+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24739 | |||||||||
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Title | A. baumannii Ribosome-TP-6076 complex: E-site tRNA 70S | |||||||||
Map data | Combined locally-refined map of A. baumannii 70S ribosome in complex with E-site tRNA and TP-6076 | |||||||||
Sample |
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Keywords | Antibiotic / Ribosome / tetracycline / Ribosome-RNA complex | |||||||||
Function / homology | Function and homology information ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii AB0057 (bacteria) / Acinetobacter baumannii (strain AB0057) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.38 Å | |||||||||
Authors | Morgan CE / Yu EW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: mBio / Year: 2021 Title: An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii. Authors: Christopher E Morgan / Zhemin Zhang / Robert A Bonomo / Edward W Yu / Abstract: Antibiotic resistance among bacterial pathogens continues to pose a serious global health threat. Multidrug-resistant (MDR) strains of the Gram-negative organism Acinetobacter baumannii utilize a ...Antibiotic resistance among bacterial pathogens continues to pose a serious global health threat. Multidrug-resistant (MDR) strains of the Gram-negative organism Acinetobacter baumannii utilize a number of resistance determinants to evade current antibiotics. One of the major resistance mechanisms employed by these pathogens is the use of multidrug efflux pumps. These pumps extrude xenobiotics directly out of bacterial cells, resulting in treatment failures when common antibiotics are administered. Here, the structure of the novel tetracycline antibiotic TP-6076, bound to both the cinetobacter rug fflux pump AdeJ and the ribosome from Acinetobacter baumannii, using single-particle cryo-electron microscopy (cryo-EM), is elucidated. In this work, the structure of the AdeJ-TP-6076 complex is solved, and we show that AdeJ utilizes a network of hydrophobic interactions to recognize this fluorocycline. Concomitant with this, we elucidate three structures of TP-6076 bound to the A. baumannii ribosome and determine that its binding is stabilized largely by electrostatic interactions. We then compare the differences in binding modes between TP-6076 and the related tetracycline antibiotic eravacycline in both targets. These differences suggest that modifications to the tetracycline core may be able to alter AdeJ binding while maintaining interactions with the ribosome. Together, this work highlights how different mechanisms are used to stabilize the binding of tetracycline-based compounds to unique bacterial targets and provides guidance for the future clinical development of tetracycline antibiotics. Treatment of antibiotic-resistant organisms such as A. baumannii represents an ongoing issue for modern medicine. The multidrug efflux pump AdeJ serves as a major resistance determinant in A. baumannii through its action of extruding antibiotics from the cell. In this work, we use cryo-EM to show how AdeJ recognizes the experimental tetracycline antibiotic TP-6076 and prevents this drug from interacting with the A. baumannii ribosome. Since AdeJ and the ribosome use different binding modes to stabilize interactions with TP-6076, exploiting these differences may guide future drug development for combating antibiotic-resistant A. baumannii and potentially other strains of MDR bacteria. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24739.map.gz | 14.3 MB | EMDB map data format | |
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Header (meta data) | emd-24739-v30.xml emd-24739.xml | 73 KB 73 KB | Display Display | EMDB header |
Images | emd_24739.png | 146.9 KB | ||
Filedesc metadata | emd-24739.cif.gz | 13.5 KB | ||
Others | emd_24739_additional_1.map.gz emd_24739_additional_2.map.gz emd_24739_additional_3.map.gz | 8.9 MB 5 MB 17.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24739 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24739 | HTTPS FTP |
-Validation report
Summary document | emd_24739_validation.pdf.gz | 382.2 KB | Display | EMDB validaton report |
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Full document | emd_24739_full_validation.pdf.gz | 381.9 KB | Display | |
Data in XML | emd_24739_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_24739_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24739 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24739 | HTTPS FTP |
-Related structure data
Related structure data | 7rygMC 7ry3C 7ryfC 7ryhC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24739.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Combined locally-refined map of A. baumannii 70S ribosome in complex with E-site tRNA and TP-6076 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.089 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Locally-refined map of A. baumannii 30S core in...
