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- EMDB-13228: Cryo-electron tomogram of a hybrid virus particle generated by co... -

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Basic information

Entry
Database: EMDB / ID: EMD-13228
TitleCryo-electron tomogram of a hybrid virus particle generated by coinfection of human Influenza A virus and Respiratory Syncytial virus on lung cells.
Map dataCryo-electron tomogram of a hybrid virus particle generated during coinfection of Influenza A virus and Respiratory Syncytial virus in lung cells.
Sample
  • Virus: Hybrid virus particle formed from RSV A2 and IAV PR8
Keywordshybrid virus / filament / glycoprotein spikes / RNPs / VIRUS
Biological speciesHybrid virus particle formed from RSV A2 and IAV PR8
Methodelectron tomography / cryo EM
AuthorsVijayakrishnan S / Haney J / Murcia PR
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N013166/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_12014/9 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_12014/7 United Kingdom
CitationJournal: Nat Microbiol / Year: 2022
Title: Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles.
Authors: Joanne Haney / Swetha Vijayakrishnan / James Streetley / Kieran Dee / Daniel Max Goldfarb / Mairi Clarke / Margaret Mullin / Stephen D Carter / David Bhella / Pablo R Murcia /
Abstract: Interactions between respiratory viruses during infection affect transmission dynamics and clinical outcomes. To identify and characterize virus-virus interactions at the cellular level, we ...Interactions between respiratory viruses during infection affect transmission dynamics and clinical outcomes. To identify and characterize virus-virus interactions at the cellular level, we coinfected human lung cells with influenza A virus (IAV) and respiratory syncytial virus (RSV). Super-resolution microscopy, live-cell imaging, scanning electron microscopy and cryo-electron tomography revealed extracellular and membrane-associated filamentous structures consistent with hybrid viral particles (HVPs). We found that HVPs harbour surface glycoproteins and ribonucleoproteins of IAV and RSV. HVPs use the RSV fusion glycoprotein to evade anti-IAV neutralizing antibodies and infect and spread among cells lacking IAV receptors. Finally, we show that IAV and RSV coinfection in primary cells of the bronchial epithelium results in viral proteins from both viruses co-localizing at the apical cell surface. Our observations define a previously unknown interaction between respiratory viruses that might affect virus pathogenesis by expanding virus tropism and enabling immune evasion.
History
DepositionJul 16, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13228.png

Downloads & links

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Map

FileDownload / File: emd_13228.map.gz / Format: CCP4 / Size: 648 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of a hybrid virus particle generated during coinfection of Influenza A virus and Respiratory Syncytial virus in lung cells.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.99 Å/pix.
x 162 pix.
= 1942.704 Å		11.99 Å/pix.
x 1024 pix.
= 12279.808 Å		11.99 Å/pix.
x 1024 pix.
= 12279.808 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: 11.992 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-6986.620600000000195 - 6655.004399999999805
Average (Standard dev.)17.468132000000001 (±175.44765000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0081
Dimensions10241024162
Spacing10241024162
CellA: 12279.808 Å / B: 12279.808 Å / C: 1942.704 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Hybrid virus particle formed from RSV A2 and IAV PR8

EntireName: Hybrid virus particle formed from RSV A2 and IAV PR8
Components
  • Virus: Hybrid virus particle formed from RSV A2 and IAV PR8

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Supramolecule #1: Hybrid virus particle formed from RSV A2 and IAV PR8

SupramoleculeName: Hybrid virus particle formed from RSV A2 and IAV PR8 / type: virus / ID: 1 / Parent: 0
Details: This sample was A549 lung fibroblasts coinfected with both the PR8 strain of Influenza A virus and the A2 strain of Respiratory Syncytial Virus.
NCBI-ID: 1972429
Sci species name: Hybrid virus particle formed from RSV A2 and IAV PR8
Sci species strain: A2 and PR8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / Strain: PR8 and A2

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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: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Blotted from backside for 5 seconds before plunging..
DetailsThis sample was A549 lung fibroblasts coinfected with the human PR8 strain of Influenza A virus and A2 strain of Respiratory Syncytial virus directly on EM grids.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: British Biocell International / Diameter: 20 nm

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.11)
Software - details: Tomograms reconstructed using Etomo module of IMOD
Details: Tilt series were aligned and dose filtered using alignframes module in IMOD; tomograms were reconstructed using weighted back projection via the etomo module in IMOD. CTF correction was ...Details: Tilt series were aligned and dose filtered using alignframes module in IMOD; tomograms were reconstructed using weighted back projection via the etomo module in IMOD. CTF correction was carried out using ctfplotter. Final tomograms were binned by 8 (bin8) to aid in visualisation and interpretation.
Number images used: 61

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