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- EMDB-54356: Genetically Encoded FerriTag as a Specific Label for Cryo-Electro... -

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Basic information

Entry
Database: EMDB / ID: EMD-54356
TitleGenetically Encoded FerriTag as a Specific Label for Cryo-Electron Tomography
Map data
Sample
  • Cell: label for cryo-ET
Keywordslabel for cryo em / METAL BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsWang C / Iacovache I / Khosrozadeh A / Zuber B
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation32NE30_185536 Switzerland
Swiss National Science FoundationCRSII_222809 Switzerland
Swiss National Science Foundation31003A_179520 Switzerland
CitationJournal: Structure / Year: 2025
Title: Genetically encoded FerriTag as a specific label for cryo-electron tomography.
Authors: Chang Wang / Amin Khosrozadeh / Ioan Iacovache / Benoît Zuber /
Abstract: Cryo-electron tomography (cryoET) provides 3D datasets of organelles and proteins at nanometer and sub-nanometer resolution. However, locating target proteins in live cells remains a significant ...Cryo-electron tomography (cryoET) provides 3D datasets of organelles and proteins at nanometer and sub-nanometer resolution. However, locating target proteins in live cells remains a significant challenge. Conventional labeling methods, such as fluorescent protein tagging and immunogold labeling, are unsuitable for small structures in vitrified samples at molecular resolution. Directly linking large, visually identifiable proteins to target proteins may alter their structure, localization, and function. To overcome this, we employed a rapamycin-induced oligomer formation system involving two tags, FK506 binding protein (FKBP) and FKBP-rapamycin binding (FRB), which bind in the presence of rapamycin. FKBP is linked to the target protein, while FRB is linked to ferritin, a large (10-12 nm) iron-binding complex that creates strong contrast in cryoET. Upon adding rapamycin to the cell medium, the iron-loaded ferritin accurately marks the target protein location. As in situ cryoET with subtomogram averaging advances, our method addresses the persistent challenge of locating target proteins in live cells.
History
DepositionJul 10, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54356.png

Downloads & links

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Map

FileDownload / File: emd_54356.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
37.12 Å/pix.
x 512 pix.
= 19005.439 Å		37.12 Å/pix.
x 250 pix.
= 9280. Å		37.12 Å/pix.
x 512 pix.
= 19005.439 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 37.12 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-249.0 - 289.0
Average (Standard dev.)20.55518 (±20.897860000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-10900
Dimensions250512512
Spacing512250512
CellA: 19005.44 Å / B: 9280.0 Å / C: 19005.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : label for cryo-ET

EntireName: label for cryo-ET
Components
  • Cell: label for cryo-ET

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Supramolecule #1: label for cryo-ET

SupramoleculeName: label for cryo-ET / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293FT

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 16 / Focused ion beam - Current: 0.11 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 500 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61
CTF correctionType: NONE

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