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- EMDB-8801: Negative-stain EM reconstruction of H3v-47 Fab in complex with A/... -

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Basic information

Entry
Database: EMDB / ID: EMD-8801
TitleNegative-stain EM reconstruction of H3v-47 Fab in complex with A/Minnesota/11/2010 H3N2v HA and FI6v Fab
Map dataReconstruction of HA in complex with H3v-47 Fab and FI6v Fab.
Sample
  • Complex: A/Minnesota/11/2010 H3N2v HA
    • Complex: H3v-47 Fab
    • Complex: FI6v Fab
Biological speciesInfluenza A virus / Homo sapiens (human) / Human (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.8 Å
AuthorsNieusma T / Ward AB
CitationJournal: JCI Insight / Year: 2016
Title: Recognition of influenza H3N2 variant virus by human neutralizing antibodies.
Authors: Sandhya Bangaru / Travis Nieusma / Nurgun Kose / Natalie J Thornburg / Jessica A Finn / Bryan S Kaplan / Hannah G King / Vidisha Singh / Rebecca M Lampley / Gopal Sapparapu / Alberto ...Authors: Sandhya Bangaru / Travis Nieusma / Nurgun Kose / Natalie J Thornburg / Jessica A Finn / Bryan S Kaplan / Hannah G King / Vidisha Singh / Rebecca M Lampley / Gopal Sapparapu / Alberto Cisneros / Kathryn M Edwards / James C Slaughter / Srilatha Edupuganti / Lilin Lai / Juergen A Richt / Richard J Webby / Andrew B Ward / James E Crowe /
Abstract: Since 2011, over 300 human cases of infection, especially in exposed children, with the influenza A H3N2 variant (H3N2v) virus that circulates in swine in the US have been reported. The structural ...Since 2011, over 300 human cases of infection, especially in exposed children, with the influenza A H3N2 variant (H3N2v) virus that circulates in swine in the US have been reported. The structural and genetic basis for the lack of protection against H3N2v induced by vaccines containing seasonal H3N2 antigens is poorly understood. We isolated 17 human monoclonal antibodies (mAbs) that neutralized H3N2v virus from subjects experimentally immunized with an H3N2v candidate vaccine. Six mAbs exhibited very potent neutralizing activity (IC < 200 ng/ml) against the H3N2v virus but not against current human H3N2 circulating strains. Fine epitope mapping and structural characterization of antigen-antibody complexes revealed that H3N2v specificity was attributable to amino acid polymorphisms in the 150-loop and the 190-helix antigenic sites on the hemagglutinin protein. H3N2v-specific antibodies also neutralized human H3N2 influenza strains naturally circulating between 1995 and 2005. These results reveal a high level of antigenic relatedness between the swine H3N2v virus and previously circulating human strains, consistent with the fact that early human H3 seasonal strains entered the porcine population in the 1990s and reentered the human population, where they had not been circulating, as H3N2v about a decade later. The data also explain the increased susceptibility to H3N2v viruses in young children, who lack prior exposure to human seasonal strains from the 1990s.
History
DepositionJun 30, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseMay 9, 2018-
UpdateApr 24, 2019-
Current statusApr 24, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8801.png

Downloads & links

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Map

FileDownload / File: emd_8801.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HA in complex with H3v-47 Fab and FI6v Fab.
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 3.6 / Movie #1: 3.6
Minimum - Maximum-5.113778 - 15.210354000000001
Average (Standard dev.)0.000000002790279 (±0.90643466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-47-47-47
Dimensions192192192
Spacing192192192
CellA=B=C: 393.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-47-47-47
NC/NR/NS192192192
D min/max/mean-5.11415.2100.000

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Supplemental data

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Sample components

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Entire : A/Minnesota/11/2010 H3N2v HA

EntireName: A/Minnesota/11/2010 H3N2v HA
Components
  • Complex: A/Minnesota/11/2010 H3N2v HA
    • Complex: H3v-47 Fab
    • Complex: FI6v Fab

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Supramolecule #1: A/Minnesota/11/2010 H3N2v HA

SupramoleculeName: A/Minnesota/11/2010 H3N2v HA / type: complex / ID: 1 / Parent: 0
Details: H3v-47 Fab in complex with A/Minnesota/11/2010 H3N2v HA and FI6v Fab
Source (natural)Organism: Influenza A virus / Strain: H3N2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK Freestyle 293-F / Recombinant plasmid: pcDNA3.1(+)
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: H3v-47 Fab

SupramoleculeName: H3v-47 Fab / type: complex / ID: 2 / Parent: 1
Details: H3v-47 Fab in complex with A/Minnesota/11/2010 H3N2v HA and FI6v Fab
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: human hybridoma cell line

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Supramolecule #3: FI6v Fab

SupramoleculeName: FI6v Fab / type: complex / ID: 3 / Parent: 1
Details: Negative-stain EM reconstruction of H3v-47 Fab in complex with A/Minnesota/11/2010 H3N2v HA and FI6v Fab
Source (natural)Organism: Human (human) / Strain: H3N2
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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
StainingType: NEGATIVE / Material: Uranyl formate
Details: The complex was diluted to 2ug/ml, applied to freshly glow discharged 400 mesh carbon coated copper grids, and negatively stained with 2% uranyl formate.
GridModel: EMS / Material: COPPER / Mesh: 400 / Support film - Material: CELLULOSE ACETATE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Carbon was evaporated upon grid prior to use.

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 20.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 24.7 e/Å2

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 1.1) / Number images used: 23175

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