3CK6

Crystal structure of ZntB cytoplasmic domain from Vibrio parahaemolyticus RIMD 2210633


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and electrostatic property of cytoplasmic domain of ZntB transporter.

Tan, K.Sather, A.Robertson, J.L.Moy, S.Roux, B.Joachimiak, A.

(2009) Protein Sci. 18: 2043-2052

  • DOI: 10.1002/pro.215

  • PubMed Abstract: 
  • ZntB is the distant homolog of CorA Mg(2+) transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn(2+) and Cd(2+), but not Mg(2+). Here, we report the 1.90 A c ...

    ZntB is the distant homolog of CorA Mg(2+) transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn(2+) and Cd(2+), but not Mg(2+). Here, we report the 1.90 A crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn(2+) or Cd(2+) binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl(-) ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl(-) ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport.


    Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative membrane transport protein
A, B, C, D, E
252Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)Mutation(s): 1 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
CorA Superfamily Ion Transporters
Protein: 
ZntB Zn+2 transporter cytoplasmic domain
Find proteins for Q87M69 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Go to UniProtKB:  Q87M69
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.390α = 90.00
b = 130.213β = 103.41
c = 79.386γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
MLPHAREphasing
HKL-3000phasing
SBC-Collectdata collection
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance