2J8S

Drug Export Pathway of Multidrug Exporter AcrB Revealed by DARPin Inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb2J8S/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2006-10-27 Released: 2007-01-23 
• Deposition Author(s): Sennhauser, G., Amstutz, P., Briand, C., Storchenegger, O., Gruetter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.271 
• R-Value Work: 0.229 
• R-Value Observed: 0.229 

Literature

Drug Export Pathway of Multidrug Exporter Acrb Revealed by Darpin Inhibitors.

Sennhauser, G., Amstutz, P., Briand, C., Storchenegger, O., Grutter, M.G.

(2007) PLoS Biol 5: E7

• PubMed: 17194213 
• DOI: https://doi.org/10.1371/journal.pbio.0050007
• Primary Citation of Related Structures:  
  2J8S


• PubMed Abstract: 
  

The multidrug exporter AcrB is the inner membrane component of the AcrAB-TolC drug efflux system in Escherichia coli and is responsible for the resistance of this organism to a wide range of drugs. Here we describe the crystal structure of the trimeric AcrB in complex with a designed ankyrin-repeat protein (DARPin) inhibitor at 2.5-A resolution. The three subunits of AcrB are locked in different conformations revealing distinct channels in each subunit. There seems to be remote conformational coupling between the channel access, exit, and the putative proton-translocation site, explaining how the proton motive force is used for drug export. Thus our structure suggests a transport pathway not through the central pore but through the identified channels in the individual subunits, which greatly advances our understanding of the multidrug export mechanism.

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Organizational Affiliation: 

University of Zurich, Zurich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 385.73 kDa 
• Atom Count: 26,771 
• Modelled Residue Count: 3,426 
• Deposited Residue Count: 3,503 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACRIFLAVINE RESISTANCE PROTEIN B	A, B, C	1,055	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMU	I [auth A]	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
LMT	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth C]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.271 
• R-Value Work: 0.229 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.18	α = 90
b = 157.41	β = 90
c = 246.04	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Sennhauser, G., Amstutz, P., Briand, C., Storchenegger, O., Gruetter, M.G.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Version format compliance