6BTX

Structure of a bacterial metal transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Calcium is an essential cofactor for metal efflux by the ferroportin transporter family.

Deshpande, C.N.Ruwe, T.A.Shawki, A.Xin, V.Vieth, K.R.Valore, E.V.Qiao, B.Ganz, T.Nemeth, E.Mackenzie, B.Jormakka, M.

(2018) Nat Commun 9: 3075-3075

  • DOI: https://doi.org/10.1038/s41467-018-05446-4
  • Primary Citation of Related Structures:  
    6BTX

  • PubMed Abstract: 

    Ferroportin (Fpn)-the only known cellular iron exporter-transports dietary and recycled iron into the blood plasma, and transfers iron across the placenta. Despite its central role in iron metabolism, our molecular understanding of Fpn-mediated iron efflux remains incomplete. Here, we report that Ca 2+ is required for human Fpn transport activity. Whereas iron efflux is stimulated by extracellular Ca 2+ in the physiological range, Ca 2+ is not transported. We determine the crystal structure of a Ca 2+ -bound BbFpn, a prokaryotic orthologue, and find that Ca 2+ is a cofactor that facilitates a conformational change critical to the transport cycle. We also identify a substrate pocket accommodating a divalent transition metal complexed with a chelator. These findings support a model of iron export by Fpn and suggest a link between plasma calcium and iron homeostasis.


  • Organizational Affiliation

    Structural Biology Program, Centenary Institute, Sydney Medical School, University of Sydney, Sydney, NSW, 2042, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 39 (Iron-regulated transporter)440Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: slc39Bd2019
Membrane Entity: Yes 
UniProt
Find proteins for Q6MLJ0 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MLJ0 
Go to UniProtKB:  Q6MLJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MLJ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.072α = 90
b = 54.109β = 103.6
c = 72.442γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references