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- EMDB-75344: A549 cell late endosome containing influenza A virus -

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Basic information

Entry
Database: EMDB / ID: EMD-75344
TitleA549 cell late endosome containing influenza A virus
Map dataA549 cell late endosome containing influenza A virus
Sample
  • Cell: A549 cell
KeywordsIFITM3 / transmembrane protein / viral restriction factor / IAV / ANTIVIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / negative staining
AuthorsButh SA / Melikian GB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI150453 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 AI190198 United States
CitationJournal: To Be Published
Title: A549 cell late endosome containing influenza A virus
Authors: Buth SA / Melikian GB
History
DepositionJan 29, 2026-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75344.png

Downloads & links

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Map

FileDownload / File: emd_75344.map.gz / Format: CCP4 / Size: 264.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA549 cell late endosome containing influenza A virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
18.93 Å/pix.
x 111 pix.
= 2101.23 Å		18.93 Å/pix.
x 791 pix.
= 14973.63 Å		18.93 Å/pix.
x 791 pix.
= 14973.63 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: 18.93 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum826.108339999999998 - 12094.038000000000466
Average (Standard dev.)8065.194300000000112 (±584.987700000000018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin121462-55
Dimensions791791111
Spacing791791111
CellA: 14973.63 Å / B: 14973.63 Å / C: 2101.23 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : A549 cell

EntireName: A549 cell
Components
  • Cell: A549 cell

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Supramolecule #1: A549 cell

SupramoleculeName: A549 cell / type: cell / ID: 1 / Parent: 0
Details: A549 cell expressing IFITM3 transmembrane protein infected with influenza A virus at MOI 1.5
Source (natural)Organism: Homo sapiens (human) / Organ: lung

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.2 / Details: DMEM media + 10% FSB
StainingType: POSITIVE / Material: Uranyl Acetate / Details: 0.1% UA in FS medium
Sugar embeddingMaterial: HM20
GridModel: EMS Formvar Carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
DetailsIAV infected cells were high pressure frozen, freeze-substituted and stained with 0.1% uranyl acetate, infiltrated with HM20 resin, and polymerized by UV Blocks were sectioned at 200-250nm.
High pressure freezingInstrument: BAL-TEC HPM 010
Details: The sapphire disc containing cell monolayer was sandwiched between two type B HPF planchettes and frozen according to manufacturer's procedure. Hexadecene-1 was used as a filler..
Cryo protectantHexadecene-1
SectioningUltramicrotomy - Instrument: Leica EM UC6 / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 250

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: OTHER / Average exposure time: 1.0 sec. / Average electron dose: 13.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 60.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 10000
Sample stageSpecimen holder model: JEOL

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Image processing

DetailsDark subtracted and gain normalized, frame alignment and summing using SerialEM on-the-fly implementation
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: eTomo / Number images used: 242
CTF correctionType: NONE

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