Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 343.39 kDa 
• Atom Count: 23378 
• Modelled Residue Count: 3066 
• Deposited Residue Count: 3159 
• Unique protein chains: 1

3AOC

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

• PDB DOI: 10.2210/pdb3AOC/pdb

• Classification: MEMBRANE PROTEIN/ANTIBIOTIC
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2010-09-23 Released: 2011-11-30 
• Deposition Author(s): Nakashima, R., Sakurai, K., Yamaguchi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free: 0.344 
• R-Value Work: 0.273 
• R-Value Observed: 0.277 

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

• PubMed: 22121023 
• DOI: 10.1038/nature10641
• Primary Citation of Related Structures:  
  3AOA, 3AOB, 3AOC, 3AOD


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A, B, C	1053	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, EcDH1_3148, 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
ERY	D [auth C]	ERYTHROMYCIN A C37 H67 N O13 ULGZDMOVFRHVEP-RWJQBGPGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free: 0.344 
• R-Value Work: 0.273 
• R-Value Observed: 0.277 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.28	α = 90
b = 134.211	β = 98.2
c = 162.054	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-23 
• Released Date: 2011-11-30 
Deposition Author(s): Nakashima, R., Sakurai, K., Yamaguchi, A.

Revision History  

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