4RVW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.48 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.317 
  • R-Value Observed: 0.320 

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
  • Structures With Same Primary Citation

  • 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
ZnuDA748Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: NMB0964
Find proteins for Q9JZN9 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZN9 
Go to UniProtKB:  Q9JZN9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.48 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.317 
  • R-Value Observed: 0.320 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.548α = 90
b = 149.592β = 90
c = 157.59γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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