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- EMDB-41473: H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41473
TitleH2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2
Map dataH2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2
Sample
  • Complex: H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2
Keywordsinfluenza / hemagglutinin / monoclonal antibody / immune complex / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Singapore/1/1957(H2N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsYang YR / Han J / Perrett HR / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2 T32 AI007244-36 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F31Al172358 United States
CitationJournal: bioRxiv / Year: 2023
Title: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.
Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita ...Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita Chopde / Masaru Kanekiyo / Katherine V Houser / Grace L Chen / Adrian B McDermott / Sarah F Andrews / Andrew B Ward /
Abstract: Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in ...Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses.
History
DepositionAug 4, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41473.png

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Map

FileDownload / File: emd_41473.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2
Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.273
Minimum - Maximum-0.80674714 - 1.5188626
Average (Standard dev.)-0.00048038914 (±0.038143877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41473_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_41473_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_41473_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal ...

EntireName: H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2
Components
  • Complex: H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2

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Supramolecule #1: H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal ...

SupramoleculeName: H2 hemagglutinin (A/Singapore/1/1957) in complex with polyclonal Fab, pAb_2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/Singapore/1/1957(H2N2))

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2wr7

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61108
FSC plot (resolution estimation)

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