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- EMDB-26486: 70S ribosome complex in an intermediate state of translocation bo... -
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Open data
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Basic information
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Title | 70S ribosome complex in an intermediate state of translocation bound to EF-G(GDP) stalled by Argyrin B | ||||||||||||
![]() | Refine3D (Relion 4.0), re-sampled after pixel calibration | ||||||||||||
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![]() | Translocation / EF-G / Argyrin / Ribosome | ||||||||||||
Function / homology | ![]() ribosome disassembly / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / positive regulation of ribosome biogenesis / translation elongation factor activity ...ribosome disassembly / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / positive regulation of ribosome biogenesis / translation elongation factor activity / translational termination / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / regulation of translation / 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 / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.58 Å | ||||||||||||
![]() | Rundlet EJ / Wieland M / Holm M / Koller TO / Blanchard SC / Wilson DN | ||||||||||||
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 | ![]() | 165.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 92 KB 92 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 210.8 KB | ||
Filedesc metadata | ![]() | 17 KB | ||
Others | ![]() ![]() ![]() | 25.5 MB 165.8 MB 165.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ug7MC ![]() 7otcC 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
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Annotation | Refine3D (Relion 4.0), re-sampled after pixel calibration | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.054 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: PostProcess(Relion 4.0), b-factor = -30, re-sampled after pixel...
File | emd_26486_additional_1.map | ||||||||||||
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Annotation | PostProcess(Relion 4.0), b-factor = -30, re-sampled after pixel calibration | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refine3D half 1 (Relion 4.0), re-sampled after pixel calibration
File | emd_26486_half_map_1.map | ||||||||||||
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Annotation | Refine3D half 1 (Relion 4.0), re-sampled after pixel calibration | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refine3D half 2 (Relion 4.0), re-sampled after pixel calibration
File | emd_26486_half_map_2.map | ||||||||||||
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Annotation | Refine3D half 2 (Relion 4.0), re-sampled after pixel calibration | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 70S ribosome in an intermediate state of translocation bound to E...
+Supramolecule #1: 70S ribosome in an intermediate state of translocation bound to E...
+Supramolecule #2: 30S ribosomal subunit
+Supramolecule #3: 50S ribosomal subunit
+Macromolecule #1: 16S rRNA
+Macromolecule #22: 23S rRNA
+Macromolecule #23: 5S rRNA
+Macromolecule #57: tRNA-fMet
+Macromolecule #58: tRNA-Phe
+Macromolecule #59: mRNA
+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 L1
+Macromolecule #25: 50S ribosomal protein L2
+Macromolecule #26: 50S ribosomal protein L3
+Macromolecule #27: 50S ribosomal protein L4
+Macromolecule #28: 50S ribosomal protein L5
+Macromolecule #29: 50S ribosomal protein L6
+Macromolecule #30: 50S ribosomal protein L9
+Macromolecule #31: 50S ribosomal protein L10
+Macromolecule #32: 50S ribosomal protein L11
+Macromolecule #33: 50S ribosomal protein L13
+Macromolecule #34: 50S ribosomal protein L14
+Macromolecule #35: 50S ribosomal protein L15
+Macromolecule #36: 50S ribosomal protein L16
+Macromolecule #37: 50S ribosomal protein L17
+Macromolecule #38: 50S ribosomal protein L18
+Macromolecule #39: 50S ribosomal protein L19
+Macromolecule #40: 50S ribosomal protein L20
+Macromolecule #41: Ribosomal protein L21
+Macromolecule #42: 50S ribosomal protein L22
+Macromolecule #43: 50S ribosomal protein L23
+Macromolecule #44: 50S ribosomal protein L24
+Macromolecule #45: 50S ribosomal protein L25
+Macromolecule #46: 50S ribosomal protein L27
+Macromolecule #47: 50S ribosomal protein L28
+Macromolecule #48: 50S ribosomal protein L29
+Macromolecule #49: 50S ribosomal protein L30
+Macromolecule #50: 50S ribosomal protein L31
+Macromolecule #51: 50S ribosomal protein L32
+Macromolecule #52: 50S ribosomal protein L33
+Macromolecule #53: 50S ribosomal protein L34
+Macromolecule #54: 50S ribosomal protein L35
+Macromolecule #55: 50S ribosomal protein L36
+Macromolecule #56: Elongation factor G
+Macromolecule #60: Argyrin B
+Macromolecule #61: 1,4-DIAMINOBUTANE
+Macromolecule #62: MAGNESIUM ION
+Macromolecule #63: SPERMIDINE
+Macromolecule #64: ZINC ION
+Macromolecule #65: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #66: N-FORMYLMETHIONINE
+Macromolecule #67: PHENYLALANINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2851902 / Average electron dose: 68.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |