4K0J

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.3 of the entry. See complete history. 


Literature

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

  • 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 bacte ...

    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.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy metal cation tricomponent efflux pump ZneA(CzcA-like) A, B, C, D, E, F1045Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: zneA, Rmet_5329
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Multi-Drug Efflux Transporters		Protein: 
ZneA Zn(II)/proton antiporter
Find proteins for Q1LCD8 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LCD8 
Go to UniProtKB:  Q1LCD8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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