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- PDB-8p2f: Staphylococcus aureus 70S ribosome with elongation factor G locke... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p2f | |||||||||||||||
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Title | Staphylococcus aureus 70S ribosome with elongation factor G locked with fusidic acid cyclopentane in post-translocational state | |||||||||||||||
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![]() | RIBOSOME / fusidic acid / EF-G / antibiotic | |||||||||||||||
Function / homology | ![]() ribosome disassembly / translation elongation factor activity / 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 ...ribosome disassembly / translation elongation factor activity / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å | |||||||||||||||
![]() | Gonzalez-Lopez, A. / Selmer, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane. Authors: Adrián González-López / Daniel S D Larsson / Ravi Kiran Koripella / Brett N Cain / Martin Garcia Chavez / Paul J Hergenrother / Suparna Sanyal / Maria Selmer / ![]() ![]() Abstract: The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome ...The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 220.5 KB | Display | |
Data in CIF | ![]() | 398.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17363MC ![]() 8p2gC ![]() 8p2hC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+50S ribosomal protein ... , 28 types, 28 molecules 123456789GHIJKMNOPQRSTUVWXYZ
-RNA chain , 5 types, 6 molecules ABDFab
#10: RNA chain | Mass: 946782.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: GenBank: CP000253 | ||||
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#11: RNA chain | Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: GenBank: CP000253.1 | ||||
#12: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #33: RNA chain | | Mass: 503117.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: GenBank: CP000253 #34: RNA chain | | Mass: 7889.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Protein , 1 types, 1 molecules E
#13: Protein | Mass: 76699.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: fusA, SAOUHSC_00529 / Production host: ![]() ![]() |
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-30S ribosomal protein ... , 19 types, 19 molecules cdefghijklmnopqrstu
#35: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FZ25 |
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#36: Protein | Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW12 |
#37: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FXK6 |
#38: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW23 |
#39: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2G113 |
#40: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: P48940 |
#41: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW20 |
#42: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW39 |
#43: Protein | Mass: 11598.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: A0A0D1JTN2 |
#44: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW31 |
#45: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: P0A0H0 |
#46: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW30 |
#47: Protein | Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW19 |
#48: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2G2Q1 |
#49: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FZ45 |
#50: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW15 |
#51: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2G111 |
#52: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FW10 |
#53: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: 8325-4 / References: UniProt: Q2FXY6 |
-Non-polymers , 8 types, 1772 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/GDP.gif)
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#54: Chemical | #55: Chemical | ChemComp-MG / #56: Chemical | ChemComp-SPD / | #57: Chemical | ChemComp-PUT / | #58: Chemical | ChemComp-GDP / | #59: Chemical | ChemComp-WUX / | Mass: 546.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H54O6 / Feature type: SUBJECT OF INVESTIGATION #60: Chemical | ChemComp-K / | #61: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: Staphylococcus aureus 70S ribosome with elongation factor G and fusidic acid cyclopentane Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 2.6 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() Strain: 8325-4 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1300 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 200 nm / Calibrated defocus max: 2400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.23 sec. / Electron dose: 27.77 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17252 |
EM imaging optics | Energyfilter name: TFS Selectris / Energyfilter slit width: 10 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 559995 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40800 / Algorithm: FOURIER SPACE / Num. of class averages: 4 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE |