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- EMDB-55000: Cryo-EM structure of the desthiobiotin-bound streptavidin prepare... -

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Basic information

Entry
Database: EMDB / ID: EMD-55000
TitleCryo-EM structure of the desthiobiotin-bound streptavidin prepared using the cryoWriter automated grid preparation system with line pattern writing
Map data
Sample
  • Complex: Desthiobiotin-bound streptavidin
    • Protein or peptide: Streptavidin
KeywordscryoWriter / cryo-EM / streptavidin / automated grid preparation / single-particle / PEPTIDE BINDING PROTEIN
Biological speciesStreptomyces avidinii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsChinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
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 3, 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_55000.png

Downloads & links

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Map

FileDownload / File: emd_55000.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 256 pix.
= 327.936 Å		1.28 Å/pix.
x 256 pix.
= 327.936 Å		1.28 Å/pix.
x 256 pix.
= 327.936 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.281 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1957633 - 1.9400346
Average (Standard dev.)0.00004115035 (±0.02308851)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 327.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55000_msk_1.map
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Half map: #2

Fileemd_55000_half_map_1.map
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Half map: #1

Fileemd_55000_half_map_2.map
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Sample components

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Entire : Desthiobiotin-bound streptavidin

EntireName: Desthiobiotin-bound streptavidin
Components
  • Complex: Desthiobiotin-bound streptavidin
    • Protein or peptide: Streptavidin

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Supramolecule #1: Desthiobiotin-bound streptavidin

SupramoleculeName: Desthiobiotin-bound streptavidin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces avidinii (bacteria)
Molecular weightTheoretical: 52 kDa/nm

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Macromolecule #1: Streptavidin

MacromoleculeName: Streptavidin / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Streptomyces avidinii (bacteria)
SequenceString:
GITGTWYNQL GSTFIVTAG A DGALTGTY ES AVGNAES RYV LTGRYD SAPA TDGSG TALGW TVAW KNNYRN AHS ATTWSGQ YV GGAEARIN T QWLLTSGTT EANAWKSTLV GHDTFTKVK

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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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: SPT Labtech self-wicking R1.2/0.8 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 2209 / Average electron dose: 60.0 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: 1.0 µm / Nominal magnification: 165000
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 (ver. v4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 47564
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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