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- EMDB-68251: Cryo-EM structure of mouse heavy-chain apoferritin at 1.24 A on C... -

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Basic information

Entry
Database: EMDB / ID: EMD-68251
TitleCryo-EM structure of mouse heavy-chain apoferritin at 1.24 A on CRYO ARM 200 II
Map dataSharpened map
Sample
  • Complex: homo 24-mer mouse heavy-chain apoferritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
  • Ligand: water
Keywordsapoferritin / METAL BINDING PROTEIN
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / Neutrophil degranulation / endocytic vesicle lumen / ferric iron binding ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / Neutrophil degranulation / endocytic vesicle lumen / 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 / identical protein binding / membrane / cytoplasm / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.24 Å
AuthorsDanev R / Yanagisawa H / Yamashita K / Eisenstein F / Kikkawa M
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02554 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121002j0004 Japan
CitationJournal: To Be Published
Title: Atomic resolution cryo-EM at 200 keV
Authors: Danev R / Yanagisawa H / Yamashita K / Eisenstein F / Kikkawa M
History
DepositionJan 9, 2026-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68251.png

Downloads & links

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Map

FileDownload / File: emd_68251.map.gz / Format: CCP4 / Size: 325 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.)
0.57 Å/pix.
x 440 pix.
= 250.592 Å		0.57 Å/pix.
x 440 pix.
= 250.592 Å		0.57 Å/pix.
x 440 pix.
= 250.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56953 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.43991497 - 1.3793277
Average (Standard dev.)-0.00008814234 (±0.025417807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 250.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68251_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Fo-Fc difference density map

Fileemd_68251_additional_1.map
AnnotationFo-Fc difference density map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68251_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68251_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homo 24-mer mouse heavy-chain apoferritin

EntireName: homo 24-mer mouse heavy-chain apoferritin
Components
  • Complex: homo 24-mer mouse heavy-chain apoferritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: homo 24-mer mouse heavy-chain apoferritin

SupramoleculeName: homo 24-mer mouse heavy-chain apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.097631 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 201 / 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

Concentration1.9 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 1 mM dithiothreitol (DTT)
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa / Details: R0.6/1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: 3 ul sample, 20 s blot time.

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
TemperatureMin: 87.0 K / Max: 87.0 K
Alignment procedureComa free - Residual tilt: 0.5 mrad
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 13654 / Average exposure time: 1.51 sec. / Average electron dose: 53.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 0.8 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 163612 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.5 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 652257
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: previous apoferritin reconstruction
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 615248
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: 3 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7a4m


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-22fx:
Cryo-EM structure of mouse heavy-chain apoferritin at 1.24 A on CRYO ARM 200 II

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