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- EMDB-47204: Fluorescently Guided FIB Milled AAVs in HeLa Cells -

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Basic information

Entry
Database: EMDB / ID: EMD-47204
TitleFluorescently Guided FIB Milled AAVs in HeLa Cells
Map dataTomographic reconstruction of fluorescently labeled AAV particles in HeLa cells captured by fluorescently-guided FIB milling.
Sample
  • Virus: adeno-associated virus 2
KeywordsAdeno-associated virus / fluorescently labelled / FIB Milled / VIRUS
Biological speciesadeno-associated virus 2
Methodelectron tomography / cryo EM
AuthorsSica A / Zaoralova M / Dahlberg P
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21GM140345 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI127401 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 FWP 100883 United States
Chan Zuckerberg Initiative2021-234593 United States
CitationJournal: To Be Published
Title: Optical Interference for the Guidance of Cryogenic Focused Ion Beam Milling Beyond the Axial Diffraction Limit
Authors: Sica AV / Zaoralova M / Antolini C / Boltje D / Penzes J / Malmqvist L / Jensen G / Kaelber J / Dahlberg P
History
DepositionOct 7, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47204.png

Downloads & links

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Map

FileDownload / File: emd_47204.map.gz / Format: CCP4 / Size: 1.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomographic reconstruction of fluorescently labeled AAV particles in HeLa cells captured by fluorescently-guided FIB milling.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.84 Å/pix.
x 450 pix.
= 4428. Å		9.84 Å/pix.
x 1024 pix.
= 10076.16 Å		9.84 Å/pix.
x 1024 pix.
= 10076.16 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: 9.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 42.536853999999998
Average (Standard dev.)5.426907 (±2.6591902)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024450
Spacing10241024450
CellA: 10076.16 Å / B: 10076.16 Å / C: 4428.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : adeno-associated virus 2

EntireName: adeno-associated virus 2
Components
  • Virus: adeno-associated virus 2

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Supramolecule #1: adeno-associated virus 2

SupramoleculeName: adeno-associated virus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10804 / Sci species name: adeno-associated virus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.2 / Focused ion beam - Duration: 6000 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Enzel. This is not in a list of allowed values {'OTHER', 'DB235'} 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: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41
CTF correctionType: NONE

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