4RVW

Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (soaked with 20 micromolar Zinc)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.477 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.317 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD.

Calmettes, C.Ing, C.Buckwalter, C.M.El Bakkouri, M.Chieh-Lin Lai, C.Pogoutse, A.Gray-Owen, S.D.Pomes, R.Moraes, T.F.

(2015) Nat Commun 6: 7996-7996

  • DOI: 10.1038/ncomms8996
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host orga ...

    Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host organism during infection. Here we demonstrate that ZnuD is required for efficient systemic infections by the causative agent of bacterial meningitis, Neisseria meningitidis, in a mouse model. We also combine X-ray crystallography and molecular dynamics simulations to gain insight into the mechanism of zinc recognition and transport across the bacterial outer-membrane by ZnuD. Because ZnuD is also considered a promising vaccine candidate against N. meningitidis, we use several ZnuD structural intermediates to map potential antigenic epitopes, and propose a mechanism by which ZnuD can maintain high sequence conservation yet avoid immune recognition by altering the conformation of surface-exposed loops.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ZnuD
A
748Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Find proteins for Q9JZN9 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q9JZN9
Small Molecules
Ligands 2 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.477 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.317 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 101.548α = 90.00
b = 149.592β = 90.00
c = 157.590γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHENIXphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references