analysis with other known bacterial ribosomes pinpoints several unique features specific to S. aureus around a conserved core, at both the protein and the RNA levels. Our work provides the structural basis for the many studies aiming at understanding translation regulation in S. aureus and for designing drugs against this often multi-resistant pathogen. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4050MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules aAB
#1: RNA chain | Mass: 500464.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 87201381 |
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#21: RNA chain | Mass: 945058.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: GenBank: 87201381 |
#22: RNA chain | Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 87201381 |
-30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst
#2: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FZ25 |
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#3: Protein | Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW12 |
#4: Protein | Mass: 22920.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FXK6 |
#5: Protein | Mass: 17639.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW23 |
#6: Protein | Mass: 11368.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2G113 |
#7: Protein | Mass: 17167.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P48940 |
#8: Protein | Mass: 14723.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW20 |
#9: Protein | Mass: 14440.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW39 |
#10: Protein | Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q931G5 |
#11: Protein | Mass: 12562.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW31 |
#12: Protein | Mass: 15131.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q5HID0 |
#13: Protein | Mass: 13487.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW30 |
#14: Protein | Mass: 7186.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW19 |
#15: Protein | Mass: 10503.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2G2Q1 |
#16: Protein | Mass: 10122.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FZ45 |
#17: Protein | Mass: 10065.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW15 |
#18: Protein | Mass: 8418.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2G111 |
#19: Protein | Mass: 9605.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW10 |
#20: Protein | Mass: 8708.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FXY6 |
+50S ribosomal protein ... , 28 types, 28 molecules DEFGHMNOPQRSTUVWXYZ012345678
-Non-polymers , 4 types, 203 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/ZN.gif)
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#51: Chemical | ChemComp-MG / #52: Chemical | ChemComp-O / #53: Chemical | ChemComp-ZN / | #54: Water | ChemComp-HOH / | |
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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 |
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Sample preparation
Component | Name: 70S ribosome from Staphylococcus aureus / Type: RIBOSOME / Entity ID: #1-#50 |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 Details: 5 mM Hepes-KOH pH 7.5 50 mM KCl 10 mM NH4Cl 10 mM Mg(OAc)2 1 mM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 5, blot waiting time 30 s |
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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: ![]() |
Electron lens | Mode: DARK FIELD |
Image recording | Average exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3850 |
Image scans | Movie frames/image: 17 / Used frames/image: 2-8 |
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Processing
Software | Name: PHENIX / Version: dev_2341: / 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: 423497 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110000 / Algorithm: FOURIER SPACE / Num. of class averages: 8 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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