2QFI

Structure of the zinc transporter YiiP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.322 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the zinc transporter YiiP.

Lu, M.Fu, D.

(2007) Science 317: 1746-1748

  • DOI: 10.1126/science.1143748

  • PubMed Abstract: 
  • YiiP is a membrane transporter that catalyzes Zn2+/H+ exchange across the inner membrane of Escherichia coli. Mammalian homologs of YiiP play critical roles in zinc homeostasis and cell signaling. Here, we report the x-ray structure of YiiP in comple ...

    YiiP is a membrane transporter that catalyzes Zn2+/H+ exchange across the inner membrane of Escherichia coli. Mammalian homologs of YiiP play critical roles in zinc homeostasis and cell signaling. Here, we report the x-ray structure of YiiP in complex with zinc at 3.8 angstrom resolution. YiiP is a homodimer held together in a parallel orientation through four Zn2+ ions at the interface of the cytoplasmic domains, whereas the two transmembrane domains swing out to yield a Y-shaped structure. In each protomer, the cytoplasmic domain adopts a metallochaperone-like protein fold; the transmembrane domain features a bundle of six transmembrane helices and a tetrahedral Zn2+ binding site located in a cavity that is open to both the membrane outer leaflet and the periplasm.


    Organizational Affiliation

    Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferrous-iron efflux pump fieF
A, B
300Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: fieF (yiiP)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Cation Diffusion Facilitator (CDF) Family
Protein: 
YiiP Zinc Transporter
Find proteins for P69380 (Escherichia coli (strain K12))
Go to UniProtKB:  P69380
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.322 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 106.660α = 90.00
b = 110.839β = 90.00
c = 130.662γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-06-27 
  • Released Date: 2007-10-16 
  • Deposition Author(s): Lu, M.

Revision History 

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance