4U8V

Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Literature

Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB.

Eicher, T., Seeger, M.A., Anselmi, C., Zhou, W., Brandstatter, L., Verrey, F., Diederichs, K., Faraldo-Gomez, J.D., Pos, K.M.

(2014) Elife 3

  • DOI: https://doi.org/10.7554/eLife.03145
  • Primary Citation of Related Structures:  
    4U8V, 4U8Y, 4U95, 4U96

  • PubMed Abstract: 

    • Membrane transporters of the RND superfamily confer multidrug resistance to pathogenic bacteria, and are essential for cholesterol metabolism and embryonic development in humans. We use high-resolution X-ray crystallography and computational methods to delineate the mechanism of the homotrimeric RND-type proton/drug antiporter AcrB, the active component of the major efflux system AcrAB-TolC in Escherichia coli, and one most complex and intriguing membrane transporters known to date ...

    Membrane transporters of the RND superfamily confer multidrug resistance to pathogenic bacteria, and are essential for cholesterol metabolism and embryonic development in humans. We use high-resolution X-ray crystallography and computational methods to delineate the mechanism of the homotrimeric RND-type proton/drug antiporter AcrB, the active component of the major efflux system AcrAB-TolC in Escherichia coli, and one most complex and intriguing membrane transporters known to date. Analysis of wildtype AcrB and four functionally-inactive variants reveals an unprecedented mechanism that involves two remote alternating-access conformational cycles within each protomer, namely one for protons in the transmembrane region and another for drugs in the periplasmic domain, 50 Å apart. Each of these cycles entails two distinct types of collective motions of two structural repeats, coupled by flanking α-helices that project from the membrane. Moreover, we rationalize how the cross-talk among protomers across the trimerization interface might lead to a more kinetically efficient efflux system.

    Organizational Affiliation: 

    Institute of Biochemistry, Goethe University, Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrB
A, B, C
1,057Escherichia coliMutation(s): 1 
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31224
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DARPin
D, E
169synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth C]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
MIY
Query on MIY
Download Ideal Coordinates CCD File 
J [auth B](4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.59α = 90
b = 161.59β = 90
c = 245.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2014-10-15 
    • Deposition Author(s): Pos, K.M.

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release