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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: To Be Published
Title: CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation
Authors: Chinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
History
DepositionSep 3, 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_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

Size
Brightness
Contrast
Others
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
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55000_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55000_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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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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