4RDT | pdb_00004rdt

Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (flexible conformation bound to a zinc ion)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.305 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.270 (Depositor) 
  • R-Value Observed: 
    0.272 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ncomms8996
  • Primary Citation Related Structures: 
    4RDR, 4RDT, 4RVW

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 169.88 kDa 
  • Atom Count: 10,159 
  • Modeled Residue Count: 1,270 
  • Deposited Residue Count: 1,496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ZnuD
A, B
748Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: NMB0964
Membrane Entity: Yes 
UniProt
Find proteins for Q9JZN9 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58))
Explore Q9JZN9 
Go to UniProtKB:  Q9JZN9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JZN9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E

Query on C8E



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.305 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.270 (Depositor) 
  • R-Value Observed: 0.272 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.34α = 90
b = 156.227β = 90
c = 158.075γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary