9GAR | pdb_00009gar

Siderophore-binding lipoprotein XusB from Barnesiella viscericola


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of iron piracy by human gut Bacteroides.

Silale, A.Soo, Y.L.Mark, H.Motz, R.N.Basle, A.Nolan, E.M.van den Berg, B.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.04.15.589501
  • Primary Citation of Related Structures:  
    9GAR, 9GBC, 9GCY, 9GCZ, 9HQ1, 9HQE, 9HQK

  • PubMed Abstract: 

    Iron is an essential element that can be growth-limiting in microbial communities, particularly those present within host organisms. To acquire iron, many bacteria secrete siderophores, secondary metabolites that chelate ferric iron. These iron chelates can be transported back into the cell via TonB-dependent transporters in the outer membrane, followed by intracellular liberation of the iron. Pathogenic Escherichia coli and Salmonella produce siderophores during gut infection. In response to iron starvation, the human gut symbiont Bacteroides thetaiotaomicron upregulates an iron piracy system, XusABC, which steals iron-bound siderophores from the invading pathogens. Here, we investigated the molecular details of xenosiderophore uptake across the outer membrane by the XusAB complex. Our crystal and cryogenic electron microscopy structures explain how the XusB lipoprotein recognises iron-bound xenosiderophores and passes them on to the XusA TonB-dependent transporter. Moreover, we show that Xus homologues can transport a variety of siderophores with different iron-chelating functional groups.


  • Organizational Affiliation
    • Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4374 domain-containing protein472Barnesiella viscericola DSM 18177Mutation(s): 0 
Gene Names: BARVI_05925
UniProt
Find proteins for W0ET74 (Barnesiella viscericola DSM 18177)
Explore W0ET74 
Go to UniProtKB:  W0ET74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0ET74
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.869α = 90
b = 184.869β = 90
c = 82.309γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom214222/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references