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TitleThe Mechanism of Mineral Nucleation and Growth in a Mini-Ferritin.
Journal, issue, pagesJ Am Chem Soc, Vol. 147, Issue 41, Page 37030-37044, Year 2025
Publish dateOct 15, 2025
AuthorsColin C Gauvin / Monika Tokmina-Lukaszewska / Hitesh Kumar Waghwani / Sterling C McBee / Trevor Douglas / Brian Bothner / C Martin Lawrence /
PubMed AbstractIron is an enigmatic element. While necessary for life, as Fe(II) it also catalyzes formation of reactive oxygen species. To mitigate this, cellular life has evolved the ferritin protein superfamily, ...Iron is an enigmatic element. While necessary for life, as Fe(II) it also catalyzes formation of reactive oxygen species. To mitigate this, cellular life has evolved the ferritin protein superfamily, which includes the 24 subunit ferritins and bacterioferritins, and 12 subunit mini-ferritins (DPS). Each catalyze the oxidation of Fe(II) to ferric oxyhydroxide, which is then sequestered within the hollow protein shell. While there is a wealth of structural information on unmineralized ferritins, high resolution information on iron loaded ferritins is lacking, and the mechanism of iron mineralization is poorly understood. To address this, we followed iron loading in a mini-ferritin by cryo-EM. We determined a 1.86 Å structure in the unmineralized state, as well as a 1.91 Å structure of an early, iron loading state in which the mini-ferritin catalyzes nucleation of ferric oxyhydroxide at the acidic 3-fold pores. Mechanistically, a conserved crucible of precisely positioned glutamates and unsaturated main chain carbonyls are employed as a template to catalyze nucleation. A 2.4 Å structure at a later time point was also determined, revealing the role of a second constellation of main-chain carbonyls on the interior surface that subsequently supports crystalline mineral growth, that then proceeds into the center of the particle. Notably, the visualized mineral is consistent with one of two competing structural descriptions for ferrihydrite. This study provides the first pseudoatomic level observation of controlled mineral nucleation and growth in any member of the ferritin superfamily, and informs general mechanisms of nucleation and biomineralization.
External linksJ Am Chem Soc / PubMed:41052476 / PubMed Central
MethodsEM (single particle)
Resolution1.86 - 2.48 Å
Structure data

46055

9cz0

EMDB-46055, PDB-9cz0:
Structure of thioferritin from Pyrococcus furiosis
Method: EM (single particle) / Resolution: 1.86 Å

46063

9cz8

EMDB-46063, PDB-9cz8:
Structure of thioferritin exhibiting iron mineral nucleation, from Pyrococcus furiosis
Method: EM (single particle) / Resolution: 1.91 Å

46064

9cz9

EMDB-46064, PDB-9cz9:
Structure of thioferritin with averaged iron mineral core, from Pyrococcus furiosis
Method: EM (single particle) / Resolution: 2.43 Å

47728

9e8s

EMDB-47728, PDB-9e8s:
Structure of thioferritin (PfDPSL) with ferrihydrite growth at a single three-fold pore.
Method: EM (single particle) / Resolution: 2.48 Å

Chemicals

ChemComp-FE:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-O:
OXYGEN ATOM

ChemComp-OXY:
OXYGEN MOLECULE

Source
  • pyrococcus furiosus (archaea)
KeywordsMETAL BINDING PROTEIN / Ferritin / thioferritin / oxidative stress / iron homeostasis / iron mineral / ferric oxyhydroxide / nucleation / biomineral / mineral core / protein cage

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