6N63

Crystal structure of an Iron binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Large protein organelles form a new iron sequestration system with high storage capacity.

Giessen, T.W.Orlando, B.J.Verdegaal, A.A.Chambers, M.G.Gardener, J.Bell, D.C.Birrane, G.Liao, M.Silver, P.A.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.46070
  • Primary Citation of Related Structures:  
    6N63, 6NJ8

  • PubMed Abstract: 

    Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and it is not known how they store iron. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from Quasibacillus thermotolerans . Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo and show interactions underlying cargo-shell co-assembly. This compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. Our results reveal a new approach for survival in diverse habitats with limited or fluctuating iron availability via an iron storage system able to store 10 to 20 times more iron than ferritin.


  • Organizational Affiliation

    Department of Systems Biology, Harvard Medical School, Boston, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENCAPSULIN CARGO PROTEIN198Bacillus thermotoleransMutation(s): 0 
Gene Names: QY95_01593
UniProt
Find proteins for A0A0F5HNH9 (Bacillus thermotolerans)
Explore A0A0F5HNH9 
Go to UniProtKB:  A0A0F5HNH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F5HNH9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.39α = 90
b = 81.39β = 90
c = 65.861γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-04-03
    Changes: Refinement description