Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 388.26 kDa 
• Atom Count: 28194 
• Residue Count: 3419 
• Unique protein chains: 2

4DX7

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop

• DOI: 10.2210/pdb4DX7/pdb

• Classification: MEMBRANE PROTEIN, TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-27 Released: 2012-05-02 
• Deposition Author(s): Eicher, T., Cha, H., Seeger, M.A., Brandstaetter, L., El-Delik, J., Bohnert, J.A., Kern, W.V., Verrey, F., Gruetter, M.G., Diederichs, K., Pos, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop.

Eicher, T., Cha, H.J., Seeger, M.A., Brandstatter, L., El-Delik, J., Bohnert, J.A., Kern, W.V., Verrey, F., Grutter, M.G., Diederichs, K., Pos, K.M.

(2012) Proc Natl Acad Sci U S A 109: 5687-5692

• PubMed: 22451937 
• DOI: 10.1073/pnas.1114944109
• Primary Citation of Related Structures:  
  4DX5, 4DX6, 4DX7


• PubMed Abstract: 
  

AcrAB-TolC is the major efflux protein complex in Escherichia coli extruding a vast variety of antimicrobial agents from the cell. The inner membrane component AcrB is a homotrimer, and it has been postulated that the monomers cycle consecutively through three conformational stages designated loose (L), tight (T), and open (O) in a concerted fashion. Binding of drugs has been shown at a periplasmic deep binding pocket in the T conformation. The initial drug-binding step and transport toward this drug-binding site has been elusive thus far. Here we report high resolution structures (1.9-2.25 Å) of AcrB/designed ankyrin repeat protein (DARPin) complexes with bound minocycline or doxorubicin. In the AcrB/doxorubicin cocrystal structure, binding of three doxorubicin molecules is apparent, with one doxorubicin molecule bound in the deep binding pocket of the T monomer and two doxorubicin molecules in a stacked sandwich arrangement in an access pocket at the lateral periplasmic cleft of the L monomer. This access pocket is separated from the deep binding pocket apparent in the T monomer by a switch-loop. The localization and conformational flexibility of this loop seems to be important for large substrates, because a G616N AcrB variant deficient in macrolide transport exhibits an altered conformation within this loop region. Transport seems to be a stepwise process of initial drug uptake in the access pocket of the L monomer and subsequent accommodation of the drug in the deep binding pocket during the L to T transition to the internal deep binding pocket of the T monomer.

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Organizational Affiliation: 

Institute of Biochemistry and Cluster of Excellence Frankfurt-Macromolecular Complexes, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A, B, C	1057	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, JW0451
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Multi-Drug Efflux Transporters	Protein:  wt AcrB/DARPin in complex with minocycline
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM2	A, B	DOXORUBICIN C27 H29 N O11 AOJJSUZBOXZQNB-TZSSRYMLSA-N
LMT	A, B, C	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
LMU	B	DODECYL-ALPHA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-YHBSTRCHSA-N
D12	A, B, C	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10	A, B, C	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
GOL	B, C	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
HEX	B, C	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.943	α = 90
b = 163.285	β = 90
c = 245.766	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-27 
• Released Date: 2012-05-02 
Deposition Author(s): Eicher, T., Cha, H., Seeger, M.A., Brandstaetter, L., El-Delik, J., Bohnert, J.A., Kern, W.V., Verrey, F., Gruetter, M.G., Diederichs, K., Pos, K.M.

Revision History 

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2014-01-29
  Changes: Source and taxonomy