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- EMDB-68355: cryo-ET subtomogram-averaged structure of mouse heavy-chain apofe... -

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Basic information

Entry
Database: EMDB / ID: EMD-68355
Titlecryo-ET subtomogram-averaged structure of mouse heavy-chain apoferritin resolved at 2.71 Angstroms
Map dataFull-sharpen-map
Sample
  • Complex: Mouse apoferritin, heavy chain
    • Protein or peptide: Ferritin heavy chain
  • Ligand: MAGNESIUM ION
Keywordscryo-ET / subtomogram-average / mouse heavy-chain apoferritin / 2.71 Angstroms / OXIDOREDUCTASE
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding / autophagosome ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding / autophagosome / iron ion transport / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 2.71 Å
AuthorsMazmanian K / Wang CH / Hsu ST / Wu KP / Chang YC
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: cryo-ET subtomogram-averaged structure of mouse heavy-chain apoferritin resolved at 2.71 Angstroms
Authors: Mazmanian K / Wang CH / Hsu ST / Wu KP / Chang YC
History
DepositionJan 13, 2026-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68355.png

Downloads & links

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Map

FileDownload / File: emd_68355.map.gz / Format: CCP4 / Size: 27.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-sharpen-map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 194 pix.
= 259.184 Å		1.34 Å/pix.
x 194 pix.
= 259.184 Å		1.34 Å/pix.
x 194 pix.
= 259.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.0039406456 - 0.0071830014
Average (Standard dev.)-0.0000010084145 (±0.00044187307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions194194194
Spacing194194194
CellA=B=C: 259.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map-2

Fileemd_68355_half_map_1.map
Annotationhalf-map-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map-1

Fileemd_68355_half_map_2.map
Annotationhalf-map-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse apoferritin, heavy chain

EntireName: Mouse apoferritin, heavy chain
Components
  • Complex: Mouse apoferritin, heavy chain
    • Protein or peptide: Ferritin heavy chain
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mouse apoferritin, heavy chain

SupramoleculeName: Mouse apoferritin, heavy chain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.097631 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKP DRDDWESGLN AMECALHLEK SVNQSLLELH KLATDKNDPH LCDFIETYYL SEQVKSIKEL GDHVTNLRKM G APEAGMAE YLFDKHTLGH GDES

UniProtKB: Ferritin heavy chain

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 38 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1.65 mg/mL
BufferpH: 7.5 / Details: 30 mM HEPES 150 mM NaCl 1 mM DTT
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 2.0) / Software - details: Warp/M / Number subtomograms used: 3635
ExtractionNumber tomograms: 17 / Number images used: 20173 / Software - Name: Warp (ver. 2.0)
CTF correctionSoftware - Name: Warp (ver. 2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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