+Open data
-Basic information
Entry | Database: PDB / ID: 7ryh | ||||||
---|---|---|---|---|---|---|---|
Title | A. baumannii Ribosome-TP-6076 complex: Empty 70S | ||||||
Components |
| ||||||
Keywords | Ribosome/RNA / Antibiotic / Ribosome / tetracycline / Ribosome-RNA complex | ||||||
Function / homology | Function and homology information large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) Acinetobacter baumannii AB0057 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.43 Å | ||||||
Authors | Morgan, C.E. / Yu, E.W. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ryh.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ryh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ryh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/7ryh ftp://data.pdbj.org/pub/pdb/validation_reports/ry/7ryh | HTTPS FTP |
---|
-Related structure data
Related structure data | 24740MC 7ry3C 7ryfC 7rygC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ
-RNA chain , 3 types, 3 molecules ABa
#5: RNA chain | Mass: 945315.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 |
---|---|
#6: RNA chain | Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: GenBank: 1577037162 |
#31: RNA chain | Mass: 500297.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: GenBank: 1211343212 |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#32: Protein | Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: V5VBC2 |
---|---|
#33: Protein | Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: V5V9N0 |
#34: Protein | Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA15 |
#35: Protein | Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA22 |
#36: Protein | Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IBC1 |
#37: Protein | Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7I7S0 |
#38: Protein | Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA25 |
#39: Protein | Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: V5VBA5 |
#40: Protein | Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A009L7S8 |
#41: Protein | Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A4R0F9S8 |
#42: Protein | Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7I7R9 |
#43: Protein | Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA17 |
#44: Protein | Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA26 |
#45: Protein | Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7I3U0 |
#46: Protein | Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A1V3DIZ9 |
#47: Protein | Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA30 |
#48: Protein | Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A022IPE7 |
#49: Protein | Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7IA35 |
#50: Protein | Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria) Strain: AB0057 / References: UniProt: B7I5N9 |
#51: Protein | Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) / Strain: AB0057 / References: UniProt: A0A0Q7FMS9 |
-Non-polymers , 3 types, 8 molecules
#52: Chemical | ChemComp-ZN / | ||
---|---|---|---|
#53: Chemical | #54: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: A. baumannii 70S ribosome in complex with TP-6076 / Type: RIBOSOME / Entity ID: #1-#51 / Source: NATURAL |
---|---|
Source (natural) | Organism: Acinetobacter baumannii AB0057 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127249 / Symmetry type: POINT |