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- EMDB-20571: Monoclonal antibody 1H09 binds head domain of influenza virus hem... -

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Basic information

Entry
Database: EMDB / ID: EMD-20571
TitleMonoclonal antibody 1H09 binds head domain of influenza virus hemagglutinin
Map dataMonoclonal antibody 1H09 binds head domain of influenza virus hemagglutinin
Sample
  • Complex: Monoclonal antibody 1F03 in complex with head domain of influenza virus hemagglutinin.
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsHan J / Ward A
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Adjuvanted H5N1 influenza vaccine enhances both cross-reactive memory B cell and strain-specific naive B cell responses in humans.
Authors: Ali H Ellebedy / Raffael Nachbagauer / Katherine J L Jackson / Ya-Nan Dai / Julianna Han / Wafaa B Alsoussi / Carl W Davis / Daniel Stadlbauer / Nadine Rouphael / Veronika Chromikova / Megan ...Authors: Ali H Ellebedy / Raffael Nachbagauer / Katherine J L Jackson / Ya-Nan Dai / Julianna Han / Wafaa B Alsoussi / Carl W Davis / Daniel Stadlbauer / Nadine Rouphael / Veronika Chromikova / Megan McCausland / Cathy Y Chang / Mario Cortese / Mary Bower / Chakravarthy Chennareddy / Aaron J Schmitz / Veronika I Zarnitsyna / Lilin Lai / Arvind Rajabhathor / Cheyann Kazemian / Rustom Antia / Mark J Mulligan / Andrew B Ward / Daved H Fremont / Scott D Boyd / Bali Pulendran / Florian Krammer / Rafi Ahmed /
Abstract: There is a need for improved influenza vaccines. In this study we compared the antibody responses in humans after vaccination with an AS03-adjuvanted versus nonadjuvanted H5N1 avian influenza virus ...There is a need for improved influenza vaccines. In this study we compared the antibody responses in humans after vaccination with an AS03-adjuvanted versus nonadjuvanted H5N1 avian influenza virus inactivated vaccine. Healthy young adults received two doses of either formulation 3 wk apart. We found that AS03 significantly enhanced H5 hemagglutinin (HA)-specific plasmablast and antibody responses compared to the nonadjuvanted vaccine. Plasmablast response after the first immunization was exclusively directed to the conserved HA stem region and came from memory B cells. Monoclonal antibodies (mAbs) derived from these plasmablasts had high levels of somatic hypermutation (SHM) and recognized the HA stem region of multiple influenza virus subtypes. Second immunization induced a plasmablast response to the highly variable HA head region. mAbs derived from these plasmablasts exhibited minimal SHM (naive B cell origin) and largely recognized the HA head region of the immunizing H5N1 strain. Interestingly, the antibody response to H5 HA stem region was much lower after the second immunization, and this suppression was most likely due to blocking of these epitopes by stem-specific antibodies induced by the first immunization. Taken together, these findings show that an adjuvanted influenza vaccine can substantially increase antibody responses in humans by effectively recruiting preexisting memory B cells as well as naive B cells into the response. In addition, we show that high levels of preexisting antibody can have a negative effect on boosting. These findings have implications toward the development of a universal influenza vaccine.
History
DepositionAug 7, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseJul 15, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20571.png

Downloads & links

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Map

FileDownload / File: emd_20571.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMonoclonal antibody 1H09 binds head domain of influenza virus hemagglutinin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 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: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.04346532 - 0.09810651
Average (Standard dev.)0.00022631955 (±0.0062031737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0430.0980.000

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Supplemental data

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Sample components

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Entire : Monoclonal antibody 1F03 in complex with head domain of influenza...

EntireName: Monoclonal antibody 1F03 in complex with head domain of influenza virus hemagglutinin.
Components
  • Complex: Monoclonal antibody 1F03 in complex with head domain of influenza virus hemagglutinin.

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Supramolecule #1: Monoclonal antibody 1F03 in complex with head domain of influenza...

SupramoleculeName: Monoclonal antibody 1F03 in complex with head domain of influenza virus hemagglutinin.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: 293F
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: 293F
Molecular weightExperimental: 120 KDa

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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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
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:

3m5g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 3790
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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