National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
75N93019C00051
United States
Citation
Journal: Cell Rep / Year: 2021 Title: Polyclonal epitope mapping reveals temporal dynamics and diversity of human antibody responses to H5N1 vaccination. Authors: Julianna Han / Aaron J Schmitz / Sara T Richey / Ya-Nan Dai / Hannah L Turner / Bassem M Mohammed / Daved H Fremont / Ali H Ellebedy / Andrew B Ward / Abstract: Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens ...Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens requires a thorough understanding of the antigenic sites targeted by the polyclonal antibody (pAb) response, which single-particle electron microscopy (EM) can sensitively detect. In this study, we employ EM polyclonal epitope mapping (EMPEM) to extensively characterize the pAb response to hemagglutinin (HA) after H5N1 immunization in humans. Cross-reactive pAbs originating from memory B cells immediately bound the stem of HA and persisted for more than a year after vaccination. In contrast, de novo pAb responses to multiple sites on the head of HA, targeting previously determined key neutralizing sites on H5 HA, expanded after the second immunization and waned quickly. Thus, EMPEM provides a robust tool for comprehensively tracking the specificity and durability of immune responses elicited by novel universal influenza vaccine candidates.
History
Deposition
Sep 2, 2020
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Header (metadata) release
Mar 3, 2021
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Map release
Mar 3, 2021
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Update
Mar 3, 2021
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Current status
Mar 3, 2021
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_22560.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 43 at day 100
Voxel size
X=Y=Z: 1.98 Å
Density
Contour Level
By AUTHOR: 0.0188 / Movie #1: 0.0188
Minimum - Maximum
-0.040136993 - 0.11461521
Average (Standard dev.)
0.00014542796 (±0.0054220925)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
160
160
160
Spacing
160
160
160
Cell
A=B=C: 316.8 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.98
1.98
1.98
M x/y/z
160
160
160
origin x/y/z
0.000
0.000
0.000
length x/y/z
316.800
316.800
316.800
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
160
160
160
D min/max/mean
-0.040
0.115
0.000
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Supplemental data
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Sample components
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Entire : Polyclonal immune complex of Fab binding the receptor binding sit...
Entire
Name: Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 43 at day 100
Components
Complex: Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 43 at day 100
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Supramolecule #1: Polyclonal immune complex of Fab binding the receptor binding sit...
Supramolecule
Name: Polyclonal immune complex of Fab binding the receptor binding site region of H5 HA from serum of subject 43 at day 100 type: complex / ID: 1 / Parent: 0
Source (natural)
Organism: Homo sapiens (human) / Location in cell: PBMC
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Experimental details
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Structure determination
Method
negative staining
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Buffer
pH: 7.4
Staining
Type: NEGATIVE / Material: 2% w/v uranyl formate
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Electron microscopy
Microscope
FEI TALOS ARCTICA
Image recording
Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
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