7O63 | pdb_00007o63

High resolution crystal structure of human mitochondrial ferritin (hMTF)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.140 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.125 (Depositor) 
  • R-Value Observed: 
    0.126 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7O63

This is version 1.2 of the entry. See complete history

Literature

Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin.

Ciambellotti, S.Pratesi, A.Tassone, G.Turano, P.Mangani, S.Pozzi, C.

(2021) Chemistry 27: 14690-14701

  • DOI: https://doi.org/10.1002/chem.202102270
  • Primary Citation Related Structures: 
    7O63, 7O64, 7O65, 7O66, 7O67, 7O68, 7O69, 7O6A, 7O6C, 7O6D, 7OWY

  • PubMed Abstract: 

    Ferritins are nanocage proteins that store iron ions in their central cavity as hydrated ferric oxide biominerals. In mammals, further the L (light) and H (heavy) chains constituting cytoplasmic maxi-ferritins, an additional type of ferritin has been identified, the mitochondrial ferritin (MTF). Human MTF (hMTF) is a functional homopolymeric H-like ferritin performing the ferroxidase activity in its ferroxidase site (FS), in which Fe(II) is oxidized to Fe(III) in the presence of dioxygen. To better investigate its ferroxidase properties, here we performed time-lapse X-ray crystallography analysis of hMTF, providing structural evidence of how iron ions interact with hMTF and of their binding to the FS. Transient iron binding sites, populating the pathway along the cage from the iron entry channel to the catalytic center, were also identified. Furthermore, our kinetic data at variable iron loads indicate that the catalytic iron oxidation reaction occurs via a diferric peroxo intermediate followed by the formation of ferric-oxo species, with significant differences with respect to human H-type ferritin.


  • Organizational Affiliation
    • Department of Chemistry "Ugo Schiff" Department of Excellence 2018-2022, University of Florence, via della Lastruccia 2, 50019, Sesto Fiorentino, Italy.

Macromolecule Content 

  • Total Structure Weight: 21.65 kDa 
  • Atom Count: 2,084 
  • Modeled Residue Count: 172 
  • Deposited Residue Count: 183 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin, mitochondrial183Homo sapiensMutation(s): 0 
Gene Names: FTMT
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4E7 (Homo sapiens)
Explore Q8N4E7 
Go to UniProtKB:  Q8N4E7
PHAROS:  Q8N4E7
GTEx:  ENSG00000181867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N4E7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
R [auth A]
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.140 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.125 (Depositor) 
  • R-Value Observed: 0.126 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.133α = 90
b = 184.133β = 90
c = 184.133γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description