X-ray crystal structure of a heavy metal efflux pump, crystal form I

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 

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This is version 1.4 of the entry. See complete history


Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter.

Pak, J.E.Ekende, E.N.Kifle, E.G.O'Connell, J.D.De Angelis, F.Tessema, M.B.Derfoufi, K.M.Robles-Colmenares, Y.Robbins, R.A.Goormaghtigh, E.Vandenbussche, G.Stroud, R.M.

(2013) Proc Natl Acad Sci U S A 110: 18484-18489

  • DOI: https://doi.org/10.1073/pnas.1318705110
  • Primary Citation of Related Structures:  
    4K0E, 4K0J

  • PubMed Abstract: 

    Efflux pumps belonging to the ubiquitous resistance-nodulation-cell division (RND) superfamily transport substrates out of cells by coupling proton conduction across the membrane to a conformationally driven pumping cycle. The heavy metal-resistant bacteria Cupriavidus metallidurans CH34 relies notably on as many as 12 heavy metal efflux pumps of the RND superfamily. Here we show that C. metallidurans CH34 ZneA is a proton driven efflux pump specific for Zn(II), and that transport of substrates through the transmembrane domain may be electrogenic. We report two X-ray crystal structures of ZneA in intermediate transport conformations, at 3.0 and 3.7 Å resolution. The trimeric ZneA structures capture protomer conformations that differ in the spatial arrangement and Zn(II) occupancies at a proximal and a distal substrate binding site. Structural comparison shows that transport of substrates through a tunnel that links the two binding sites, toward an exit portal, is mediated by the conformation of a short 14-aa loop. Taken together, the ZneA structures presented here provide mechanistic insights into the conformational changes required for substrate efflux by RND superfamily transporters.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Center for the Structure of Membrane Proteins, Membrane Protein Expression Center, University of California, San Francisco, CA 94158.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
A, B, C, D, E
A, B, C, D, E, F
1,045Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: zneARmet_5329
Membrane Entity: Yes 
Find proteins for Q1LCD8 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LCD8 
Go to UniProtKB:  Q1LCD8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LCD8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.627α = 90
b = 129.056β = 94.62
c = 392.374γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references, Structure summary
  • Version 1.2: 2013-11-06
    Changes: Structure summary
  • Version 1.3: 2013-12-04
    Changes: Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description