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- EMDB-26586: Negative stain EM map of Y2 COBRA hemagglutinin in complex with m... -

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Basic information

Entry
Database: EMDB / ID: EMD-26586
TitleNegative stain EM map of Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
Map dataNegative stain EM map of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Sample
  • Complex: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
    • Complex: Y2 COBRA hemagglutinin
    • Complex: P1-05 monoclonal antibody
Biological speciesCricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / negative staining / Resolution: 11.0 Å
AuthorsHan J / Dzimianski JV / DuBois RM / Ward A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: J Immunol / Year: 2022
Title: The Pre-Existing Human Antibody Repertoire to Computationally Optimized Influenza H1 Hemagglutinin Vaccines.
Authors: Kaito Nagashima / John V Dzimianski / Julianna Han / Nada Abbadi / Aaron D Gingerich / Fredejah Royer / Sara O'Rourke / Giuseppe A Sautto / Ted M Ross / Andrew B Ward / Rebecca M DuBois / Jarrod J Mousa /
Abstract: Computationally optimized broadly reactive Ag (COBRA) hemagglutinin (HA) immunogens have previously been generated for several influenza subtypes to improve vaccine-elicited Ab breadth. As nearly all ...Computationally optimized broadly reactive Ag (COBRA) hemagglutinin (HA) immunogens have previously been generated for several influenza subtypes to improve vaccine-elicited Ab breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA Ags. Cross-reactivity between wild-type HA and H1 COBRA HA proteins P1, X6, and Y2 were observed for isolated mAbs. The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 HA head and stem domains, and most mAbs had hemagglutination inhibition and neutralizing activity against 2009 pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had hemagglutination inhibition and neutralizing activity against a prepandemic H1 strain. One mAb, P1-05, targeted the stem region of H1 HA, but did not compete with a known stem-targeting H1 mAb. We determined that mAb P1-05 recognizes a recently discovered HA epitope, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by mAb P1-05, suggesting the importance of protein design for vaccine formulations. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA-reactive B cells that target head, central stalk, and anchor epitopes, and they demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes.
History
DepositionApr 1, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26586.png

Downloads & links

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Map

FileDownload / File: emd_26586.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 180 pix.
= 356.4 Å		1.98 Å/pix.
x 180 pix.
= 356.4 Å		1.98 Å/pix.
x 180 pix.
= 356.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-0.470915 - 3.3580077
Average (Standard dev.)-0.0244092 (±0.26363954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 356.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Negative stain EM half map A of Y2...

Fileemd_26586_half_map_1.map
AnnotationNegative stain EM half map A of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain EM half map B of Y2...

Fileemd_26586_half_map_2.map
AnnotationNegative stain EM half map B of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05

EntireName: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
Components
  • Complex: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
    • Complex: Y2 COBRA hemagglutinin
    • Complex: P1-05 monoclonal antibody

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Supramolecule #1: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05

SupramoleculeName: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / Organ: ovaries
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

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Supramolecule #2: Y2 COBRA hemagglutinin

SupramoleculeName: Y2 COBRA hemagglutinin / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Details: HA antigen based on A/California/04/2009 H1N1 HA
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / Organ: ovaries
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

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Supramolecule #3: P1-05 monoclonal antibody

SupramoleculeName: P1-05 monoclonal antibody / type: complex / Chimera: Yes / ID: 3 / Parent: 1
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / Organ: ovaries
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate / Details: 2% w/v
GridModel: Homemade / Pretreatment - Type: PLASMA CLEANING

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 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: PDB ENTRY
PDB model - PDB ID:

4m4y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12717
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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