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- EMDB-5793: A common solution to group 2 influenza virus neutralization -

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Basic information

Entry
Database: EMDB / ID: EMD-5793
TitleA common solution to group 2 influenza virus neutralization
Map dataInfluenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutralizing antibody CR8043
Sample
  • Sample: Influenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutralizing antibody CR8043
  • Protein or peptide: CR8043 Fab
  • Protein or peptide: Influenza A/Hong Kong/1/1968 (H3N2) hemagglutinin
KeywordsAntibody recognition / Hemagglutinin
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsFriesen RHE / Leeb PS / Stoop EJM / Hoffman RMB / Ekiert DC / Bhabha G / Yu W / Juraszek J / Koudstaal W / Jongeneelen M ...Friesen 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 / ...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.
History
DepositionNov 14, 2013-
Header (metadata) releaseDec 11, 2013-
Map releaseDec 11, 2013-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5793_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5793.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfluenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutralizing antibody CR8043
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.08 / Movie #1: 8.08
Minimum - Maximum-15.70829487 - 35.731815339999997
Average (Standard dev.)0.0699385 (±1.80856657)
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-15.70835.7320.070

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Supplemental data

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Sample components

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Entire : Influenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutr...

EntireName: Influenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutralizing antibody CR8043
Components
  • Sample: Influenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutralizing antibody CR8043
  • Protein or peptide: CR8043 Fab
  • Protein or peptide: Influenza A/Hong Kong/1/1968 (H3N2) hemagglutinin

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Supramolecule #1000: Influenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutr...

SupramoleculeName: Influenza (A/Hong Kong/1/1968, H3N2) hemagglutinin bound to neutralizing antibody CR8043
type: sample / ID: 1000 / Oligomeric state: One HA trimer bound to three Fabs / Number unique components: 2
Molecular weightTheoretical: 288 KDa

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Macromolecule #1: CR8043 Fab

MacromoleculeName: CR8043 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 44 KDa
Recombinant expressionOrganism: unidentified baculovirus

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Macromolecule #2: Influenza A/Hong Kong/1/1968 (H3N2) hemagglutinin

MacromoleculeName: Influenza A/Hong Kong/1/1968 (H3N2) hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Influenza A virus / Strain: A/Hong Kong/1/1968
Molecular weightTheoretical: 157 KDa
Recombinant expressionOrganism: unidentified baculovirus

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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

Concentration0.01 mg/mL
BufferpH: 7.4 / Details: TBS
StainingType: NEGATIVE
Details: Samples were applied to freshly glow-discharged grids and stained with 2% uranyl formate (20 seconds).
GridDetails: 400 mesh copper with nitrocellulose and thin layer of carbon
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureAverage: 293 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism corrected at 100,000 times magnification.
DateMay 18, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 243
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55

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Image processing

DetailsProjection matching seeded with a low-pass filtered hemagglutinin
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: Appion, Spider, Xmipp, Eman1, Sparx / Number images used: 10033

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