Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 183.26 kDa 
• Atom Count: 12835 
• Modelled Residue Count: 1635 
• Deposited Residue Count: 1635 
• Unique protein chains: 1

5N9Y

The full-length structure of ZntB

• PDB DOI: 10.2210/pdb5N9Y/pdb
• EM Map EMD-3605:EMDBEMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2017-02-27 Released: 2017-11-15 
• Deposition Author(s): Cornelius, G., Stetsenko, A., Scheres, S.H.W., Slotboom, D.J., Guskov, A.
• Funding Organization(s): NWO

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The structural basis of proton driven zinc transport by ZntB.

Gati, C., Stetsenko, A., Slotboom, D.J., Scheres, S.H.W., Guskov, A.

(2017) Nat Commun 8: 1313-1313

• PubMed: 29101379 
• DOI: 10.1038/s41467-017-01483-7
• Primary Citation of Related Structures:  
  5N9Y


• PubMed Abstract: 
  

Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc concentration have evolved. In Enterobacteriaceae, several membrane transporters are involved in zinc homeostasis and linked to virulence. ZntB has been proposed to play a role in the export of zinc, but the transport mechanism of ZntB is poorly understood and based only on experimental characterization of its distant homologue CorA magnesium channel. Here, we report the cryo-electron microscopy structure of full-length ZntB from Escherichia coli together with the results of isothermal titration calorimetry, and radio-ligand uptake and fluorescent transport assays on ZntB reconstituted into liposomes. Our results show that ZntB mediates Zn ²⁺ uptake, stimulated by a pH gradient across the membrane, using a transport mechanism that does not resemble the one proposed for homologous CorA channels.

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Organizational Affiliation: 

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc transport protein ZntB	A, B, C, D, E	327	Escherichia coli K-12	Mutation(s): 0  Gene Names: zntB, ydaN, b1342, JW1336 Membrane Entity: Yes
UniProt
Find proteins for P64423 (Escherichia coli (strain K12)) Explore P64423  Go to UniProtKB:  P64423

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-27 
• Released Date: 2017-11-15 
Deposition Author(s): Cornelius, G., Stetsenko, A., Scheres, S.H.W., Slotboom, D.J., Guskov, A.

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Funding Organization	Location	Grant Number
NWO	Netherlands	723.014.002

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references
• Version 1.2: 2019-10-02
  Changes: Data collection, Other
• Version 1.3: 2019-10-23
  Changes: Data collection, Other