9C0B | pdb_00009c0b

E.coli GroEL + PBZ1587 inhibitor

  • Classification: CHAPERONE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-05-25 Released: 2024-08-07 
  • Deposition Author(s): Watson, E.R., Lander, G.C.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9C0B

This is version 1.1 of the entry. See complete history

Literature

Bis-sulfonamido-2-phenylbenzoxazoles Validate the GroES/EL Chaperone System as a Viable Antibiotic Target.

Godek, J.Sivinski, J.Watson, E.R.Lebario, F.Xu, W.Stevens, M.Zerio, C.J.Ambrose, A.J.Zhu, X.Trindl, C.A.Zhang, D.D.Johnson, S.M.Lander, G.C.Chapman, E.

(2024) J Am Chem Soc 146: 20845-20856

  • DOI: https://doi.org/10.1021/jacs.4c05057
  • Primary Citation Related Structures: 
    9C0B, 9C0C, 9C0D

  • PubMed Abstract: 

    We recently reported on small-molecule inhibitors of the GroES/GroEL chaperone system as potential antibiotics against Escherichia coli 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 bis -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, Enterococcus faecium . 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 E. faecium 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.


  • Organizational Affiliation
    • College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States.

Macromolecule Content 

  • Total Structure Weight: 807.51 kDa 
  • Atom Count: 54,229 
  • Modeled Residue Count: 7,336 
  • Deposited Residue Count: 7,672 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
60 kDa chaperonin548Escherichia coliMutation(s): 0 
Gene Names: groELgroLmopABN17_41231BU34_16740ECs5124LF82_0923
EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Explore P0A6F5 
Go to UniProtKB:  P0A6F5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095892
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesS10OD021634
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM120350

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Database references