File | emd_24739_additional_1.map | ||||||||||||
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Annotation | Locally-refined map of A. baumannii 30S core in complex with E-site tRNA and TP-6076 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Locally-refined map of A. baumannii 30S head in...
File | emd_24739_additional_2.map | ||||||||||||
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Annotation | Locally-refined map of A. baumannii 30S head in complex with E-site tRNA and TP-6076 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Locally-refined map of A. baumannii 50S subunit in...
File | emd_24739_additional_3.map | ||||||||||||
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Annotation | Locally-refined map of A. baumannii 50S subunit in complex with E-site tRNA and TP-6076 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : A. baumannii 70S ribosome in complex with E-site tRNA and TP-6076
+Supramolecule #1: A. baumannii 70S ribosome in complex with E-site tRNA and TP-6076
+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 #7: 50S ribosomal protein L2
+Macromolecule #8: 50S ribosomal protein L3
+Macromolecule #9: 50S ribosomal protein L4
+Macromolecule #10: 50S ribosomal protein L5
+Macromolecule #11: 50S ribosomal protein L6
+Macromolecule #12: 50S ribosomal protein L9
+Macromolecule #13: 50S ribosomal protein L13
+Macromolecule #14: 50S ribosomal protein L14
+Macromolecule #15: 50S ribosomal protein L15
+Macromolecule #16: 50S ribosomal protein L16
+Macromolecule #17: 50S ribosomal protein L17
+Macromolecule #18: 50S ribosomal protein L18
+Macromolecule #19: 50S ribosomal protein L19
+Macromolecule #20: 50S ribosomal protein L20
+Macromolecule #21: 50S ribosomal protein L21
+Macromolecule #22: 50S ribosomal protein L22
+Macromolecule #23: 50S ribosomal protein L23
+Macromolecule #24: 50S ribosomal protein L24
+Macromolecule #25: 50S ribosomal protein L25
+Macromolecule #26: 50S ribosomal protein L27
+Macromolecule #27: 50S ribosomal protein L28
+Macromolecule #28: 50S ribosomal protein L29
+Macromolecule #29: 50S ribosomal protein L30
+Macromolecule #30: 50S ribosomal protein L32
+Macromolecule #32: 30S ribosomal protein S2
+Macromolecule #33: 30S ribosomal protein S3
+Macromolecule #34: 30S ribosomal protein S4
+Macromolecule #35: 30S ribosomal protein S5
+Macromolecule #36: 30S ribosomal protein S6
+Macromolecule #37: 30S ribosomal protein S7
+Macromolecule #38: 30S ribosomal protein S8
+Macromolecule #39: 30S ribosomal protein S9
+Macromolecule #40: 30S ribosomal protein S10
+Macromolecule #41: 30S ribosomal protein S11
+Macromolecule #42: 30S ribosomal protein S12
+Macromolecule #43: 30S ribosomal protein S13
+Macromolecule #44: 30S ribosomal protein S14
+Macromolecule #45: 30S ribosomal protein S15
+Macromolecule #46: 30S ribosomal protein S16
+Macromolecule #47: 30S ribosomal protein S17
+Macromolecule #48: 30S ribosomal protein S18
+Macromolecule #49: 30S ribosomal protein S19
+Macromolecule #50: 30S ribosomal protein S20
+Macromolecule #51: 30S ribosomal protein S21
+Macromolecule #5: 23S ribosomal RNA
+Macromolecule #6: 5S ribosomal RNA
+Macromolecule #31: 16S Ribosomal RNA
+Macromolecule #52: tRNA-met
+Macromolecule #53: mRNA
+Macromolecule #54: ZINC ION
+Macromolecule #55: (4S,4aS,5aR,12aS)-4-(diethylamino)-3,10,12,12a-tetrahydroxy-1,11-...
+Macromolecule #56: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155853 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |