3AOB

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket

Nakashima, R.Sakurai, K.Yamasaki, S.Nishino, K.Yamaguchi, A.

(2011) Nature 480: 565-569

  • DOI: 10.1038/nature10641
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AcrB and its homologues are the principal multidrug transporters in Gram-negative bacteria and are important in antibiotic drug tolerance. AcrB is a homotrimer that acts as a tripartite complex with the outer membrane channel TolC and the membrane fu ...

    AcrB and its homologues are the principal multidrug transporters in Gram-negative bacteria and are important in antibiotic drug tolerance. AcrB is a homotrimer that acts as a tripartite complex with the outer membrane channel TolC and the membrane fusion protein AcrA. Minocycline and doxorubicin have been shown to bind to the phenylalanine cluster region of the binding monomer. Here we report the crystal structures of AcrB bound to the high-molecular-mass drugs rifampicin and erythromycin. These drugs bind to the access monomer, and the binding sites are located in the proximal multisite binding pocket, which is separated from the phenylalanine cluster region (distal pocket) by the Phe-617 loop. Our structures indicate that there are two discrete multisite binding pockets along the intramolecular channel. High-molecular-mass drugs first bind to the proximal pocket in the access state and are then forced into the distal pocket in the binding state by a peristaltic mechanism involving subdomain movements that include a shift of the Phe-617 loop. By contrast, low-molecular-mass drugs, such as minocycline and doxorubicin, travel through the proximal pocket without specific binding and immediately bind to the distal pocket. The presence of two discrete, high-volume multisite binding pockets contributes to the remarkably broad substrate recognition of AcrB.


    Organizational Affiliation

    Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acriflavine resistance protein B
A, B, C
1053Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acrB (acrE)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Multi-Drug Efflux Transporters
Protein: 
AcrB bacterial multi-drug efflux transporter
Find proteins for P31224 (Escherichia coli (strain K12))
Go to UniProtKB:  P31224
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RFP
Query on RFP

Download SDF File 
Download CCD File 
C
RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 223.897α = 90.00
b = 134.314β = 98.10
c = 161.766γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references
  • Version 1.2: 2017-10-11
    Type: Refinement description