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- EMDB-23314: Negative stain map of monoclonal Fab 45 binding the esterase doma... -

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Basic information

Entry
Database: EMDB / ID: EMD-23314
TitleNegative stain map of monoclonal Fab 45 binding the esterase domain of H1 HA
Map dataNegative stain map of monoclonal Fab 45 binding the esterase domain of H1 HA
Sample
  • Complex: Negative stain map of monoclonal Fab 45 binding the lateral patch of H1 HA
    • Complex: Monoclonal Fab 45
    • Complex: Hemagglutinin (H1)
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsHan J / Freyn AW / Ward AB
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: Proc Natl Acad Sci U S A / Year: 2021
Title: Influenza hemagglutinin-specific IgA Fc-effector functionality is restricted to stalk epitopes.
Authors: Alec W Freyn / Julianna Han / Jenna J Guthmiller / Mark J Bailey / Karlynn Neu / Hannah L Turner / Victoria C Rosado / Veronika Chromikova / Min Huang / Shirin Strohmeier / Sean T H Liu / ...Authors: Alec W Freyn / Julianna Han / Jenna J Guthmiller / Mark J Bailey / Karlynn Neu / Hannah L Turner / Victoria C Rosado / Veronika Chromikova / Min Huang / Shirin Strohmeier / Sean T H Liu / Viviana Simon / Florian Krammer / Andrew B Ward / Peter Palese / Patrick C Wilson / Raffael Nachbagauer /
Abstract: In this study, we utilized a panel of human immunoglobulin (Ig) IgA monoclonal antibodies isolated from the plasmablasts of eight donors after 2014/2015 influenza virus vaccination (Fluarix) to study ...In this study, we utilized a panel of human immunoglobulin (Ig) IgA monoclonal antibodies isolated from the plasmablasts of eight donors after 2014/2015 influenza virus vaccination (Fluarix) to study the binding and functional specificities of this isotype. In this cohort, isolated IgA monoclonal antibodies were primarily elicited against the hemagglutinin protein of the H1N1 component of the vaccine. To compare effector functionalities, an H1-specific subset of antibodies targeting distinct epitopes were expressed as monomeric, dimeric, or secretory IgA, as well as in an IgG1 backbone. When expressed with an IgG Fc domain, all antibodies elicited Fc-effector activity in a primary polymorphonuclear cell-based assay which differs from previous observations that found only stalk-specific antibodies activate the low-affinity FcγRIIIa. However, when expressed with IgA Fc domains, only antibodies targeting the stalk domain showed Fc-effector activity in line with these previous findings. To identify the cause of this discrepancy, we then confirmed that IgG signaling through the high-affinity FcγI receptor was not restricted to stalk epitopes. Since no corresponding high-affinity Fcα receptor exists, the IgA repertoire may therefore be limited to stalk-specific epitopes in the context of Fc receptor signaling.
History
DepositionJan 20, 2021-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23314.png

Downloads & links

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Map

FileDownload / File: emd_23314.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of monoclonal Fab 45 binding the esterase domain of H1 HA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.039933782 - 0.077987656
Average (Standard dev.)0.00041641935 (±0.0059265895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 283.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z283.200283.200283.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0400.0780.000

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Supplemental data

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Sample components

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Entire : Negative stain map of monoclonal Fab 45 binding the lateral patch...

EntireName: Negative stain map of monoclonal Fab 45 binding the lateral patch of H1 HA
Components
  • Complex: Negative stain map of monoclonal Fab 45 binding the lateral patch of H1 HA
    • Complex: Monoclonal Fab 45
    • Complex: Hemagglutinin (H1)

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Supramolecule #1: Negative stain map of monoclonal Fab 45 binding the lateral patch...

SupramoleculeName: Negative stain map of monoclonal Fab 45 binding the lateral patch of H1 HA
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Monoclonal Fab 45

SupramoleculeName: Monoclonal Fab 45 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Supramolecule #3: Hemagglutinin (H1)

SupramoleculeName: Hemagglutinin (H1) / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Influenza A virus / Strain: A/California/04/2009(H1N1)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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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

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (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: Tecnai F20 / 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: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 3688
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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