Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 21.10 kDa 
• Atom Count: 1683 
• Residue Count: 171 
• Unique protein chains: 1

1R03

crystal structure of a human mitochondrial ferritin

• DOI: 10.2210/pdb1R03/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-19 Released: 2004-06-29 
• Deposition Author(s): Corsi, B., Santambrogio, P., Arosio, P., Levi, S., Langlois d'Estaintot, B., Granier, T., Gallois, B., Chevallier, J.M., Precigoux, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.180 

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

• PubMed: 15201052 
• DOI: 10.1016/j.jmb.2004.04.036
• Primary Citation of Related Structures:  
  1R03


• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mitochondrial ferritin	A	182	Homo sapiens	Mutation(s): 0  Gene Names: FTMT EC: 1.16.3.1
Find proteins for Q8N4E7 (Homo sapiens) Explore Q8N4E7  Go to UniProtKB:  Q8N4E7
NIH Common Fund Data Resources
PHAROS:  Q8N4E7 GTEx:  ENSG00000181867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.180 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.41	α = 90
b = 181.41	β = 90
c = 181.41	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-19 
• Released Date: 2004-06-29 
Deposition Author(s): Corsi, B., Santambrogio, P., Arosio, P., Levi, S., Langlois d'Estaintot, B., Granier, T., Gallois, B., Chevallier, J.M., Precigoux, G.

Revision History 

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