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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: IUCrJ / Year: 2026
Title: Atomic resolution cryo-EM at 200 keV.
Authors: Radostin Danev / Haruaki Yanagisawa / Keitaro Yamashita / Fabian Eisenstein / Masahide Kikkawa /
Abstract: Atomic resolution in cryo-electron microscopy was first demonstrated six years ago. This was accomplished using 300 kV electron microscopes equipped with new hardware that provided narrower energy ...Atomic resolution in cryo-electron microscopy was first demonstrated six years ago. This was accomplished using 300 kV electron microscopes equipped with new hardware that provided narrower energy spread, aberration correction and energy filtering. Here, we report the achievement of 1.24 Å atomic resolution on an upgraded 200 kV electron microscope featuring a cold field emission gun, a high-resolution objective lens polepiece and an energy filter. These components transform the instrument into a cost-effective single-particle cryo-EM platform with performance comparable to that of significantly more expensive 300 kV systems. The microscope can also be operated at 100 kV and by using a high-speed hybrid-pixel detector we were able to reach sub-2 Å resolution.
History
DepositionJan 8, 2026-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68204.png

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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
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Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.78 Å
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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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