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- EMDB-49096: Representative tomogram of influenza (PR8/34) -

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Basic information

Entry
Database: EMDB / ID: EMD-49096
TitleRepresentative tomogram of influenza (PR8/34)
Map data
Sample
  • Virus: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
KeywordsHemagglutinin / Glycoprotein / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Puerto Rico/8/1934(H1N1))
Methodelectron tomography / cryo EM
AuthorsHuang QJ / Song K / Schiffer CA / Somasundaran M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143773 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151996 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryoelectron tomography.
Authors: Qiuyu J Huang / Ryan Kim / Kangkang Song / Nikolaus Grigorieff / James B Munro / Celia A Schiffer / Mohan Somasundaran /
Abstract: Influenza viruses are enveloped, negative-sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80 to 90% of influenza glycoprotein and plays a ...Influenza viruses are enveloped, negative-sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80 to 90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of purified receptor-free and receptor-bound HA, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryoelectron tomography to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even interglycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and the formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8 to 10 Å reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.
History
DepositionFeb 5, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49096.png

Downloads & links

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Map

FileDownload / File: emd_49096.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.35 Å/pix.
x 352 pix.
= 2939.2 Å		8.35 Å/pix.
x 1440 pix.
= 12024.001 Å		8.35 Å/pix.
x 1024 pix.
= 8550.4 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: 8.35 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3.0 - 3.0
Average (Standard dev.)0.006018491 (±0.9249915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-13
Dimensions14401024352
Spacing10241440352
CellA: 8550.4 Å / B: 12024.001 Å / C: 2939.2002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Influenza A virus (A/Puerto Rico/8/1934(H1N1))

EntireName: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Components
  • Virus: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

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Supramolecule #1: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

SupramoleculeName: Influenza A virus (A/Puerto Rico/8/1934(H1N1)) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Purchased from Charles River Laboratories. / NCBI-ID: 211044
Sci species name: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 198 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Instrument: EMS-002 RAPID IMMERSION FREEZER
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: SIgma-Aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.86 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: Warp (ver. 1.1) / Number images used: 62

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