9EQ9 | pdb_00009eq9

Iron loaded mitochondrial ferritin, anaerobic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.247 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Observation of the Assembly of the Nascent Mineral Core at the Nucleation Site of Human Mitochondrial Ferritin.

Bradley, J.M.Bugg, Z.Moore, G.R.Hemmings, A.M.Le Brun, N.E.

(2025) J Am Chem Soc 147: 13699-13710

  • DOI: https://doi.org/10.1021/jacs.5c01337
  • Primary Citation of Related Structures:  
    9EQ8, 9EQ9, 9EQA, 9EQB, 9EQC

  • PubMed Abstract: 

    Ferritins play a crucial role in iron homeostasis and detoxification in organisms from all kingdoms of life. They are composed of 24 α-helical subunits arranged around an interior cavity where an iron-containing mineral core can be reversibly stored. Despite decades of study, leading to significant progress in defining the routes of Fe 2+ uptake and the mechanism of its subsequent oxidation to Fe 3+ at diiron catalytic sites termed ferroxidase centers, the process of core synthesis from the product of ferroxidase center activity remains poorly understood. In large part, this is due to the lack of high-resolution structural data on ferritin cores anchored to their nucleation sites on the inner surface of the protein. Mitochondrial ferritins are atypical of those found in higher eukaryotes in that they are homopolymers in which all subunits contain both a ferroxidase center and a presumed but undefined core nucleation site. Here, in conjunction with a novel method for producing iron-enriched ferritin crystals, we exploit these unusual features to structurally characterize both the nucleation site of mitochondrial ferritin and a pentanuclear, ferrihydrite-like iron-oxo cluster formed there. Kinetic data for wild-type and variant proteins confirmed the functional importance of this site, indicating a critical role for E61 in the transfer of Fe 3+ from the ferroxidase center to the nascent mineral core.


  • Organizational Affiliation
    • Centre for Molecular and Structural Biochemistry, School of Chemistry, Pharmacy and Pharmacology, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin, mitochondrial174Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth A]
Q [auth A]
R [auth A]
S [auth A]
T [auth A]
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [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],
N [auth A],
O [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.43α = 90
b = 177.43β = 90
c = 177.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R002363/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references