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- EMDB-26044: H10ssF: ferritin-based nanoparticle displaying H10 hemagglutinin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-26044
TitleH10ssF: ferritin-based nanoparticle displaying H10 hemagglutinin stabilized stem epitopes
Map dataFerritin nanoparticle with HA-stem complexes inserted at the 3-fold axes. The HA-stem complexes are flexible compared to the ferritin core.
Sample
  • Complex: H10ssF
    • Protein or peptide: H10ssF
Biological speciesInfluenza A virus / Helicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsGallagher JR / Harris 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: Immunity / Year: 2022
Title: Co-immunization with hemagglutinin stem immunogens elicits cross-group neutralizing antibodies and broad protection against influenza A viruses.
Authors: Syed M Moin / Jeffrey C Boyington / Seyhan Boyoglu-Barnum / Rebecca A Gillespie / Gabriele Cerutti / Crystal Sao-Fong Cheung / Alberto Cagigi / John R Gallagher / Joshua Brand / Madhu ...Authors: Syed M Moin / Jeffrey C Boyington / Seyhan Boyoglu-Barnum / Rebecca A Gillespie / Gabriele Cerutti / Crystal Sao-Fong Cheung / Alberto Cagigi / John R Gallagher / Joshua Brand / Madhu Prabhakaran / Yaroslav Tsybovsky / Tyler Stephens / Brian E Fisher / Adrian Creanga / Sila Ataca / Reda Rawi / Kizzmekia S Corbett / Michelle C Crank / Gunilla B Karlsson Hedestam / Jason Gorman / Adrian B McDermott / Audray K Harris / Tongqing Zhou / Peter D Kwong / Lawrence Shapiro / John R Mascola / Barney S Graham / Masaru Kanekiyo /
Abstract: Current influenza vaccines predominantly induce immunity to the hypervariable hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, the immunosubdominant yet conserved HA ...Current influenza vaccines predominantly induce immunity to the hypervariable hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, the immunosubdominant yet conserved HA stem harbors a supersite that is targeted by broadly neutralizing antibodies (bnAbs), representing a prime target for universal vaccines. Here, we showed that the co-immunization of two HA stem immunogens derived from group 1 and 2 influenza A viruses elicits cross-group protective immunity and neutralizing antibody responses in mice, ferrets, and nonhuman primates (NHPs). Immunized mice were protected from multiple group 1 and 2 viruses, and all animal models showed broad serum-neutralizing activity. A bnAb isolated from an immunized NHP broadly neutralized and protected against diverse viruses, including H5N1 and H7N9. Genetic and structural analyses revealed strong homology between macaque and human bnAbs, illustrating common biophysical constraints for acquiring cross-group specificity. Vaccine elicitation of stem-directed cross-group-protective immunity represents a step toward the development of broadly protective influenza vaccines.
History
DepositionJan 24, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26044.png

Downloads & links

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Map

FileDownload / File: emd_26044.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFerritin nanoparticle with HA-stem complexes inserted at the 3-fold axes. The HA-stem complexes are flexible compared to the ferritin core.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 228 pix.
= 325.584 Å		1.43 Å/pix.
x 228 pix.
= 325.584 Å		1.43 Å/pix.
x 228 pix.
= 325.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.428 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0786
Minimum - Maximum-0.13865036 - 0.43645984
Average (Standard dev.)0.0014071696 (±0.020033848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 325.58398 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Low-pass filtered map to 8A that resolves the...

Fileemd_26044_additional_1.map
AnnotationLow-pass filtered map to 8A that resolves the flexible HA-stem complexes inserted at the ferritin 3-fold symmetry axes.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H10ssF

EntireName: H10ssF
Components
  • Complex: H10ssF
    • Protein or peptide: H10ssF

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Supramolecule #1: H10ssF

SupramoleculeName: H10ssF / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: Fusion protein of H10 stabilized hemagglutinin stem construct and H. pylori ferritin.
Source (natural)Organism: Influenza A virus / Strain: H10N8 (A/Jiangxi-Donghu/346/2013)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: H10ssF

MacromoleculeName: H10ssF / type: protein_or_peptide / ID: 1
Details: influenza HA, H10 subtype, stem construct (N-terminal) fusion protein with H. pylori Ferritin (C-terminal).
Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKICLGHHAV ANGTIVKTLT NEQEEVTNAT ELVFPGCGVL MLATGMRNVP EGLFGAIAGF LENGWEGMVD GWYGFRHQNA QGTGQAADYK STQAAIDQIT GMVNRVVELM EQGGPDCYLA ELLVAMLNQH VIDMADSEMR NLYERVRKQL RQNAEEDGKG CFEIYHACDD ...String:
DKICLGHHAV ANGTIVKTLT NEQEEVTNAT ELVFPGCGVL MLATGMRNVP EGLFGAIAGF LENGWEGMVD GWYGFRHQNA QGTGQAADYK STQAAIDQIT GMVNRVVELM EQGGPDCYLA ELLVAMLNQH VIDMADSEMR NLYERVRKQL RQNAEEDGKG CFEIYHACDD SCMESIRNNT YDHSQYREEA LLNRLNINSG GDIIKLLNEQ VNKEMNSSNL YMSMSSWCYT HSLDGAGLFL FDHAAEEYEH AKKLIIFLNE NNVPVQLTSI SAPEHKFEGL TQIFQKAYEH EQHISESINN IVDHAIKSKD HATFNFLQWY VAEQHEEEVL FKDILDKIEL IGNENHGLYL ADQYVKGIAK SRK

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
1.8 mMKH2PO4Potassium phosphate
10.0 mMNa2HPO4Sodium phosphate
137.0 mMNaClSodium chloride
2.7 mMKClPotassium chloride

Details: PBS
GridModel: Quantifoil / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number real images: 4027 / Average exposure time: 4.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 78000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 693018
Startup modelType of model: OTHER / Details: solid sphere
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 118473
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2)
FSC plot (resolution estimation)

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