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- EMDB-5794: A common solution to group 2 influenza virus neutralization -

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Entry
Database: EMDB / ID: EMD-5794
TitleA common solution to group 2 influenza virus neutralization
Map data
SampleInfluenza (A/Bangkok/1/1979, H3N2) hemagglutinin bound to neutralizing antibody CR8043
  • CR8043 Fab
  • Influenza A/Bangkok/1/1979 (H3N2) hemagglutinin
KeywordsAntibody recognition / Hemagglutinin
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 23 Å
AuthorsFriesen RHE / Leeb PS / Stoop EJM / Hoffman RMB / Ekiert DC / Bhabha G / Yu W / Juraszek J / Koudstaal W / Jongeneelen M / Korse HJWM / Ophorst C / Brinkman-van der Linden ECM / Throsby M / Kwakkenbos MJ / Bakkerd AQ / Beaumont Y / Spits H / Kwaks T / Vogels R / Ward AB / Goudsmit J / Wilson IA
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: A common solution to group 2 influenza virus neutralization.
Authors: Robert H E Friesen / Peter S Lee / Esther J M Stoop / Ryan M B Hoffman / Damian C Ekiert / Gira Bhabha / Wenli Yu / Jarek Juraszek / Wouter Koudstaal / Mandy Jongeneelen / Hans J W M Korse / Carla Ophorst / Els C M Brinkman-van der Linden / Mark Throsby / Mark J Kwakkenbos / Arjen Q Bakker / Tim Beaumont / Hergen Spits / Ted Kwaks / Ronald Vogels / Andrew B Ward / Jaap Goudsmit / Ian A Wilson /
Abstract: The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the ...The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the design of universal influenza vaccines. Only one human bnAb (CR8020) specifically recognizing group 2 influenza A viruses has been previously characterized that binds to a highly conserved epitope at the base of the hemagglutinin (HA) stem and has neutralizing activity against H3, H7, and H10 viruses. Here, we report a second group 2 bnAb, CR8043, which was derived from a different germ-line gene encoding a highly divergent amino acid sequence. CR8043 has in vitro neutralizing activity against H3 and H10 viruses and protects mice against challenge with a lethal dose of H3N2 and H7N7 viruses. The crystal structure and EM reconstructions of the CR8043-H3 HA complex revealed that CR8043 binds to a site similar to the CR8020 epitope but uses an alternative angle of approach and a distinct set of interactions. The identification of another antibody against the group 2 stem epitope suggests that this conserved site of vulnerability has great potential for design of therapeutics and vaccines.
DateDeposition: Nov 14, 2013 / Header (metadata) release: Dec 11, 2013 / Map release: Dec 11, 2013 / Update: Feb 17, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5794.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 192 pix.
= 393.6 Å
2.05 Å/pix.
x 192 pix.
= 393.6 Å
2.05 Å/pix.
x 192 pix.
= 393.6 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
Contour LevelBy AUTHOR: 10.699999999999999 / Movie #1: 10.7
Minimum - Maximum-22.681745530000001 - 48.457839970000002
Average (Standard dev.)0.02987161 (±2.88823533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
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-96-96-96
NC/NR/NS192192192
D min/max/mean-22.68248.4580.030

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Supplemental data

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Sample components

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Entire Influenza (A/Bangkok/1/1979, H3N2) hemagglutinin bound to neutral...

EntireName: Influenza (A/Bangkok/1/1979, H3N2) hemagglutinin bound to neutralizing antibody CR8043
Number of components: 2 / Oligomeric State: One HA trimer bound to three Fabs
MassTheoretical: 288 kDa

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Component #1: protein, CR8043 Fab

ProteinName: CR8043 Fab / Oligomeric Details: Monomer / Number of Copies: 3 / Recombinant expression: Yes
MassTheoretical: 44 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: unidentified baculovirus

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Component #2: protein, Influenza A/Bangkok/1/1979 (H3N2) hemagglutinin

ProteinName: Influenza A/Bangkok/1/1979 (H3N2) hemagglutinin / Oligomeric Details: trimer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 157 kDa
SourceSpecies: Influenza A virus / Strain: A/Hong Kong/1/1968
Source (engineered)Expression System: unidentified baculovirus

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: negative staining
Sample solutionSpecimen conc.: 0.01 mg/mL / Buffer solution: TBS / pH: 7.4
Support film400 mesh copper with nitrocellulose and thin layer of carbon
StainingSamples were applied to freshly glow-discharged grids and stained with 2% uranyl formate (20s seconds).
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Mar 26, 2013
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (calibrated)
Astigmatism: Objective lens astigmatism corrected at 100,000 times magnification.
Imaging mode: BRIGHT FIELD / Defocus: 1000 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 ° / Temperature: 293
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 206

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 7009
Details: Projection matching seeded with a low-pass filtered hemagglutinin
3D reconstructionAlgorithm: Projection matching / Software: Appion, Spider, Xmipp, Eman1, Sparx / Resolution: 23 Å / Resolution method: FSC 0.5, semi-independent

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