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- EMDB-27233: Tomogram of Flublok vaccine hemagglutinin starfish complexes -

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Basic information

Entry
Database: EMDB / ID: EMD-27233
TitleTomogram of Flublok vaccine hemagglutinin starfish complexes
Map datatomogram of Flublok hemagglutinin "starfish" particles.
Sample
  • Complex: Expressed hemagglutinin protein from these influenza viruses: A/Michigan/45/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016 B/Phuket/3073/2013
    • Complex: A/Michigan/45/2015 hemagglutinin protein
    • Complex: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein
    • Complex: B/Maryland/15/2016 hemagglutinin protein
    • Complex: B/Phuket/3073/2013 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_27233.png

Downloads & links

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Map

FileDownload / File: emd_27233.map.gz / Format: CCP4 / Size: 684.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationtomogram of Flublok hemagglutinin "starfish" particles.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.61 Å/pix.
x 152 pix.
= 700.066 Å		4.61 Å/pix.
x 1537 pix.
= 7078.961 Å		4.61 Å/pix.
x 1537 pix.
= 7078.961 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: 4.6057 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2333.0 - 2348.0
Average (Standard dev.)136.35982 (±392.25223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-768-768-76
Dimensions15371537152
Spacing15371537152
CellA: 7078.961 Å / B: 7078.961 Å / C: 700.0664 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: subtomogram of Flublok hemagglutinin starfish, processed with nonlinear...

Fileemd_27233_additional_1.map
Annotationsubtomogram of Flublok hemagglutinin starfish, 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 : Expressed hemagglutinin protein from these influenza viruses: A/M...

EntireName: Expressed hemagglutinin protein from these influenza viruses: A/Michigan/45/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016 B/Phuket/3073/2013
Components
  • Complex: Expressed hemagglutinin protein from these influenza viruses: A/Michigan/45/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016 B/Phuket/3073/2013
    • Complex: A/Michigan/45/2015 hemagglutinin protein
    • Complex: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein
    • Complex: B/Maryland/15/2016 hemagglutinin protein
    • Complex: B/Phuket/3073/2013 hemagglutinin protein

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Supramolecule #1: Expressed hemagglutinin protein from these influenza viruses: A/M...

SupramoleculeName: Expressed hemagglutinin protein from these influenza viruses: A/Michigan/45/2015 A/Singapore/INFIMH-16-0019/2016 B/Maryland/15/2016 B/Phuket/3073/2013
type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Influenza A virus

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Supramolecule #2: A/Michigan/45/2015 hemagglutinin protein

SupramoleculeName: A/Michigan/45/2015 hemagglutinin protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1

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Supramolecule #3: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein

SupramoleculeName: A/Singapore/INFIMH-16-0019/2016 hemagglutinin protein / type: complex / ID: 3 / Chimera: Yes / Parent: 1

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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

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Supramolecule #5: B/Phuket/3073/2013 hemagglutinin protein

SupramoleculeName: B/Phuket/3073/2013 hemagglutinin protein / type: complex / ID: 5 / Chimera: Yes / Parent: 1

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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: 99 % / 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
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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