+Open data
-Basic information
Entry | Database: PDB / ID: 9c0d | ||||||||||||
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Title | E.Faecium GroEL | ||||||||||||
Components | Chaperonin GroEL | ||||||||||||
Keywords | CHAPERONE / GroEL / ANTIBIOTIC | ||||||||||||
Function / homology | Function and homology information mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / chaperonin ATPase / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production ...mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / chaperonin ATPase / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of T cell activation / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / ATP binding Similarity search - Function | ||||||||||||
Biological species | Enterococcus faecium (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å | ||||||||||||
Authors | Watson, E.R. / Lander, G.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J Am Chem Soc / Year: 2024 Title: Bis-sulfonamido-2-phenylbenzoxazoles Validate the GroES/EL Chaperone System as a Viable Antibiotic Target. Authors: Jack Godek / Jared Sivinski / Edmond R Watson / Felicidad Lebario / Wenli Xu / Mckayla Stevens / Christopher J Zerio / Andrew J Ambrose / Xiaoyi Zhu / Carlee A Trindl / Donna D Zhang / ...Authors: Jack Godek / Jared Sivinski / Edmond R Watson / Felicidad Lebario / Wenli Xu / Mckayla Stevens / Christopher J Zerio / Andrew J Ambrose / Xiaoyi Zhu / Carlee A Trindl / Donna D Zhang / Steven M Johnson / Gabriel C Lander / Eli Chapman / Abstract: We recently reported on small-molecule inhibitors of the GroES/GroEL chaperone system as potential antibiotics against and the ESKAPE pathogens but were unable to establish GroES/GroEL as the ...We recently reported on small-molecule inhibitors of the GroES/GroEL chaperone system as potential antibiotics against and the ESKAPE pathogens but were unable to establish GroES/GroEL as the cellular target, leading to cell death. In this study, using two of our most potent -sulfonamido-2-phenylbenzoxazoles (PBZs), we established the binding site of the PBZ molecules using cryo-EM and found that GroEL was the cellular target responsible for the mode of action. Cryo-EM revealed that PBZ1587 binds at the GroEL ring-ring interface (RRI). A cellular reporter assay confirmed that PBZ1587 engaged GroEL in cells, but cellular rescue experiments showed potential off-target effects. This prompted us to explore a closely related analogue, PBZ1038, which is also bound to the RRI. Biochemical characterization showed potent inhibition of Gram-negative chaperonins but much lower potency of chaperonin from a Gram-positive organism, . A cellular reporter assay showed that PBZ1038 also engaged GroEL in cells and that the cytotoxic phenotype could be rescued by a chromosomal copy of GroEL/GroES or by expressing a recalcitrant RRI mutant. These data argue that PBZ1038's antimicrobial action is exerted through inhibition of GroES/GroEL, validating this chaperone system as an antibiotic target. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9c0d.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9c0d.ent.gz | 974.5 KB | Display | PDB format |
PDBx/mmJSON format | 9c0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9c0d_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 9c0d_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9c0d_validation.xml.gz | 182.2 KB | Display | |
Data in CIF | 9c0d_validation.cif.gz | 278.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/9c0d ftp://data.pdbj.org/pub/pdb/validation_reports/c0/9c0d | HTTPS FTP |
-Related structure data
Related structure data | 45080MC 9c0bC 9c0cC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 57243.074 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: groL, groEL, GBM44_11620, GBM73_12310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A132Z3A5, chaperonin ATPase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E.faecium GroEL / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Enterococcus faecium (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 62.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10837 / Symmetry type: POINT | ||||||||||||||||||||||||
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