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- EMDB-68204: 100 kV cryo-EM structure of apoferritin at 1.91 A with DECTRIS SI... -

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Basic information

Entry
Database: EMDB / ID: EMD-68204
Title100 kV cryo-EM structure of apoferritin at 1.91 A with DECTRIS SINGLA detector on CRYO ARM 200 II
Map dataSharpened map
Sample
  • Complex: homo 24-mer mouse heavy-chain apoferritin
    • Protein or peptide: apoferritin
Keywordsapoferritin / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.91 Å
AuthorsDanev R / Yanagisawa H / Yamashita K / Eisenstein F / Kikkawa M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H02554 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 8, 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_68204.png

Downloads & links

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Map

FileDownload / File: emd_68204.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 180 pix.
= 140.4 Å		0.78 Å/pix.
x 180 pix.
= 140.4 Å		0.78 Å/pix.
x 180 pix.
= 140.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.860582 - 1.7168232
Average (Standard dev.)0.0031407245 (±0.16639504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 140.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68204_msk_1.map
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Additional map: Unsharpened map

Fileemd_68204_additional_1.map
AnnotationUnsharpened map
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Half map: Half map B

Fileemd_68204_half_map_1.map
AnnotationHalf map B
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Half map: Half map A

Fileemd_68204_half_map_2.map
AnnotationHalf map A
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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: apoferritin

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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: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: apoferritin

MacromoleculeName: apoferritin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKPD RDDWESGLNA MECALHLEKS VNQSLLELHK LATDKNDPHL CDFIETYYLS EQVKSIKELG DHVTNLRKMG APEAGMAEYL FDKHTLGHGD ES

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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 R1.2/1.3 / 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: 3 ul sample, 10 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: 1.2 mrad
DetailsThe 500000 for the microscope magnification and the 641026 for the calibrated magnification were the actual values for the experiment.
Image recordingFilm or detector model: DECTRIS SINGLA (1k x 1k) / Number grids imaged: 1 / Number real images: 17424 / Average exposure time: 3.0 sec. / Average electron dose: 52.2 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.8 µm / Calibrated defocus min: 0.2 µm / Calibrated magnification: 100000 / 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: 49999
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 349779
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: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 250077
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: 100 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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