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- EMDB-57470: Cryo-EM structure of mouse heavy-chain apoferritin on continuous ... -

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Basic information

Entry
Database: EMDB / ID: EMD-57470
TitleCryo-EM structure of mouse heavy-chain apoferritin on continuous carbon from 300 kV Titan Krios
Map datamasked map from relion_postprocess with deposited half maps and mask
Sample
  • Complex: Mouse heavy-chain apoferritin
    • Protein or peptide: Ferritin heavy chain
Keywordsiron storage / cryo-EM benchmark / METAL BINDING PROTEIN
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / protein complex oligomerization / ferroxidase activity / autolysosome / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / ferroxidase / negative regulation of ferroptosis / protein complex oligomerization / ferroxidase activity / autolysosome / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / membrane / identical protein binding / cytosol / cytoplasm
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.09 Å
AuthorsFromm SA / Mattei S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2026
Title: LowDoseWizard: rapid and standardized setup of low-dose cryo-TEM imaging in SerialEM.
Authors: Simon A Fromm / Simone Mattei /
Abstract: Structure elucidation of biological macromolecules by single-particle cryogenic electron microscopy (SPA cryo-EM) or cryogenic electron tomography (cryo-ET) relies on low-dose imaging on cryogenic ...Structure elucidation of biological macromolecules by single-particle cryogenic electron microscopy (SPA cryo-EM) or cryogenic electron tomography (cryo-ET) relies on low-dose imaging on cryogenic transmission electron microscopes (cryo-TEMs). Routine microscope setup remains technically demanding and can be time-consuming, particularly for inexperienced or infrequent users. We present LowDoseWizard, a guided workflow implemented in SerialEM that enables rapid and standardized setup of cryo-TEM imaging conditions. From minimal user input, the workflow configures microscope optics, camera parameters and image-shift settings for all low-dose states, and guides the user through key daily alignment procedures, including beam-shift offset calibration, objective-lens astigmatism correction and coma-free alignment. The workflow is organized into modular routines that can be executed sequentially or independently, while microscope-specific acquisition parameters are defined in editable configuration files, allowing flexible adaptation to different instruments without modification of the core scripts. Across user sessions on three microscopes at EMBL Heidelberg, the complete setup required on average less than 15 min. To assess whether predefined imaging conditions generated by the workflow are compatible with high-resolution data collection, we acquired apoferritin data on a 200 kV Glacios and a 300 kV Titan Krios. These datasets yielded reconstructions at 1.62 and 1.09 Å resolution, respectively, demonstrating that rapid, guided setup can support near-atomic and atomic-resolution SPA cryo-EM. LowDoseWizard lowers the barrier to robust cryo-TEM setup, reduces the time spent on routine parameter selection and alignment, and helps users focus on sample-specific aspects of data acquisition such as target selection. The workflow should be particularly valuable in shared instrumentation environments, where accessibility, reproducibility and efficient microscope use are critical.
#1: Journal: Biorxiv / Year: 2026
Title: LowDoseWizard - rapid and standardised setup of low-dose cryo-TEM imaging in SerialEM
Authors: Fromm SA / Mattei S
History
DepositionApr 16, 2026-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57470.png

Downloads & links

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Map

FileDownload / File: emd_57470.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked map from relion_postprocess with deposited half maps and mask
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.38 Å/pix.
x 576 pix.
= 219.456 Å		0.38 Å/pix.
x 576 pix.
= 219.456 Å		0.38 Å/pix.
x 576 pix.
= 219.456 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.381 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4185622 - 2.0363715
Average (Standard dev.)0.0012331449 (±0.037967052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 219.45601 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_57470_msk_1.map
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Half map: #1

Fileemd_57470_half_map_1.map
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Half map: #2

Fileemd_57470_half_map_2.map
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Sample components

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Entire : Mouse heavy-chain apoferritin

EntireName: Mouse heavy-chain apoferritin
Components
  • Complex: Mouse heavy-chain apoferritin
    • Protein or peptide: Ferritin heavy chain

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Supramolecule #1: Mouse heavy-chain apoferritin

SupramoleculeName: Mouse heavy-chain apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEK LMKLQNQRGG RIFLQDIKKP DRDDWESGLN AMECALHLEK SVNQSLLELH K LATDKNDP HLCDFIETYY LSEQVKSIKE LGDHVTNLRK MGAPEAGMAE YLFDKHTLGH GD ES

UniProtKB: Ferritin heavy chain

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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

Concentration3.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
80.0 mMsodim chlorideNaCl
1.7 mMDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Details: Quorum GloQube, 25 mA, neg polarity
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 281 K / Instrument: LEICA EM GP / Details: front side blotting.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3417 / Average exposure time: 1.3 sec. / Average electron dose: 40.0 e/Å2 / Details: saved as EER
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 244755 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.25 µm / Nominal magnification: 215000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailssupersampled 2x during motion correction
Particle selectionNumber selected: 593971
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1), cryoSPARC (ver. 5.0.0))
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0) / Number images used: 453035
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
FSC plot (resolution estimation)

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