1R03

crystal structure of a human mitochondrial ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure and Biochemical Properties of the Human Mitochondrial Ferritin and its Mutant Ser144Ala

Langlois d'Estaintot, B.Santambrogio, P.Granier, T.Gallois, B.Chevallier, J.M.Precigoux, G.Levi, S.Arosio, P.

(2004) J.Mol.Biol. 340: 277-293

  • DOI: 10.1016/j.jmb.2004.04.036

  • PubMed Abstract: 
  • Mitochondrial ferritin is a recently identified protein precursor encoded by an intronless gene. It is specifically taken up by the mitochondria and processed to a mature protein that assembles into functional ferritin shells. The full mature recombi ...

    Mitochondrial ferritin is a recently identified protein precursor encoded by an intronless gene. It is specifically taken up by the mitochondria and processed to a mature protein that assembles into functional ferritin shells. The full mature recombinant protein and its S144A mutant were produced to study structural and functional properties. They yielded high quality crystals from Mg(II) solutions which diffracted up to 1.38 Angstrom resolution. The 3D structures of the two proteins resulted very similar to that of human H-ferritin, to which they have high level of sequence identity (approximately 80%). Metal-binding sites were identified in the native crystals and in those soaked in Mn(II) and Zn(II) solutions. The ferroxidase center binds binuclear iron at the sites A and B, and the structures showed that the A site was always fully occupied by Mg(II), Mn(II) or Zn(II), while the occupancy of the B site was variable. In addition, distinct Mg(II) and Zn(II)-binding sites were found in the 3-fold axes to block the hydrophilic channels. Other metal-binding sites, never observed before in H-ferritin, were found on the cavity surface near the ferroxidase center and near the 4-fold axes. Mitochondrial ferritin showed biochemical properties remarkably similar to those of human H-ferritin, except for the difficulty in renaturing to yield ferritin shells and for a reduced ( approximately 41%) rate in ferroxidase activity. This was partially rescued by the substitution of the bulkier Ser144 with Ala, which occurs in H-ferritin. The residue is exposed on a channel that connects the ferroxidase center with the cavity. The finding that the mutation increased both catalytic activity and the occupancy of the B site demonstrated that the channel is functionally important. In conclusion, the present data define the structure of human mitochondrial ferritin and provide new data on the iron pathways within the H-type ferritin shell.


    Related Citations: 
    • A human mitochondrial ferritin encoded by an intronless gene
      Levi, S.,Corsi, B.,Bosisio, M.,Invernizzi, R.,Volz, A.,Sanford, D.,Arosio, P.,Drysdale, J.
      (2001) J.Biol.Chem. 270: 24437
    • Comparison of the three-dimensional structures of recombinant human H and horse L ferritins at high resolution ferritins at high resolution
      Hempstead, P.D.,Yewdall, S.J.,Alistair, R.,Lawson, D.M.,Artymiuk, P.J.,Rice, D.W.,Ford, G.C.,Harrison, P.M.
      (1997) J.Mol.Biol. 268: 424


    Organizational Affiliation

    Unité de Biophysique Structurale, Bât. B8 avenue des Facultés, Université Bordeaux I, 33405 Talence Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ferritin
A
182Homo sapiensGene Names: FTMT
EC: 1.16.3.1
Find proteins for Q8N4E7 (Homo sapiens)
Go to Gene View: FTMT
Go to UniProtKB:  Q8N4E7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 181.410α = 90.00
b = 181.410β = 90.00
c = 181.410γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance