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- EMDB-47728: Structure of thioferritin (PfDPSL) with ferrihydrite growth at a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47728
TitleStructure of thioferritin (PfDPSL) with ferrihydrite growth at a single three-fold pore.
Map dataSharpened map
Sample
  • Complex: Thioferritin dodecamer with loaded ferroxidase centers and mineral at single 3-fold pore
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: FE (III) ION
  • Ligand: OXYGEN MOLECULE
  • Ligand: OXYGEN ATOM
  • Ligand: water
KeywordsFerritin / thioferritin / oxidative stress / iron homeostasis / iron mineral / ferric oxyhydroxide / mineral core / protein cage / METAL BINDING PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / nucleoid / ferroxidase activity / ferric iron binding / intracellular iron ion homeostasis / heme binding / DNA binding / cytosol
Similarity search - Function
: / DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
DNA protection during starvation protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsGauvin CC / Waghwani HK / Tokmina-Lukaszewska M / Bothner B / Douglas T / Lawrence CM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI-1828765 United States
CitationJournal: J Am Chem Soc / Year: 2025
Title: The Mechanism of Mineral Nucleation and Growth in a Mini-Ferritin.
Authors: Colin C Gauvin / Monika Tokmina-Lukaszewska / Hitesh Kumar Waghwani / Sterling C McBee / Trevor Douglas / Brian Bothner / C Martin Lawrence /
Abstract: 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, ...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.
History
DepositionNov 6, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47728.png

Downloads & links

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Map

FileDownload / File: emd_47728.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 448 pix.
= 309.12 Å		0.69 Å/pix.
x 448 pix.
= 309.12 Å		0.69 Å/pix.
x 448 pix.
= 309.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.59409386 - 0.90383387
Average (Standard dev.)0.0013479458 (±0.024548344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 309.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_47728_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_47728_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Thioferritin dodecamer with loaded ferroxidase centers and minera...

EntireName: Thioferritin dodecamer with loaded ferroxidase centers and mineral at single 3-fold pore
Components
  • Complex: Thioferritin dodecamer with loaded ferroxidase centers and mineral at single 3-fold pore
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: FE (III) ION
  • Ligand: OXYGEN MOLECULE
  • Ligand: OXYGEN ATOM
  • Ligand: water

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Supramolecule #1: Thioferritin dodecamer with loaded ferroxidase centers and minera...

SupramoleculeName: Thioferritin dodecamer with loaded ferroxidase centers and mineral at single 3-fold pore
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 256 KDa

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Macromolecule #1: DNA protection during starvation protein

MacromoleculeName: DNA protection during starvation protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: Oxidoreductases; Oxidizing metal ions
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 21.387254 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPEHNRRLVE RTGIDVEKLL ELLIKAAAAE FTTYYYYTIL RNHATGLEGE AIKEIIEDAR LEDRNHFEAL VPRIYELGGE LPRDIREFA DLASCRDAYL PEEPTIENIL KVLLEAERCA VGVYTEICNY TFGKDPRTYD LALAILHEEI EHEAWFEELL T GKPSGHFR RGKPGESPYV SKFLKTR

UniProtKB: DNA protection during starvation protein

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Macromolecule #2: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 37 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 3 / Number of copies: 12 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #4: OXYGEN ATOM

MacromoleculeName: OXYGEN ATOM / type: ligand / ID: 4 / Number of copies: 18 / Formula: O
Molecular weightTheoretical: 15.999 Da
Chemical component information

ChemComp-O:
OXYGEN ATOM

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 144 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
50.0 mMC6H13NO4S2-(N-morpholino)ethanesulfonic acid
100.0 mMNaClSodium Chloride

Details: 50 mM MES, 100 mM NaCl, pH 6.5
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample formed a thin monodispersed layer.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9094 / Average exposure time: 6.0 sec. / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 57000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

DetailsImages were motion corrected using patch motion correction software in CryoSPARC.
Particle selectionNumber selected: 3153592
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 395423
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7stw


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsModel was fit to map using ChimeraX fitmap, and then refined in PHENIX.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 58.4 / Target criteria: Cross-correlation coefficient
Output model

PDB-9e8s:
Structure of thioferritin (PfDPSL) with ferrihydrite growth at a single three-fold pore.

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