28JY | pdb_000028jy

Iron loaded E61A human H-chain ferritin, anaerobic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Ferritin Iron Mineralisation: Route of Fe 3+ Transfer From the Ferroxidase Centre to the Inner Cavity of Human H-Chain Ferritin.

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

(2026) Angew Chem Int Ed Engl : e1203843-e1203843

  • DOI: https://doi.org/10.1002/anie.1203843
  • Primary Citation Related Structures: 
    28JY, 28JZ, 28KA, 28KB, 28KC, 28LZ

  • PubMed Abstract: 

    Ferritin-catalysed Fe 2+ oxidation by reaction with O 2 occurs at an intra-subunit diiron site known as the ferroxidase centre (FoC). Currently, how Fe 3+ , the key substrate for iron core nucleation/mineralisation, transfers from the FoC to the inner protein surface/central cavity where the mineral is laid down is unknown. Iron-binding sites that become occupied following exposure of anaerobic, Fe 2+ -bound human cytosolic H-chain ferritin (HuHF) to O 2 were identified by time-resolved x-ray crystallography. In addition to the two FoC iron sites, three further sites were identified, each involving Glu61 as a coordinating residue. Substitution by a non-coordinating residue (variant E61A) eliminated binding at these additional iron sites. Solution kinetic studies of Fe 2+ oxidation and iron core mineralisation in wild-type HuHF and its E61A variant showed that rapid Fe 2+ oxidation was unaffected by loss of Glu61, ruling out an important role for these sites in either guiding Fe 2+ to the FoC, or in the mechanism of FoC-catalysed Fe 2+ oxidation. Conversely, the transfer of Fe 3+ out of the FoC and core mineralisation were both severely affected in the E61A variant. A mechanism for Fe 3+ transfer from the FoC to the inner protein surface is proposed.


  • Organizational Affiliation
    • Centre For Molecular and Structural Biochemistry, School of Chemistry, Pharmacy and Pharmacology, University of East Anglia, Norwich, UK.

Macromolecule Content 

  • Total Structure Weight: 21.53 kDa 
  • Atom Count: 1,731 
  • Modeled Residue Count: 173 
  • Deposited Residue Count: 182 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferritin heavy chain, N-terminally processed182Homo sapiensMutation(s): 1 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
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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]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



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

Query on MG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.7α = 90
b = 182.7β = 90
c = 182.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-10
    Type: Initial release