Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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High resolution crystal structures of amphibian red-cell L ferritin: potential roles for structural plasticity and solvation in function.

Trikha, J.Theil, E.C.Allewell, N.M.

(1995) J Mol Biol 248: 949-967

  • DOI: https://doi.org/10.1006/jmbi.1995.0274
  • Primary Citation of Related Structures:  
    1RCC, 1RCD, 1RCE, 1RCG, 1RCI

  • PubMed Abstract: 

    Ferritin is a highly conserved multisubunit protein in animals, plants and microbes which assembles with cubic symmetry and transports hydrated iron ions and protons to and from a mineralized core in the protein interior. We report here the high resolution structures of recombinant amphibian red-cell L ferritin and two mutants solved under two sets of conditions. In one mutant, Glu56, 57, 58 and 60 were replaced with Ala, producing a lag phase in the kinetics of iron uptake. In the second mutant, His25 was replaced with Tyr with, at most, subtle effects on function. A molecule of betaine, used in the purification, is bound in all structures at the 2-fold axis near the recently identified heme binding site of bacterioferritin and horse spleen L ferritin. Comparisons of the five amphibian structures identify two regions of the molecule in which conformational flexibility may be related to function. The positions and interactions of a set of 10 to 18 side-chains, most of which are on the inner surface of the protein, are sensitive both to solution conditions and to the Glu-->Ala mutation. A subset of these side-chains and a chain of ordered solvent molecules extends from the vicinity of Glu56 to 58 and Glu60 to the 3-fold channel in the wild type protein and may be involved in the transport of either iron or protons. The "spine of hydration" is disrupted in the Glu-->Ala mutant. In contrast, H25Y mutation shifts the positions of backbone atoms between the site of the mutation and the 4-fold axis and side-chain positions throughout the structure; the largest changes in the position of backbone atoms are in the DE loop and E helix, approximately 10 A from the mutation site. In combination, these results indicate that solvation, structural plasticity and cooperative structural changes may play a role in ferritin function. Analogies with the structure and function of ion channel proteins such as annexins are noted.

  • Organizational Affiliation

    Department of Biochemistry, University of Minnesota, St. Paul 55108, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L FERRITIN173Aquarana catesbeianaMutation(s): 0 
Gene Names: CDNA
Find proteins for P07797 (Aquarana catesbeiana)
Explore P07797 
Go to UniProtKB:  P07797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07797
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BET

Download Ideal Coordinates CCD File 
C5 H12 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.355α = 90
b = 182.355β = 90
c = 182.355γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
XENGENdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-11-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other