[English] 日本語
Yorodumi- EMDB-51351: Fusidic acid-locked Escherichia coli 70S ribosome with Staphyloco... -
+
Open data
-
Basic information
| Entry | ![]() | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Fusidic acid-locked Escherichia coli 70S ribosome with Staphylococcus aureus EF-G in post-translocational state (POST) | |||||||||||||||
Map data | Local filtered map | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | RIBOSOME / fusidic acid / EF-G / antibiotic | |||||||||||||||
| Function / homology | Function and homology informationribosome disassembly / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / transcriptional attenuation / endoribonuclease inhibitor activity ...ribosome disassembly / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / translation elongation factor activity / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / response to reactive oxygen species / ribosome assembly / transcription elongation factor complex / DNA endonuclease activity / transcription antitermination / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / large ribosomal subunit / regulation of translation / ribosome binding / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
| Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) / ![]() | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.21 Å | |||||||||||||||
Authors | Gonzalez-Lopez A / Selmer M | |||||||||||||||
| Funding support | Sweden, 4 items
| |||||||||||||||
Citation | Journal: Nat Commun / Year: 2025Title: Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis. Authors: Adrián González-López / Xueliang Ge / Daniel S D Larsson / Carina Sihlbom Wallem / Suparna Sanyal / Maria Selmer / ![]() Abstract: The antibiotic resistance protein FusB rescues protein synthesis from inhibition by fusidic acid (FA), which locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis. Here, we present ...The antibiotic resistance protein FusB rescues protein synthesis from inhibition by fusidic acid (FA), which locks elongation factor G (EF-G) to the ribosome after GTP hydrolysis. Here, we present time-resolved single-particle cryo-EM structures explaining the mechanism of FusB-mediated rescue. FusB binds to the FA-trapped EF-G on the ribosome, causing large-scale conformational changes of EF-G that break interactions with the ribosome, tRNA, and mRNA. This leads to dissociation of EF-G from the ribosome, followed by FA release. We also observe two independent binding sites of FusB on the classical-state ribosome, overlapping with the binding site of EF-G to each of the ribosomal subunits, yet not inhibiting tRNA delivery. The affinity of FusB to the ribosome and the concentration of FusB in S. aureus during FusB-mediated resistance support that direct binding of FusB to ribosomes could occur in the cell. Our results reveal an intricate resistance mechanism involving specific interactions of FusB with both EF-G and the ribosome, and a non-canonical release pathway of EF-G. | |||||||||||||||
| History |
|
-
Structure visualization
| Supplemental images |
|---|
-
Downloads & links
-EMDB archive
| Map data | emd_51351.map.gz | 86.1 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-51351-v30.xml emd-51351.xml | 92 KB 92 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_51351_fsc.xml | 22.4 KB | Display | FSC data file |
| Images | emd_51351.png | 107.3 KB | ||
| Masks | emd_51351_msk_1.map | 824 MB | Mask map | |
| Filedesc metadata | emd-51351.cif.gz | 16.8 KB | ||
| Others | emd_51351_additional_1.map.gz emd_51351_half_map_1.map.gz emd_51351_half_map_2.map.gz | 411.5 MB 765.4 MB 765.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-51351 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51351 | HTTPS FTP |
-Validation report
| Summary document | emd_51351_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
|---|---|---|---|---|
| Full document | emd_51351_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | emd_51351_validation.xml.gz | 29.7 KB | Display | |
| Data in CIF | emd_51351_validation.cif.gz | 39.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51351 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51351 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9ghbMC ![]() 9ghaC ![]() 9ghcC ![]() 9ghdC ![]() 9gheC ![]() 9ghfC ![]() 9ghgC ![]() 9ghhC M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_51351.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Local filtered map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
