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- EMDB-54970: Cryo-EM structure of horse spleen apoferritin using the cryoWrite... -

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Basic information

Entry
Database: EMDB / ID: EMD-54970
TitleCryo-EM structure of horse spleen apoferritin using the cryoWriter automated grid preparation system with one-time writing with a line pattern
Map data
Sample
  • Complex: Horse spleen apoferritin light chain
Keywordsautomated grid preparation / single-particle cryo-EM / cryoWriter / apoferritin / METAL TRANSPORT
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.02 Å
AuthorsChinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_200628 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM structure of horse spleen apoferritin using the cryoWriter automated grid preparation system with one-time writing with a line pattern
Authors: Chinmaya KV / Stahlberg H / Kube M
History
DepositionSep 2, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54970.png

Downloads & links

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Map

FileDownload / File: emd_54970.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0936
Minimum - Maximum-0.21356745 - 0.4570324
Average (Standard dev.)-0.000014371625 (±0.019714985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54970_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54970_half_map_1.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_54970_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 : Horse spleen apoferritin light chain

EntireName: Horse spleen apoferritin light chain
Components
  • Complex: Horse spleen apoferritin light chain

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Supramolecule #1: Horse spleen apoferritin light chain

SupramoleculeName: Horse spleen apoferritin light chain / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Equus caballus (horse)
Molecular weightTheoretical: 483 kDa/nm

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 290 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 4932 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
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

Particle selectionNumber selected: 4923
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 230450
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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