4RDR

Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked conformation bound to zinc and cadmium ions)

• PDB DOI:  https://doi.org/10.2210/pdb4RDR/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2014-09-19 Released: 2015-08-19 
• Deposition Author(s): Calmettes, C., Moraes, T.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

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

• PubMed: 26282243 
• DOI: https://doi.org/10.1038/ncomms8996
• Primary Citation of 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.23 kDa 
• Atom Count: 5,985 
• Modelled Residue Count: 706 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZnuD	A	748	Neisseria meningitidis MC58	Mutation(s): 0  Gene Names: NMB0964 Membrane Entity: Yes
UniProt
Find proteins for Q9JZN9 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JZN9  Go to UniProtKB:  Q9JZN9

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	AA [auth A], BA [auth A], CA [auth A], DA [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	EA [auth A], FA [auth A], GA [auth A], HA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.248 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.073	α = 90
b = 155.819	β = 90
c = 159.607	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Calmettes, C., Moraes, T.F.

Revision History  

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