9BFM | pdb_00009bfm

Cryo-EM co-structure of AcrB with the EPM35 efflux pump inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9BFM/pdb
• EM Map EMD-44500: EMDB EMDataResource

• Classification: TRANSLOCASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-04-18 Released: 2024-05-08 
• Deposition Author(s): Su, C.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Bacterial efflux pump modulators prevent bacterial growth in macrophages and under broth conditions that mimic the host environment.

Allgood, S.C., Su, C.C., Crooks, A.L., Meyer, C.T., Zhou, B., Betterton, M.D., Barbachyn, M.R., Yu, E.W., Detweiler, C.S.

(2023) mBio 14: e0249223

• PubMed: 37921493 
• DOI: https://doi.org/10.1128/mbio.02492-23
• Primary Citation Related Structures: 
  9BFH, 9BFM, 9BFN, 9BFT


• PubMed Abstract: 
  

  Bacterial efflux pumps are critical for resistance to antibiotics and for virulence. We previously identified small molecules that inhibit efflux pumps (efflux pump modulators, EPMs) and prevent pathogen replication in host cells. Here, we used medicinal chemistry to increase the activity of the EPMs against pathogens in cells into the nanomolar range. We show by cryo-electron microscopy that these EPMs bind an efflux pump subunit. In broth culture, the EPMs increase the potency (activity), but not the efficacy (maximum effect), of antibiotics. We also found that bacterial exposure to the EPMs appear to enable the accumulation of a toxic metabolite that would otherwise be exported by efflux pumps. Thus, inhibitors of bacterial efflux pumps could interfere with infection not only by potentiating antibiotics, but also by allowing toxic waste products to accumulate within bacteria, providing an explanation for why efflux pumps are needed for virulence in the absence of antibiotics.

---

Organizational Affiliation: 
• Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA.
Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, USA.
Duet Biosystems, Nashville, Tennessee, USA.
Antimicrobial Research Consortium (ARC) Labs, Boulder, Colorado, USA.
Department of Physics, University of Colorado, Boulder, Colorado, USA.
Center for Computational Biology, Flatiron Institute, New York, New York, USA.
Barbachyn Consulting, LLC, Kalamazoo, Michigan, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 341.46 kDa 
• Atom Count: 23,597 
• Modeled Residue Count: 3,100 
• Deposited Residue Count: 3,147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,049	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AON (Subject of Investigation/LOI)	D [auth A]	(2S)-1-(3,4-dichlorophenoxy)-3-(4-{[4-(trifluoromethyl)pyrimidin-2-yl]amino}piperidin-1-yl)propan-2-ol C19 H21 Cl2 F3 N4 O2 DEXPLCIUOWIUDC-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Su, C.C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection, Structure summary