|
-Supplemental data
-Mask #1
| File | emd_51351_msk_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Additional map: Unsharpened map
| File | emd_51351_additional_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Unsharpened map | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: Half map A
| File | emd_51351_half_map_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Half map A | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: Half map B
| File | emd_51351_half_map_2.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Half map B | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-
Sample components
+Entire : Staphylococcus aureus EF-G on 70S ribosomes
+Supramolecule #1: Staphylococcus aureus EF-G on 70S ribosomes
+Supramolecule #2: Staphylococcus aureus EF-G
+Supramolecule #3: mRNA
+Supramolecule #4: 70S ribosome
+Macromolecule #1: 50S ribosomal protein L33
+Macromolecule #2: 50S ribosomal protein L34
+Macromolecule #3: 50S ribosomal protein L35
+Macromolecule #4: 50S ribosomal protein L36
+Macromolecule #5: 50S ribosomal protein L31
+Macromolecule #8: 30S ribosomal protein S2
+Macromolecule #9: 30S ribosomal protein S3
+Macromolecule #10: 30S ribosomal protein S4
+Macromolecule #11: 30S ribosomal protein S5
+Macromolecule #12: 30S ribosomal protein S6
+Macromolecule #13: 30S ribosomal protein S7
+Macromolecule #14: 30S ribosomal protein S8
+Macromolecule #15: 30S ribosomal protein S9
+Macromolecule #16: 30S ribosomal protein S10
+Macromolecule #17: Small ribosomal subunit protein uS11
+Macromolecule #18: 30S ribosomal protein S12
+Macromolecule #19: 30S ribosomal protein S13
+Macromolecule #20: 30S ribosomal protein S14
+Macromolecule #21: 30S ribosomal protein S15
+Macromolecule #22: 30S ribosomal protein S16
+Macromolecule #23: 30S ribosomal protein S17
+Macromolecule #24: 30S ribosomal protein S18
+Macromolecule #25: 30S ribosomal protein S19
+Macromolecule #26: 30S ribosomal protein S20
+Macromolecule #27: 30S ribosomal protein S21
+Macromolecule #28: Elongation factor G
+Macromolecule #32: 50S ribosomal protein L2
+Macromolecule #33: 50S ribosomal protein L3
+Macromolecule #34: 50S ribosomal protein L4
+Macromolecule #35: 50S ribosomal protein L5
+Macromolecule #36: 50S ribosomal protein L6
+Macromolecule #37: 50S ribosomal protein L9
+Macromolecule #38: 50S ribosomal protein L13
+Macromolecule #39: 50S ribosomal protein L14
+Macromolecule #40: 50S ribosomal protein L15
+Macromolecule #41: Large ribosomal subunit protein uL16
+Macromolecule #42: 50S ribosomal protein L17
+Macromolecule #43: 50S ribosomal protein L18
+Macromolecule #44: 50S ribosomal protein L19
+Macromolecule #45: 50S ribosomal protein L20
+Macromolecule #46: 50S ribosomal protein L21
+Macromolecule #47: 50S ribosomal protein L22
+Macromolecule #48: 50S ribosomal protein L23
+Macromolecule #49: 50S ribosomal protein L24
+Macromolecule #50: 50S ribosomal protein L25
+Macromolecule #51: 50S ribosomal protein L27
+Macromolecule #52: 50S ribosomal protein L28
+Macromolecule #53: 50S ribosomal protein L29
+Macromolecule #54: 50S ribosomal protein L30
+Macromolecule #55: 50S ribosomal protein L32
+Macromolecule #6: mRNA
+Macromolecule #7: 16S rRNA
+Macromolecule #29: tRNA
+Macromolecule #30: 23S rRNA
+Macromolecule #31: 5S rRNA
+Macromolecule #56: ZINC ION
+Macromolecule #57: POTASSIUM ION
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #60: FUSIDIC ACID
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Buffer | pH: 7.5 Component:
| ||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | ||||||||||||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
| Microscope | TFS KRIOS |
|---|---|
| Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 24479 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.7000000000000001 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 |
+
Image processing
-Atomic model buiding 1
| Initial model |
| ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Space: REAL | ||||||||||||
| Output model | ![]() PDB-9ghb: |
Movie
Controller
About Yorodumi



Keywords
Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Authors
Sweden, 4 items
Citation





















Z (Sec.)
Y (Row.)
X (Col.)






















































FIELD EMISSION GUN



