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- EMDB-18950: 70S Escherichia coli ribosome with Paenilamicin B2 bound with A- ... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | 70S Escherichia coli ribosome with Paenilamicin B2 bound with A- and P-site tRNA. | |||||||||
![]() | Post processed masked map | |||||||||
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![]() | Ribosome / 70S / Paenilamicin / Antibiotic | |||||||||
Function / homology | ![]() 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 / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...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 / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / 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 / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
![]() | Koller TO / Wilson DN | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Paenilamicins from the honey bee pathogen are context-specific translocation inhibitors of protein synthesis. Authors: Timm O Koller / Max J Berger / Martino Morici / Helge Paternoga / Timur Bulatov / Adriana Di Stasi / Tam Dang / Andi Mainz / Karoline Raulf / Caillan Crowe-McAuliffe / Marco Scocchi / Mario ...Authors: Timm O Koller / Max J Berger / Martino Morici / Helge Paternoga / Timur Bulatov / Adriana Di Stasi / Tam Dang / Andi Mainz / Karoline Raulf / Caillan Crowe-McAuliffe / Marco Scocchi / Mario Mardirossian / Bertrand Beckert / Nora Vázquez-Laslop / Alexander Mankin / Roderich D Süssmuth / Daniel N Wilson / ![]() ![]() ![]() ![]() Abstract: The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive pathogens, such as . While ...The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen that display activity against Gram-positive pathogens, such as . While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by . We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 85.7 KB 85.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21 KB | Display | ![]() |
Images | ![]() | 96.4 KB | ||
Filedesc metadata | ![]() | 15.2 KB | ||
Others | ![]() ![]() ![]() ![]() | 671.2 MB 771.7 MB 671.4 MB 671.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r6cMC ![]() 8r8mC ![]() 9fbvC 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 | Post processed masked map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: 3D refined map
File | emd_18950_additional_1.map | ||||||||||||
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Annotation | 3D refined map | ||||||||||||
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-Additional map: Post processed map
File | emd_18950_additional_2.map | ||||||||||||
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Annotation | Post processed map | ||||||||||||
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-Half map: Half map 2
File | emd_18950_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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-Half map: Half map 1
File | emd_18950_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
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Sample components
+Entire : Paenilamicin B2 bound to the 70S Escherichia coli ribosome
+Supramolecule #1: Paenilamicin B2 bound to the 70S Escherichia coli ribosome
+Supramolecule #2: 70S Escherichia coli ribosome
+Supramolecule #3: Paenilamicin B2
+Macromolecule #1: Large ribosomal subunit protein bL33
+Macromolecule #2: Large ribosomal subunit protein bL34
+Macromolecule #3: Large ribosomal subunit protein bL35
+Macromolecule #4: Large ribosomal subunit protein bL36A
+Macromolecule #5: Large ribosomal subunit protein bL31A
+Macromolecule #8: 30S ribosomal protein S2
+Macromolecule #9: Small ribosomal subunit protein uS3
+Macromolecule #10: Small ribosomal subunit protein uS4
+Macromolecule #11: Small ribosomal subunit protein uS5
+Macromolecule #12: 30S ribosomal protein S6, fully modified isoform
+Macromolecule #13: 30S ribosomal protein S7
+Macromolecule #14: Small ribosomal subunit protein uS8
+Macromolecule #15: Small ribosomal subunit protein uS9
+Macromolecule #16: Small ribosomal subunit protein uS10
+Macromolecule #17: Small ribosomal subunit protein uS11
+Macromolecule #18: Small ribosomal subunit protein uS12
+Macromolecule #19: Small ribosomal subunit protein uS13
+Macromolecule #20: Small ribosomal subunit protein uS14
+Macromolecule #21: Small ribosomal subunit protein uS15
+Macromolecule #22: 30S ribosomal protein S16
+Macromolecule #23: Small ribosomal subunit protein uS17
+Macromolecule #24: Small ribosomal subunit protein bS18
+Macromolecule #25: Small ribosomal subunit protein uS19
+Macromolecule #26: 30S ribosomal protein S20
+Macromolecule #27: Small ribosomal subunit protein bS21
+Macromolecule #33: Large ribosomal subunit protein uL2
+Macromolecule #34: Large ribosomal subunit protein uL3
+Macromolecule #35: Large ribosomal subunit protein uL4
+Macromolecule #36: Large ribosomal subunit protein uL5
+Macromolecule #37: Large ribosomal subunit protein uL6
+Macromolecule #38: Large ribosomal subunit protein bL9
+Macromolecule #39: Large ribosomal subunit protein uL13
+Macromolecule #40: Large ribosomal subunit protein uL14
+Macromolecule #41: 50S ribosomal protein L15
+Macromolecule #42: Large ribosomal subunit protein uL16
+Macromolecule #43: Large ribosomal subunit protein bL17
+Macromolecule #44: Large ribosomal subunit protein uL18
+Macromolecule #45: Large ribosomal subunit protein bL19
+Macromolecule #46: Large ribosomal subunit protein bL20
+Macromolecule #47: Large ribosomal subunit protein bL21
+Macromolecule #48: Large ribosomal subunit protein uL22
+Macromolecule #49: Large ribosomal subunit protein uL23
+Macromolecule #50: Large ribosomal subunit protein uL24
+Macromolecule #51: 50S ribosomal protein L25
+Macromolecule #52: Large ribosomal subunit protein bL27
+Macromolecule #53: Large ribosomal subunit protein bL28
+Macromolecule #54: Large ribosomal subunit protein uL29
+Macromolecule #55: Large ribosomal subunit protein uL30
+Macromolecule #56: Large ribosomal subunit protein bL32
+Macromolecule #57: Paenilamicin B2
+Macromolecule #6: N-Formylmethionine tRNA
+Macromolecule #7: 16S ribosomal RNA
+Macromolecule #28: mRNA
+Macromolecule #29: Isoeucine-tRNA
+Macromolecule #30: Leucine-tRNA
+Macromolecule #31: 23S ribosomal RNA
+Macromolecule #32: 5S ribosomal RNA
+Macromolecule #58: ZINC ION
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: POTASSIUM ION
+Macromolecule #61: water
-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: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Details | 8 OD/mL of Ribosome |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |