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- EMDB-49235: Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-00... -

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Entry
Database: EMDB / ID: EMD-49235
TitleRecombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2
Map dataRecombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2
Sample
  • Complex: Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2
KeywordsAvian Influenza H5N1 monoclonal antibody / VIRAL PROTEIN
Biological speciesH5N1 subtype (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsSmith G / Patel A / Rehman A
Funding support1 items
OrganizationGrant numberCountry
Other privateNovavax, Inc.
CitationJournal: Nat Commun / Year: 2025
Title: Single-dose avian influenza A(H5N1) Clade 2.3.4.4b hemagglutinin-Matrix-M nanoparticle vaccine induces neutralizing responses in nonhuman primates.
Authors: Nita Patel / Asma Rehman / Jessica F Trost / Rhonda Flores / Zach Longacre / Mimi Guebre-Xabier / Haixia Zhou / Bin Zhou / Kelsey Jacobson / Desheng Jiang / Xiaoyun Bai / Rafia Khatoon / ...Authors: Nita Patel / Asma Rehman / Jessica F Trost / Rhonda Flores / Zach Longacre / Mimi Guebre-Xabier / Haixia Zhou / Bin Zhou / Kelsey Jacobson / Desheng Jiang / Xiaoyun Bai / Rafia Khatoon / Thomas Kort / James Norton / M Madhangi / Melinda Hersey / Ann M Greene / Filip Dubovsky / Gale Smith /
Abstract: With the recent rise in cases of highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b infection in humans and animals, there is an associated increase in the risk of human-to-human ...With the recent rise in cases of highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b infection in humans and animals, there is an associated increase in the risk of human-to-human transmission. In this study, we characterize a recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b vaccine. Purified recombinant A/AW/SC/2021 HA trimers formulated with Matrix-M adjuvant, saponin-cholesterol-phospholipid combination arranged in cage-like particles, are found to non-covalently anchor to the vertices of the Matrix-M and form A(H5N1) HA-Matrix-M nanoparticles (H5-MNPs). In naïve female mice, two intranasal (IN) or intramuscular (IM) doses of A/AW/SC/2021 H5-MNP vaccine induces robust antibody- and cell-mediated immune responses, including neutralizing antibodies against A(H5N1). In non-human primates (NHPs) primed with seasonal influenza vaccine, a single IM or IN dose of the A/AW/SC/2021 H5-MNP vaccine induces geometric mean serum A(H5N1) clade 2.3.4.4b pseudovirus neutralizing titers of 1:1160 and 1:54, respectively; above the generally accepted seroconverting neutralizing titer of 1:40. Immunization with H5-MNP vaccine induces antibody responses against conserved epitopes in the A(H5N1) HA stem, vestigial esterase subdomain, and receptor binding site. This A(H5N1) H5-MNP IN and IM vaccine is immunogenic in female rodents and NHPs as a potential A(H5N1) pandemic single-dose vaccine.
History
DepositionFeb 14, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49235.png

Downloads & links

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Map

FileDownload / File: emd_49235.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 384 pix.
= 295.296 Å		0.77 Å/pix.
x 384 pix.
= 295.296 Å		0.77 Å/pix.
x 384 pix.
= 295.296 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.769 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0218
Minimum - Maximum-0.3015561 - 0.41202947
Average (Standard dev.)0.00013360204 (±0.008304721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 295.296 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49235_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_49235_half_map_2.map
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Sample components

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Entire : Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-00...

EntireName: Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2
Components
  • Complex: Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2

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Supramolecule #1: Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-00...

SupramoleculeName: Recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b nanoparticle in complex with mouse monoclonal antibody NVX.73.2
type: complex / ID: 1 / Parent: 0
Details: purified FL-H5N1-HA protein co-mixed with monoclonal antibody NVX.73.2
Source (natural)Organism: H5N1 subtype (virus)

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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

Concentration0.8 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 4 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 752 / Average exposure time: 10.4 sec. / Average electron dose: 36.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 91000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 79000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 300000
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 253288
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 1 / Avg.num./class: 50000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL

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