5XGO

The Ferritin E-Domain: Toward Understanding Its Role in Protein Cage Assembly Through the Crystal Structure of a Maxi-/Mini-Ferritin Chimera


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


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Literature

The Crystal Structure of a Maxi/Mini-Ferritin Chimera Reveals Guiding Principles for the Assembly of Protein Cages.

Cornell, T.A.Srivastava, Y.Jauch, R.Fan, R.Orner, B.P.

(2017) Biochemistry 56: 3894-3899

  • DOI: https://doi.org/10.1021/acs.biochem.7b00312
  • Primary Citation of Related Structures:  
    5XGO

  • PubMed Abstract: 

    Cage proteins assemble into nanoscale structures with large central cavities. They play roles, including those as virus capsids and chaperones, and have been applied to drug delivery and nanomaterials. Furthermore, protein cages have been used as model systems to understand and design protein quaternary structure. Ferritins are ubiquitous protein cages that manage iron homeostasis and oxidative damage. Two ferritin subfamilies have strongly similar tertiary structure yet distinct quaternary structure: maxi-ferritins normally assemble into 24-meric, octahedral cages with C-terminal E-helices centered around 4-fold symmetry axes, and mini-ferritins are 12-meric, tetrahedral cages with 3-fold axes defined by C-termini lacking E-domains. To understand the role E-domains play in ferritin quaternary structure, we previously designed a chimera of a maxi-ferritin E-domain fused to the C-terminus of a mini-ferritin. The chimera is a 12-mer cage midway in size between those of the maxi- and mini-ferritin. The research described herein sets out to understand (a) whether the increase in size over a typical mini-ferritin is due to a frozen state where the E-domain is flipped out of the cage and (b) whether the symmetrical preference of the E-domain in the maxi-ferritin (4-fold axis) overrules the C-terminal preference in the mini-ferritin (3-fold axis). With a 1.99 Å resolution crystal structure, we determined that the chimera assembles into a tetrahedral cage that can be nearly superimposed with the parent mini-ferritin, and that the E-domains are flipped external to the cage at the 3-fold symmetry axes.


  • Organizational Affiliation

    Department of Chemistry, King's College London , London, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA protection during starvation protein,Bacterioferritin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
200Escherichia coli K-12Mutation(s): 0 
Gene Names: dpspexBvtmb0812JW0797bfrb3336JW3298
EC: 1.16 (PDB Primary Data), 1.16.3.1 (PDB Primary Data)
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Explore P0ABD3 
Go to UniProtKB:  P0ABD3
Find proteins for P0ABT2 (Escherichia coli (strain K12))
Explore P0ABT2 
Go to UniProtKB:  P0ABT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABT2P0ABD3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.139α = 90
b = 104.723β = 90
c = 207.756γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
A*STARSingapore--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Refinement description