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- EMDB-68815: Subtomogram average structure of human apoferritin at 1.98 Angstr... -

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Basic information

Entry
Database: EMDB / ID: EMD-68815
TitleSubtomogram average structure of human apoferritin at 1.98 Angstrom resolution(using CR-BIS data collection on Falcon4i).
Map dataCryo-EM density map of human ferritin at 1.98 angstrom resolution.
Sample
  • Complex: Human apo-ferritin
Keywordsron storage protein / ferritin-like fold / 24-mer nanocage / octahedral symmetry / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 1.98 Å
AuthorsYang Q / Huang XJ / Zhang XZ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32325027 China
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Nat Commun / Year: 2026
Title: Ultra-rapid cryo-EM data acquisition method enabled by continuous recording based beam image shift.
Authors: Qi Yang / Xiaojun Huang / Chunling Wu / Yan Zeng / Xinzheng Zhang /
Abstract: Cryo-electron microscopy (cryo-EM) data acquisition is time-intensive given that a large amount of data is required to obtain a high-resolution reconstruction. Here, we eliminate camera-induced delay ...Cryo-electron microscopy (cryo-EM) data acquisition is time-intensive given that a large amount of data is required to obtain a high-resolution reconstruction. Here, we eliminate camera-induced delay time by continuously recording during beam-image shift acquisition using a method called Continuous Recording Beam-Image Shift (CR-BIS). The utilization of CR-BIS with K3 and Falcon 4 direct electron detectors and conventional data acquisition conditions enables the acquisition of ~34,000 micrographs and ~1,000 tilt series per 24 h in single-particle analysis mode and cryo-electron tomography mode, respectively. Three-dimensional reconstructions of single-particle and tomographic datasets show that CR-BIS accelerates data collection and maintains data quality. CR-BIS is broadly applicable for efficient high-resolution cryo-EM since it can be implemented into existing acquisition software through scripting and it does not require hardware modification.
History
DepositionJan 30, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68815.png

Downloads & links

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Map

FileDownload / File: emd_68815.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of human ferritin at 1.98 angstrom resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 356 pix.
= 259.524 Å		0.73 Å/pix.
x 356 pix.
= 259.524 Å		0.73 Å/pix.
x 356 pix.
= 259.524 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00156
Minimum - Maximum-0.0072783167 - 0.014199938
Average (Standard dev.)-0.00000032740198 (±0.00062502193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 259.524 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68815_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map 1 used for the gold-standard FSC...

Fileemd_68815_half_map_1.map
AnnotationUnfiltered half-map 1 used for the gold-standard FSC resolution calculation and refinement of human ferritin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map 2 used for the gold-standard FSC...

Fileemd_68815_half_map_2.map
AnnotationUnfiltered half-map 2 used for the gold-standard FSC resolution calculation and refinement of human ferritin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human apo-ferritin

EntireName: Human apo-ferritin
Components
  • Complex: Human apo-ferritin

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Supramolecule #1: Human apo-ferritin

SupramoleculeName: Human apo-ferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 18252
ExtractionNumber tomograms: 53 / Number images used: 31800 / Software - Name: Warp
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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