3LNN

Crystal structure of ZneB from Cupriavidus metallidurans

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems.

De Angelis, F., Lee, J.K., O'Connell, J.D., Miercke, L.J., Verschueren, K.H., Srinivasan, V., Bauvois, C., Govaerts, C., Robbins, R.A., Ruysschaert, J.M., Stroud, R.M., Vandenbussche, G.

(2010) Proc.Natl.Acad.Sci.USA 107: 11038-11043

  • DOI: 10.1073/pnas.1003908107

  • PubMed Abstract: 

    • Resistance nodulation cell division (RND)-based efflux complexes mediate multidrug and heavy-metal resistance in many Gram-negative bacteria. Efflux of toxic compounds is driven by membrane proton/substrate antiporters (RND protein) in the plasma mem ...

    Resistance nodulation cell division (RND)-based efflux complexes mediate multidrug and heavy-metal resistance in many Gram-negative bacteria. Efflux of toxic compounds is driven by membrane proton/substrate antiporters (RND protein) in the plasma membrane, linked by a membrane fusion protein (MFP) to an outer-membrane protein. The three-component complex forms an efflux system that spans the entire cell envelope. The MFP is required for the assembly of this complex and is proposed to play an important active role in substrate efflux. To better understand the role of MFPs in RND-driven efflux systems, we chose ZneB, the MFP component of the ZneCAB heavy-metal efflux system from Cupriavidus metallidurans CH34. ZneB is shown to be highly specific for Zn(2+) alone. The crystal structure of ZneB to 2.8 A resolution defines the basis for metal ion binding in the coordination site at a flexible interface between the beta-barrel and membrane proximal domains. The conformational differences observed between the crystal structures of metal-bound and apo forms are monitored in solution by spectroscopy and chromatography. The structural rearrangements between the two states suggest an active role in substrate efflux through metal binding and release.

    Organizational Affiliation: 

    Laboratoire de Structure et Fonction des Membranes Biologiques, Faculté des Sciences, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles, B-1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
A, B
359Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)Mutation(s): 0 
Gene Names: zneB
Find proteins for Q1LCD7 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Go to UniProtKB:  Q1LCD7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.796 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.237 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 137.111α = 90.00
b = 137.111β = 90.00
c = 202.898γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance