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- EMDB-49222: Influenza A(H5N1) Clade 2.3.4.4b in complex with head specific mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-49222
TitleInfluenza A(H5N1) Clade 2.3.4.4b in complex with head specific monoclonal antibody NVX.361.4
Map datarecombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b vaccine bound to NVX.361.4 monoclonal antibody fab (mouse)
Sample
  • Complex: Full-length recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b protein
    • Complex: Recombinant Full-length Influenza H5N1-HA Vaccine in-complex with Monoclonal mouse antibody NVX.361.4
      • Other: Hemagglutinin
      • Other: Monoclonal Antibody NVX.361.4
KeywordsPandemic Flu / Influenza HA / H5N1 / VIRAL PROTEIN
Biological speciesH5N1 subtype (virus) / unidentified influenza virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsPatel N / Rehman A / Gale S
Funding support United States, 1 items
OrganizationGrant numberCountry
Other privateNovavax, Inc. United States
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 13, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49222.png

Downloads & links

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Map

FileDownload / File: emd_49222.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 vaccine bound to NVX.361.4 monoclonal antibody fab (mouse)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.769 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0253
Minimum - Maximum-0.3563604 - 0.4720886
Average (Standard dev.)0.00015513472 (±0.0070535396)
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: #2

Fileemd_49222_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49222_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length recombinant A(H5N1) A/American Wigeon/South Carolina/...

EntireName: Full-length recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b protein
Components
  • Complex: Full-length recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b protein
    • Complex: Recombinant Full-length Influenza H5N1-HA Vaccine in-complex with Monoclonal mouse antibody NVX.361.4
      • Other: Hemagglutinin
      • Other: Monoclonal Antibody NVX.361.4

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Supramolecule #1: Full-length recombinant A(H5N1) A/American Wigeon/South Carolina/...

SupramoleculeName: Full-length recombinant A(H5N1) A/American Wigeon/South Carolina/22/000345-001/2021 (A/AW/SC/2021) clade 2.3.4.4b protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: purified FL-H5N1-HA protein co-mixed with monoclonal antibody NVX.361.4
Source (natural)Organism: H5N1 subtype (virus)

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Supramolecule #2: Recombinant Full-length Influenza H5N1-HA Vaccine in-complex with...

SupramoleculeName: Recombinant Full-length Influenza H5N1-HA Vaccine in-complex with Monoclonal mouse antibody NVX.361.4
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: unidentified influenza virus

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: other / ID: 1 / Classification: other
Source (natural)Organism: H5N1 subtype (virus)
SequenceString: MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCD LNGVKPLILK DCSVAGWLLG NPMCDEFIRV PEWSYIVERA N PANDLCYP GSLNDYEELK HMLSRINHFE KILIIPKSSW PNHETSLGVS AA CPYQGAP SFFRNVVWLI ...String:
MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCD LNGVKPLILK DCSVAGWLLG NPMCDEFIRV PEWSYIVERA N PANDLCYP GSLNDYEELK HMLSRINHFE KILIIPKSSW PNHETSLGVS AA CPYQGAP SFFRNVVWLI KKNDAYPTIK ISYNNTNRED LLILWGIHHS NNA EEQTNL YKNPTTYISV GTSTLNQRLA PKIATRSQVN GQRGRMDFFW TILK PDDAI HFESNGNFIA PEYAYKIVKK GDSTIMKSGV EYGHCNTKCQ TPVGA INSS MPFHNIHPLT IGECPKYVKS NKLVLATGLR NSPLREKRRK RGLFGA IAG FIEGGWQGMV DGWYGYHHSN EQGSGYAADK ESTQKAIDGV TNKVNSI ID KMNTQFEAVG REFNNLERRI ENLNKKMEDG FLDVWTYNAE LLVLMENE R TLDFHDSNVK NLYDKVRLQL RDNAKELGNG CFEFYHKCDN ECMESVRNG TYDYPQYSEE ARLKREEISG VKLESVGTYQ ILSIYSTAAS SLALAIMMAG LSLWMCSNG SLQCRICI

GENBANK: GENBANK: OQ789275.1
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM

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Macromolecule #2: Monoclonal Antibody NVX.361.4

MacromoleculeName: Monoclonal Antibody NVX.361.4 / type: other / ID: 2 / Details: Mouse Monoclonal Antibody NVX.361.4 / Classification: other
Source (natural)Organism: Mus musculus (house mouse)
SequenceString: MGWSYIILFL VATATGVHSQ VQVQQSGSEL VKPGASVRLS CKASGYNFTT YYMYWVKQRP GQGLEWI GE INPTNGISNF NERFKNKATL TVDKSSSTAY MQLSSLTSED SAVYYCTRAS DYYGGSWFAY WGQGT LVTV S MESQTQVF VYMLLWLSGV DGDIVMTQSQ ...String:
MGWSYIILFL VATATGVHSQ VQVQQSGSEL VKPGASVRLS CKASGYNFTT YYMYWVKQRP GQGLEWI GE INPTNGISNF NERFKNKATL TVDKSSSTAY MQLSSLTSED SAVYYCTRAS DYYGGSWFAY WGQGT LVTV S MESQTQVF VYMLLWLSGV DGDIVMTQSQ KFMSTSVGDR VSVTCKASQN VYTNVAWYQQ KPGQSPKAL IYSASFRYNG VPDRFTGSGS GTDFTLTISN VQSEDLADYF CQQYNNYPLT FGAGTKLELK

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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

Concentration0.5 mg/mL
BufferpH: 7.2 / Details: 1X PBS
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: 990 / 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: OTHER / 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

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66000
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC
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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