3LNN

Crystal structure of ZneB from Cupriavidus metallidurans

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 

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 U S A 107: 11038-11043

  • DOI: 10.1073/pnas.1003908107
  • Primary Citation of Related Structures:  
    3LNN

  • 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 membrane, linked by a membrane fusion protein (MFP) to an outer-membrane protein ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)A, B359Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: Rmet_5330, zneB
UniProt
Find proteins for Q1LCD7 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LCD7 
Go to UniProtKB:  Q1LCD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LCD7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.111α = 90
b = 137.111β = 90
c = 202.898γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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