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- EMDB-19429: Escherichia coli 50S subunit in complex with the antimicrobial pe... -
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Open data
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Basic information
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Title | Escherichia coli 50S subunit in complex with the antimicrobial peptide Api88 - conformation III | ||||||||||||||||||
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![]() | ribosome / antimicrobial peptide / RNA / ribosomal protein / PrAMP / proline-rich peptide / antibiotics / 50S / Api88 | ||||||||||||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity ...negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / 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 / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.44 Å | ||||||||||||||||||
![]() | Lauer S / Nikolay R / Spahn C | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88. Authors: Simon M Lauer / Maren Reepmeyer / Ole Berendes / Dorota Klepacki / Jakob Gasse / Sara Gabrielli / Helmut Grubmüller / Lars V Bock / Andor Krizsan / Rainer Nikolay / Christian M T Spahn / Ralf Hoffmann / ![]() ![]() Abstract: Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized ...Proline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized derivative of honeybee PrAMP apidaecin, inhibits protein expression by trapping release factors (RFs), which interact with stop codons on ribosomes to terminate translation. This study uses cryo-EM, functional assays and molecular dynamic (MD) simulations to show that Api137 additionally occupies a second binding site near the exit of the PET and can repress translation independently of RF-trapping. Api88, a C-terminally amidated (-CONH) analog of Api137 (-COOH), binds to the same sites, occupies a third binding pocket and interferes with the translation process presumably without RF-trapping. In conclusion, apidaecin-derived PrAMPs inhibit bacterial ribosomes by multimodal mechanisms caused by minor structural changes and thus represent a promising pool for drug development efforts. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 89.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 52.2 KB 52.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.8 KB | Display | ![]() |
Images | ![]() | 121.7 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 10.2 KB | ||
Others | ![]() ![]() | 165 MB 165 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rq2MC ![]() 8rpyC ![]() 8rpzC ![]() 8rq0C M: atomic model generated by this map C: citing same article ( |
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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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Voxel size | X=Y=Z: 0.998 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : Api88 in complex with the large ribosomal subunit - conformation III
+Supramolecule #1: Api88 in complex with the large ribosomal subunit - conformation III
+Supramolecule #2: Large ribosomal subunit
+Supramolecule #3: Api88
+Macromolecule #1: Large ribosomal subunit protein bL32
+Macromolecule #2: Large ribosomal subunit protein bL33
+Macromolecule #3: Large ribosomal subunit protein bL34
+Macromolecule #4: Large ribosomal subunit protein bL35
+Macromolecule #5: Large ribosomal subunit protein bL36A
+Macromolecule #6: Large ribosomal subunit protein bL31
+Macromolecule #9: Large ribosomal subunit protein uL2
+Macromolecule #10: Large ribosomal subunit protein uL3
+Macromolecule #11: Large ribosomal subunit protein uL4
+Macromolecule #12: Large ribosomal subunit protein uL5
+Macromolecule #13: Large ribosomal subunit protein uL6
+Macromolecule #14: Large ribosomal subunit protein bL9
+Macromolecule #15: Large ribosomal subunit protein uL13
+Macromolecule #16: Large ribosomal subunit protein uL14
+Macromolecule #17: Large ribosomal subunit protein uL15
+Macromolecule #18: Large ribosomal subunit protein uL16
+Macromolecule #19: Large ribosomal subunit protein bL17
+Macromolecule #20: Large ribosomal subunit protein uL18
+Macromolecule #21: Large ribosomal subunit protein bL19
+Macromolecule #22: Large ribosomal subunit protein bL20
+Macromolecule #23: Large ribosomal subunit protein bL21
+Macromolecule #24: Large ribosomal subunit protein uL22
+Macromolecule #25: Large ribosomal subunit protein uL23
+Macromolecule #26: Large ribosomal subunit protein uL24
+Macromolecule #27: Large ribosomal subunit protein bL25
+Macromolecule #28: Large ribosomal subunit protein bL27
+Macromolecule #29: Large ribosomal subunit protein bL28
+Macromolecule #30: Large ribosomal subunit protein uL29
+Macromolecule #31: Large ribosomal subunit protein uL30
+Macromolecule #32: Apidaecins type 88
+Macromolecule #7: 23S ribosomal RNA
+Macromolecule #8: 5S ribosomal RNA
-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: 7.6 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8rq2: |