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- EMDB-13058: Cryo-EM structure of an Escherichia coli 70S ribosome in complex ... -
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Open data
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Basic information
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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 | |||||||||
![]() | Locally filtered and merged multibody refined map of an E. coli 70S - EF-G - Argyrin B complex | |||||||||
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![]() | antibiotic / ribosome / translation | |||||||||
Function / homology | ![]() translation elongation factor activity / large ribosomal subunit / small ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding ...translation elongation factor activity / large ribosomal subunit / small 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 / GTPase activity / mRNA binding / GTP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Wieland M / Koller TO | |||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 22.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 72.4 KB 72.4 KB | Display Display | ![]() |
Images | ![]() | 210.1 KB | ||
Filedesc metadata | ![]() | 14.8 KB | ||
Others | ![]() | 18 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 467.8 KB | Display | ![]() |
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Full document | ![]() | 467.3 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7otcMC ![]() 7ug7C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Locally filtered and merged multibody refined map of an E. coli 70S - EF-G - Argyrin B complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Locally filtered polished map of an E. coli...
File | emd_13058_additional_1.map | ||||||||||||
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Annotation | Locally filtered polished map of an E. coli 70S - EF-G - Argyrin B complex | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Cryo-EM structure of an Escherichia coli 70S ribosome in complex ...
+Supramolecule #1: Cryo-EM structure of an Escherichia coli 70S ribosome in complex ...
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: 23S ribosomal RNA
+Macromolecule #23: 5S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #24: 50S ribosomal protein L2
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L13
+Macromolecule #30: 50S ribosomal protein L14
+Macromolecule #31: 50S ribosomal protein L15
+Macromolecule #32: 50S ribosomal protein L16
+Macromolecule #33: 50S ribosomal protein L17
+Macromolecule #34: 50S ribosomal protein L18
+Macromolecule #35: 50S ribosomal protein L19
+Macromolecule #36: 50S ribosomal protein L20
+Macromolecule #37: 50S ribosomal protein L21
+Macromolecule #38: 50S ribosomal protein L22
+Macromolecule #39: 50S ribosomal protein L23
+Macromolecule #40: 50S ribosomal protein L24
+Macromolecule #41: 50S ribosomal protein L25
+Macromolecule #42: 50S ribosomal protein L27
+Macromolecule #43: 50S ribosomal protein L28
+Macromolecule #44: 50S ribosomal protein L29
+Macromolecule #45: 50S ribosomal protein L30
+Macromolecule #46: 50S ribosomal protein L31
+Macromolecule #47: 50S ribosomal protein L32
+Macromolecule #48: 50S ribosomal protein L33
+Macromolecule #49: 50S ribosomal protein L34
+Macromolecule #50: 50S ribosomal protein L35
+Macromolecule #51: 50S ribosomal protein L36
+Macromolecule #52: Elongation factor G
+Macromolecule #53: MAGNESIUM ION
+Macromolecule #54: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: 1,4-DIAMINOBUTANE
+Macromolecule #56: SPERMIDINE
+Macromolecule #57: ZINC ION
+Macromolecule #58: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #59: Argyrin B
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |