2QFI | pdb_00002qfi

Structure of the zinc transporter YiiP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.329 (Depositor), 0.333 (DCC) 
  • R-Value Work: 
    0.322 (Depositor), 0.348 (DCC) 
  • R-Value Observed: 
    0.323 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Structure of the zinc transporter YiiP.

Lu, M., Fu, D.

(2007) Science 317: 1746-1748

  • DOI: https://doi.org/10.1126/science.1143748
  • Primary Citation Related Structures: 
    2QFI

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 66.37 kDa 
  • Atom Count: 4,417 
  • Modeled Residue Count: 572 
  • Deposited Residue Count: 600 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferrous-iron efflux pump fieF
A, B
300Escherichia coliMutation(s): 0 
Gene Names: fieF
Membrane Entity: Yes 
UniProt
Find proteins for P69380 (Escherichia coli (strain K12))
Explore P69380 
Go to UniProtKB:  P69380
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69380
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.329 (Depositor), 0.333 (DCC) 
  • R-Value Work:  0.322 (Depositor), 0.348 (DCC) 
  • R-Value Observed: 0.323 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.66α = 90
b = 110.839β = 90
c = 130.662γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description