4U8Y

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: 2.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMTClick on this verticalbar to view detailsBest fitted MIYClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


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: e03145

  • 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. 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug efflux pump subunit AcrB
A, B, C
1,057Escherichia coli K-12Mutation(s): 1 
Gene Names: acrBacrEb0462JW0451
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DARPin
D, E
169synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.88α = 90
b = 161.16β = 90
c = 245.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMTClick on this verticalbar to view detailsBest fitted MIYClick on this verticalbar to view details

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
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary