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- EMDB-21780: Polyclonal immune complex of Fab binding the stem of H3 HA from s... -

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Entry
Database: EMDB / ID: EMD-21780
TitlePolyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
Map dataPolyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
Sample
  • Complex: Polyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
    • Complex: Fab
    • Complex: H3 HA
Biological speciesHomo sapiens (human) / unidentified influenza virus
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsHan J / Ward A / Richey ST / Yang YR
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: Nature / Year: 2020
Title: Human germinal centres engage memory and naive B cells after influenza vaccination.
Authors: Jackson S Turner / Julian Q Zhou / Julianna Han / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / Tingting Lei / Mostafa Amor / Katherine M McIntire / Philip Meade / Shirin Strohmeier / ...Authors: Jackson S Turner / Julian Q Zhou / Julianna Han / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / Tingting Lei / Mostafa Amor / Katherine M McIntire / Philip Meade / Shirin Strohmeier / Rafael I Brent / Sara T Richey / Alem Haile / Yuhe R Yang / Michael K Klebert / Teresa Suessen / Sharlene Teefey / Rachel M Presti / Florian Krammer / Steven H Kleinstein / Andrew B Ward / Ali H Ellebedy /
Abstract: Influenza viruses remain a major public health threat. Seasonal influenza vaccination in humans primarily stimulates pre-existing memory B cells, which differentiate into a transient wave of ...Influenza viruses remain a major public health threat. Seasonal influenza vaccination in humans primarily stimulates pre-existing memory B cells, which differentiate into a transient wave of circulating antibody-secreting plasmablasts. This recall response contributes to 'original antigenic sin'-the selective increase of antibody species elicited by previous exposures to influenza virus antigens. It remains unclear whether such vaccination can also induce germinal centre reactions in the draining lymph nodes, where diversification and maturation of recruited B cells can occur. Here we used ultrasound-guided fine needle aspiration to serially sample the draining lymph nodes and investigate the dynamics and specificity of germinal centre B cell responses after influenza vaccination in humans. Germinal centre B cells that bind to influenza vaccine could be detected as early as one week after vaccination. In three out of eight participants, we detected vaccine-binding germinal centre B cells up to nine weeks after vaccination. Between 12% and 88% of the responding germinal centre B cell clones overlapped with B cells detected among early circulating plasmablasts. These shared B cell clones had high frequencies of somatic hypermutation and encoded broadly cross-reactive monoclonal antibodies. By contrast, vaccine-induced B cell clones detected only in the germinal centre compartment exhibited significantly lower frequencies of somatic hypermutation and predominantly encoded strain-specific monoclonal antibodies, which suggests a naive B cell origin. Some of these strain-specific monoclonal antibodies recognized epitopes that were not targeted by the early plasmablast response. Thus, influenza virus vaccination in humans can elicit a germinal centre reaction that recruits B cell clones that can target new epitopes, thereby broadening the spectrum of vaccine-induced protective antibodies.
History
DepositionApr 17, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21780.png

Downloads & links

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Map

FileDownload / File: emd_21780.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPolyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.02606389 - 0.09559721
Average (Standard dev.)0.00037061068 (±0.00596884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0260.0960.000

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Supplemental data

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Sample components

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Entire : Polyclonal immune complex of Fab binding the stem of H3 HA from s...

EntireName: Polyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
Components
  • Complex: Polyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
    • Complex: Fab
    • Complex: H3 HA

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Supramolecule #1: Polyclonal immune complex of Fab binding the stem of H3 HA from s...

SupramoleculeName: Polyclonal immune complex of Fab binding the stem of H3 HA from serum of participant 4 at day 28
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Fab

SupramoleculeName: Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Location in cell: PBMC

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Supramolecule #3: H3 HA

SupramoleculeName: H3 HA / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: unidentified influenza virus

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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: 2% w/v uranyl formate
GridDetails: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

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

3m5g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1460
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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