4K0E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.713 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.USA 110: 18484-18489

  • DOI: 10.1073/pnas.1318705110
  • Primary Citation of Related Structures:  

  • 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 b ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy metal cation tricomponent efflux pump ZneA(CzcA-like)
A, B, C
1045Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)Mutation(s): 0 
Gene Names: zneA
Membrane protein
mpstruct
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))
Go to UniProtKB:  Q1LCD8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.713 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 215.342α = 90.00
b = 127.068β = 93.12
c = 163.331γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references, Structure summary
  • Version 1.2: 2013-11-06
    Type: Structure summary
  • Version 1.3: 2013-12-04
    Type: Database references
  • Version 1.4: 2013-12-11
    Type: Structure summary