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Yorodumi- PDB-7otc: Cryo-EM structure of an Escherichia coli 70S ribosome in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7otc | ||||||
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Title | Cryo-EM structure of an Escherichia coli 70S ribosome in complex with elongation factor G and the antibiotic Argyrin B | ||||||
Components |
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Keywords | RIBOSOME / antibiotic / translation | ||||||
Function / homology | Function and homology information translation elongation factor activity / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...translation elongation factor activity / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Wieland, M. / Koller, T.O. / Wilson, D.N. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation. Authors: Maximiliane Wieland / Mikael Holm / Emily J Rundlet / Martino Morici / Timm O Koller / Tinashe P Maviza / Domen Pogorevc / Ilya A Osterman / Rolf Müller / Scott C Blanchard / Daniel N Wilson / Abstract: Argyrins are a family of naturally produced octapeptides that display promising antimicrobial activity against Pseudomonas aeruginosa. Argyrin B (ArgB) has been shown to interact with an elongated ...Argyrins are a family of naturally produced octapeptides that display promising antimicrobial activity against Pseudomonas aeruginosa. Argyrin B (ArgB) has been shown to interact with an elongated form of the translation elongation factor G (EF-G), leading to the suggestion that argyrins inhibit protein synthesis by interfering with EF-G binding to the ribosome. Here, using a combination of cryo-electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET), we demonstrate that rather than interfering with ribosome binding, ArgB rapidly and specifically binds EF-G on the ribosome to inhibit intermediate steps of the translocation mechanism. Our data support that ArgB inhibits conformational changes within EF-G after GTP hydrolysis required for translocation and factor dissociation, analogous to the mechanism of fusidic acid, a chemically distinct antibiotic that binds a different region of EF-G. These findings shed light on the mechanism of action of the argyrin-class antibiotics on protein synthesis as well as the nature and importance of rate-limiting, intramolecular conformational events within the EF-G-bound ribosome during late-steps of translocation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7otc.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7otc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7otc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7otc ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7otc | HTTPS FTP |
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-Related structure data
Related structure data | 13058MC 7ug7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules aAB
#1: RNA chain | Mass: 497061.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1758835854 |
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#22: RNA chain | Mass: 941505.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) |
#23: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 1845283434 |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#2: Protein | Mass: 25200.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140NFK2 |
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#3: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N4K1 |
#4: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N548 |
#5: Protein | Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N6Z9 |
#6: Protein | Mass: 12326.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140NGG7 |
#7: Protein | Mass: 17619.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N6W8 |
#8: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N537 |
#9: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N2Z9 |
#10: Protein | Mass: 11325.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N6Y5 |
#11: Protein | Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N7L9 |
#12: Protein | Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N4H3 |
#13: Protein | Mass: 12738.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N5B4 |
#14: Protein | Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N7K8 |
#15: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N811 |
#16: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N7D8 |
#17: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N6Z6 |
#18: Protein | Mass: 7893.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140NGH1 |
#19: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N528 |
#20: Protein | Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140NFU3 |
#21: Protein | Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N8B4 |
+50S ribosomal protein ... , 28 types, 28 molecules CDEFGJKLMNOPQRSTUVWXYZ501234
-Protein , 1 types, 1 molecules w
#52: Protein | Mass: 77571.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: A0A140N7C7 |
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-Non-polymers , 7 types, 307 molecules
#53: Chemical | ChemComp-MG / #54: Chemical | ChemComp-ATP / | #55: Chemical | ChemComp-PUT / #56: Chemical | #57: Chemical | #58: Chemical | ChemComp-GDP / | #59: Chemical | ChemComp-1I7 / | |
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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 |
-Sample preparation
Component | Name: Cryo-EM structure of an Escherichia coli 70S ribosome in complex with elongation factor G and the antibiotic ArgyrinB Type: RIBOSOME / Entity ID: #1-#52 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3/3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 28 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Particle selection | Num. of particles selected: 610946 | ||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153360 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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