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- EMDB-55027: Cryo-EM structure of horse spleen apoferritin using the cryoWrite... -

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Basic information

Entry
Database: EMDB / ID: EMD-55027
TitleCryo-EM structure of horse spleen apoferritin using the cryoWriter automated grid preparation system with two-time writing with spiral pattern
Map data
Sample
  • Complex: Horse spleen apoferritin
Keywordson-grid mixing / cryo-EM / cryoWriter / single-particle / automated grid preparation / apoF / horse spleen apoferritin / METAL TRANSPORT
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.71 Å
AuthorsChinmaya KV / Kube M / Stahlberg H
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_200628 Switzerland
European Research Council (ERC)101118656European Union
CitationJournal: Nat Commun / Year: 2026
Title: CryoWriter: a robotic solution for improved Cryo-EM grid preparation.
Authors: Chinmaya Kv / Babatunde Ekundayo / Marta Di Fabrizio / Inayathulla Mohammed / Julika Radecke / Henning Stahlberg / Massimo Kube /
Abstract: Cryo-electron microscopy (cryo-EM) structure determination relies on preparing thin, vitreous films of sample solution on EM grids. Cryo-EM is a mature technology, but preparing the grids remains a ...Cryo-electron microscopy (cryo-EM) structure determination relies on preparing thin, vitreous films of sample solution on EM grids. Cryo-EM is a mature technology, but preparing the grids remains a major bottleneck. Here, we evaluate the cryoWriter, a blotting-free, microfluidic grid-preparation robot that writes nanoliter volumes onto EM grids in a controlled environment. Using capillary-writing in spiral or line patterns, we prepared high-quality grids from minimal sample volumes and obtained near-atomic reconstructions for test specimens, including TMV, apoferritin, and the membrane protein TRPM4. We further demonstrate programmable deposition modes, such as writing the sample twice to boost particle density, or two-line writing for on-grid mixing to visualize time-resolved protein-ligand binding. In a challenging case (NrS-1 DNA polymerase), the cryoWriter grids exhibited reduced orientation bias relative to conventional blotting, enabling a more isotropic reconstruction. These results show that the cryoWriter provides a versatile platform for reproducible low volume cryo-EM grid preparation and for on-grid biochemical workflows.
History
DepositionSep 5, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55027.png

Downloads & links

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Map

FileDownload / File: emd_55027.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.41 Å/pix.
x 600 pix.
= 246.72 Å		0.41 Å/pix.
x 600 pix.
= 246.72 Å		0.41 Å/pix.
x 600 pix.
= 246.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.4112 Å
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Contour LevelBy AUTHOR: 0.0607
Minimum - Maximum-0.28281817 - 0.39206526
Average (Standard dev.)0.000008713496 (±0.012576838)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 246.71999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55027_msk_1.map
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Half map: #1

Fileemd_55027_half_map_1.map
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Half map: #2

Fileemd_55027_half_map_2.map
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Sample components

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Entire : Horse spleen apoferritin

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

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Supramolecule #1: Horse spleen apoferritin

SupramoleculeName: Horse spleen apoferritin / 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

Concentration5 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 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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
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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 760785
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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