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- EMDB-50022: Influenza virus neuraminidase N1 NC13 ectodomain with a tetrabrac... -

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Basic information

Entry
Database: EMDB / ID: EMD-50022
TitleInfluenza virus neuraminidase N1 NC13 ectodomain with a tetrabrachio-domain stalk
Map data
Sample
  • Complex: Influenza N1 NC13 with part of stalk replaced by tetrabrachion tetramerization domain
    • Protein or peptide: Neuraminidase
KeywordsNeuraminidase / Tetrabrachion / VIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/North Carolina/07/2013(H1N1)) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRoelofs MC / Zeev-Ben-Mordehai T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: NPJ Vaccines / Year: 2024
Title: Nanoparticle display of neuraminidase elicits enhanced antibody responses and protection against influenza A virus challenge.
Authors: M N Pascha / M Ballegeer / M C Roelofs / L Meuris / I C Albulescu / F J M van Kuppeveld / D L Hurdiss / B J Bosch / T Zeev-Ben-Mordehai / X Saelens / C A M de Haan /
Abstract: Current Influenza virus vaccines primarily induce antibody responses against variable epitopes in hemagglutinin (HA), necessitating frequent updates. However, antibodies against neuraminidase (NA) ...Current Influenza virus vaccines primarily induce antibody responses against variable epitopes in hemagglutinin (HA), necessitating frequent updates. However, antibodies against neuraminidase (NA) can also confer protection against influenza, making NA an attractive target for the development of novel vaccines. In this study, we aimed to enhance the immunogenicity of recombinant NA antigens by presenting them multivalently on a nanoparticle carrier. Soluble tetrameric NA antigens of the N1 and N2 subtypes, confirmed to be correctly folded by cryo-electron microscopy structural analysis, were conjugated to Mi3 self-assembling protein nanoparticles using the SpyTag-SpyCatcher system. Immunization of mice with NA-Mi3 nanoparticles induced higher titers of NA-binding and -inhibiting antibodies and improved protection against a lethal challenge compared to unconjugated NA. Additionally, we explored the co-presentation of N1 and N2 antigens on the same Mi3 particles to create a mosaic vaccine candidate. These mosaic nanoparticles elicited antibody titers that were similar or superior to the homotypic nanoparticles and effectively protected against H1N1 and H3N2 challenge viruses. The NA-Mi3 nanoparticles represent a promising vaccine candidate that could complement HA-directed approaches for enhanced potency and broadened protection against influenza A virus.
History
DepositionApr 4, 2024-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50022.png

Downloads & links

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Map

FileDownload / File: emd_50022.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 384 pix.
= 399.744 Å		1.04 Å/pix.
x 384 pix.
= 399.744 Å		1.04 Å/pix.
x 384 pix.
= 399.744 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.041 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7877257 - 2.9744463
Average (Standard dev.)0.00010716364 (±0.058595154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 399.74402 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50022_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_50022_half_map_2.map
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Sample components

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Entire : Influenza N1 NC13 with part of stalk replaced by tetrabrachion te...

EntireName: Influenza N1 NC13 with part of stalk replaced by tetrabrachion tetramerization domain
Components
  • Complex: Influenza N1 NC13 with part of stalk replaced by tetrabrachion tetramerization domain
    • Protein or peptide: Neuraminidase

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Supramolecule #1: Influenza N1 NC13 with part of stalk replaced by tetrabrachion te...

SupramoleculeName: Influenza N1 NC13 with part of stalk replaced by tetrabrachion tetramerization domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus (A/North Carolina/07/2013(H1N1))

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 42.385258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VKLAGNSSLC PVSGWAIYSK DNSVRIGSKG DVFVIREPFI SCSPLECRTF FLTQGALLND KHSNGTIKDR SPYRTLMSCP IGEVPSPYN SRFESVAWSA SACHDGINWL TIGISGPDSG AVAVLKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTI M TDGPSDGQ ...String:
VKLAGNSSLC PVSGWAIYSK DNSVRIGSKG DVFVIREPFI SCSPLECRTF FLTQGALLND KHSNGTIKDR SPYRTLMSCP IGEVPSPYN SRFESVAWSA SACHDGINWL TIGISGPDSG AVAVLKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTI M TDGPSDGQ ASYKIFRIEK GKIVKSVEMN APNYHYEECS CYPDSSEITC VCRDNWHGSN RPWVSFNQNL EYQIGYICSG VF GDNPRPN DKTGSCGPVS SNGANGVKGF SFKYGNGVWI GRTKSISSRK GFEMIWDPNG WTGTDNNFSI KQDIVGINEW SGY SGSFVQ HPELTGLDCI RPCFWVELIR GRPEENTIWT SGSSISFCGV NSDTVGWSWP DGAELPFTI

UniProtKB: Neuraminidase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.2 sec. / Average electron dose: 48.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199724
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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