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- EMDB-2146: Electron microscopy of Influenza hemagglutinin (Malaysia/2506/200... -

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Basic information

Entry
Database: EMDB / ID: EMD-2146
TitleElectron microscopy of Influenza hemagglutinin (Malaysia/2506/2004) in complex with neutralizing antibody (Fab CR9114
Map dataInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
Sample
  • Sample: Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
  • Protein or peptide: Influenza Hemagglutinin
KeywordsInfluenza hemagglutinin (Malaysia/2506/2004) / neutralizing antibody (Fab CR9114) / negative stained / single particle analysis
Biological speciesInfluenza B virus (B/Malaysia/2506/2004)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsKhayat R / Lee JH / Ekiert DC / Dreyfus C / Wilson IA / Ward AB
CitationJournal: Science / Year: 2012
Title: Highly conserved protective epitopes on influenza B viruses.
Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt ...Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt / Mohammed Lamrani / Hans J W M Korse / Eric Geelen / Özcan Sahin / Martijn Sieuwerts / Just P J Brakenhoff / Ronald Vogels / Olive T W Li / Leo L M Poon / Malik Peiris / Wouter Koudstaal / Andrew B Ward / Ian A Wilson / Jaap Goudsmit / Robert H E Friesen /
Abstract: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. ...Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.
History
DepositionJun 26, 2012-
Header (metadata) releaseJul 9, 2012-
Map releaseAug 22, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / 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_2146.png

Downloads & links

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Map

FileDownload / File: emd_2146.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 160 pix.
= 348.8 Å		2.18 Å/pix.
x 160 pix.
= 348.8 Å		2.18 Å/pix.
x 160 pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6 / Movie #1: 3.6
Minimum - Maximum-10.304110530000001 - 20.881387709999998
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-10.30420.8810.000

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Supplemental data

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Sample components

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Entire : Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibo...

EntireName: Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
Components
  • Sample: Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
  • Protein or peptide: Influenza Hemagglutinin

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Supramolecule #1000: Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibo...

SupramoleculeName: Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
type: sample / ID: 1000 / Details: The sample was monodisperse
Oligomeric state: One trimer of hemagglutining binds to three Fabs
Number unique components: 2
Molecular weightExperimental: 282 KDa / Theoretical: 282 KDa / Method: Amino acid sequence

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Macromolecule #1: Influenza Hemagglutinin

MacromoleculeName: Influenza Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Influenza B virus (B/Malaysia/2506/2004) / synonym: Influenza
Molecular weightExperimental: 49 KDa / Theoretical: 49 KDa
Recombinant expressionOrganism: Sf9 / Recombinant plasmid: pDCE198

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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

Concentration0.1 mg/mL
BufferpH: 8 / Details: 20 mM HEPES 8.0, 50mM NaCl
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl formate for 30 seconds
GridDetails: 400 mesh gold grid with thin carbon support, glow discharged in amylamine atmosphere
VitrificationCryogen name: NONE / Chamber humidity: 18 % / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateJul 18, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 10.9 µm / Number real images: 200 / Average electron dose: 16 e/Å2 / Od range: 1.4 / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using DoG Picker and processed using a combination of EMAN2 and Sparx.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, and, Sparx / Number images used: 7128

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Atomic model buiding 1

Initial modelPDB ID:

4fqh

SoftwareName: Molrep, Chimera
DetailsProtocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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Atomic model buiding 2

Initial modelPDB ID:

4fqk

SoftwareName: Molrep, Chimera
DetailsProtocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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