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- EMDB-46063: Structure of thioferritin exhibiting iron mineral nucleation, fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-46063
TitleStructure of thioferritin exhibiting iron mineral nucleation, from Pyrococcus furiosis
Map data
Sample
  • Complex: Thioferritin dodecamer with loaded ferroxidase centers and no mineral core.
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: FE (III) ION
  • Ligand: OXYGEN ATOM
  • Ligand: water
KeywordsFerritin / thioferritin / oxidative stress / iron homeostasis / iron mineral / ferric oxyhydroxide / nucleation / biomineral / 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: 1.91 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: To Be Published
Title: Structure of thioferritin from Pyrococcus furiosis.
Authors: Gauvin CC / Waghwani HK / Tokmina-Lukaszewska M / Bothner B / Douglas T / Lawrence CM
History
DepositionAug 4, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46063.png

Downloads & links

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Map

FileDownload / File: emd_46063.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 3.5
Minimum - Maximum-28.478289 - 63.388058000000001
Average (Standard dev.)0.000000000075277 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_46063_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46063_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46063_half_map_2.map
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 no min...

EntireName: Thioferritin dodecamer with loaded ferroxidase centers and no mineral core.
Components
  • Complex: Thioferritin dodecamer with loaded ferroxidase centers and no mineral core.
    • Protein or peptide: DNA protection during starvation protein
  • Ligand: FE (III) ION
  • Ligand: OXYGEN ATOM
  • Ligand: water

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Supramolecule #1: Thioferritin dodecamer with loaded ferroxidase centers and no min...

SupramoleculeName: Thioferritin dodecamer with loaded ferroxidase centers and no mineral core.
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: 19.548141 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
IDVEKLLELL IKAAAAEFTT YYYYTILRNH ATGLEGEAIK EIIEDARLED RNHFEALVPR IYELGGELPR DIREFADLAS CRDAYLPEE PTIENILKVL LEAERCAVGV YTEICNYTFG KDPRTYDLAL AILHEEIEHE AWFEELLTGK PSGHFRRGKP G ESPYVSKF LK

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: 68 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: OXYGEN ATOM

MacromoleculeName: OXYGEN ATOM / type: ligand / ID: 3 / Number of copies: 68 / Formula: O
Molecular weightTheoretical: 15.999 Da
Chemical component information

ChemComp-O:
OXYGEN ATOM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 516 / 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 crystalline monolayer.

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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: 3094 / 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: 1742467
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: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 1619884
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: 75.5 / Target criteria: Cross-correlation coefficient
Output model

PDB-9cz8:
Structure of thioferritin exhibiting iron mineral nucleation, from Pyrococcus furiosis

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