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- EMDB-15488: Cryo-EM structure of the proline-rich antimicrobial peptide droso... -
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Open data
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Basic information
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Title | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | |||||||||
![]() | Masked post-processed map | |||||||||
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![]() | E.coli / 70S / Drosocin / Dro1 / antimicrobial peptide / proline-rich / PrAMP / Release factor 1 / RF1 / RIBOSOME | |||||||||
Function / homology | ![]() translation release factor activity, codon specific / ornithine decarboxylase inhibitor activity / four-way junction DNA binding / translational termination / DNA endonuclease activity / ribosomal large subunit assembly / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding ...translation release factor activity, codon specific / ornithine decarboxylase inhibitor activity / four-way junction DNA binding / translational termination / DNA endonuclease activity / ribosomal large subunit assembly / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / 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 / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Koller TO / Morici M / Wilson DN | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for translation inhibition by the glycosylated drosocin peptide. Authors: Timm O Koller / Martino Morici / Max Berger / Haaris A Safdari / Deepti S Lele / Bertrand Beckert / Kanwal J Kaur / Daniel N Wilson / ![]() ![]() ![]() Abstract: The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post- ...The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 79.1 KB 79.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 20.9 KB | Display | ![]() |
Images | ![]() | 105 KB | ||
Others | ![]() ![]() ![]() ![]() | 772.7 MB 670.9 MB 671.1 MB 670.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aknMC ![]() 8am9C ![]() 8anaC 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 | Masked post-processed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8 Å | ||||||||||||||||||||
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: post-processed map
File | emd_15488_additional_1.map | ||||||||||||
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Annotation | post-processed map | ||||||||||||
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-Additional map: 3Drefined map
File | emd_15488_additional_2.map | ||||||||||||
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Annotation | 3Drefined map | ||||||||||||
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-Half map: Half-map2
File | emd_15488_half_map_1.map | ||||||||||||
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Annotation | Half-map2 | ||||||||||||
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-Half map: Half-map1
File | emd_15488_half_map_2.map | ||||||||||||
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Annotation | Half-map1 | ||||||||||||
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Sample components
+Entire : Cryo-EM structure of the proline-rich antimicrobial peptide droso...
+Supramolecule #1: Cryo-EM structure of the proline-rich antimicrobial peptide droso...
+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 #6: Drosocin1
+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, fully modified isoform
+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: 30S ribosomal protein S11
+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: Peptide chain release factor RF1
+Macromolecule #34: 50S ribosomal protein L2
+Macromolecule #35: 50S ribosomal protein L3
+Macromolecule #36: 50S ribosomal protein L4
+Macromolecule #37: 50S ribosomal protein L5
+Macromolecule #38: 50S ribosomal protein L6
+Macromolecule #39: 50S ribosomal protein L9
+Macromolecule #40: 50S ribosomal protein L13
+Macromolecule #41: 50S ribosomal protein L14
+Macromolecule #42: 50S ribosomal protein L15
+Macromolecule #43: 50S ribosomal protein L16
+Macromolecule #44: 50S ribosomal protein L17
+Macromolecule #45: 50S ribosomal protein L18
+Macromolecule #46: 50S ribosomal protein L19
+Macromolecule #47: 50S ribosomal protein L20
+Macromolecule #48: 50S ribosomal protein L21
+Macromolecule #49: 50S ribosomal protein L22
+Macromolecule #50: 50S ribosomal protein L23
+Macromolecule #51: 50S ribosomal protein L24
+Macromolecule #52: 50S ribosomal protein L25
+Macromolecule #53: 50S ribosomal protein L27
+Macromolecule #54: 50S ribosomal protein L28
+Macromolecule #55: 50S ribosomal protein L29
+Macromolecule #56: 50S ribosomal protein L30
+Macromolecule #57: 50S ribosomal protein L32
+Macromolecule #7: 16S ribosomal RNA
+Macromolecule #29: Phenylalanine-tRNA
+Macromolecule #30: mRNA
+Macromolecule #31: Isoleucine-tRNA
+Macromolecule #32: 23S ribosomal RNA
+Macromolecule #33: 5S ribosomal RNA
+Macromolecule #58: ZINC ION
+Macromolecule #59: 2-acetamido-2-deoxy-alpha-D-galactopyranose
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: SPERMINE
+Macromolecule #62: 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 Component:
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Grid | Model: Quantifoil R3/3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | 8 OD260/mL |
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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: 40.0 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 |