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- EMDB-27232: Subtomogram of Fluad vaccine hemagglutinin spiked nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-27232
TitleSubtomogram of Fluad vaccine hemagglutinin spiked nanodisc
Map datasubtomogram of Fluad nanodisc, raw
Sample
  • Complex: Hemagglutinin protein extracted from these influenza viruses: A/Singapore/GP1908/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016
    • Complex: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein
    • Complex: A/Singapore/GP1908/2015 hemagglutinin protein
    • Complex: B/Maryland/15/2016 hemagglutinin protein
Biological speciesInfluenza A virus
Methodelectron tomography / cryo EM
AuthorsGallagher JR / Audray AK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI001180 United States
CitationJournal: Nat Commun / Year: 2023
Title: Commercial influenza vaccines vary in HA-complex structure and in induction of cross-reactive HA antibodies.
Authors: Mallory L Myers / John R Gallagher / Alexander J Kim / Walker H Payne / Samantha Maldonado-Puga / Haralabos Assimakopoulos / Kevin W Bock / Udana Torian / Ian N Moore / Audray K Harris /
Abstract: Influenza virus infects millions of people annually and can cause global pandemics. Hemagglutinin (HA) is the primary component of commercial influenza vaccines (CIV), and antibody titer to HA is a ...Influenza virus infects millions of people annually and can cause global pandemics. Hemagglutinin (HA) is the primary component of commercial influenza vaccines (CIV), and antibody titer to HA is a primary correlate of protection. Continual antigenic variation of HA requires that CIVs are reformulated yearly. Structural organization of HA complexes have not previously been correlated with induction of broadly reactive antibodies, yet CIV formulations vary in how HA is organized. Using electron microscopy to study four current CIVs, we find structures including: individual HAs, starfish structures with up to 12 HA molecules, and novel spiked-nanodisc structures that display over 50 HA molecules along the complex's perimeter. CIV containing these spiked nanodiscs elicit the highest levels of heterosubtypic cross-reactive antibodies in female mice. Here, we report that HA structural organization can be an important CIV parameter and can be associated with the induction of cross-reactive antibodies to conserved HA epitopes.
History
DepositionJun 7, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27232.png

Downloads & links

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Map

FileDownload / File: emd_27232.map.gz / Format: CCP4 / Size: 25.1 MB / Type: IMAGE STORED AS SIGNED BYTE
Annotationsubtomogram of Fluad nanodisc, raw
Voxel sizeX=Y=Z: 4.6057 Å
Density
Minimum - Maximum-37.0 - 60.0
Average (Standard dev.)15.814323 (±4.906499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1445-1333145
Dimensions301301290
Spacing301301290
CellA: 1386.3157 Å / B: 1386.3157 Å / C: 1335.653 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: subtomogram of Fluad nanodisc, processed with nonlinear anisotropic...

Fileemd_27232_additional_1.map
Annotationsubtomogram of Fluad nanodisc, processed with nonlinear anisotropic diffusion.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hemagglutinin protein extracted from these influenza viruses: A/S...

EntireName: Hemagglutinin protein extracted from these influenza viruses: A/Singapore/GP1908/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016
Components
  • Complex: Hemagglutinin protein extracted from these influenza viruses: A/Singapore/GP1908/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016
    • Complex: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein
    • Complex: A/Singapore/GP1908/2015 hemagglutinin protein
    • Complex: B/Maryland/15/2016 hemagglutinin protein

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Supramolecule #1: Hemagglutinin protein extracted from these influenza viruses: A/S...

SupramoleculeName: Hemagglutinin protein extracted from these influenza viruses: A/Singapore/GP1908/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Details: formulated in MF59C.1 adjuvant
Source (natural)Organism: Influenza A virus

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Supramolecule #2: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein

SupramoleculeName: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Details: formulated in MF59C.1 adjuvant

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Supramolecule #3: A/Singapore/GP1908/2015 hemagglutinin protein

SupramoleculeName: A/Singapore/GP1908/2015 hemagglutinin protein / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Details: formulated with MF59C.1 adjuvant

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Supramolecule #4: B/Maryland/15/2016 hemagglutinin protein

SupramoleculeName: B/Maryland/15/2016 hemagglutinin protein / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Details: formulated with MF59C.1 adjuvant

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 310 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Electron Microscopy Sciences / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.64 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 61

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