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- EMDB-2149: Electron microscopy of Influenza hemagglutinin (Wisconsin/1/1966 ... -

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Basic information

Entry
Database: EMDB / ID: 2149
TitleElectron microscopy of Influenza hemagglutinin (Wisconsin/1/1966 (H9N2)) in complex with neutralizing antibody (Fab CR9114)
KeywordsInfluenza hemagglutinin (Wisconsin/1/1966 (H9N2))) / neutralizing antibody (Fab CR9114) / negative stained / single particle analysis
SampleInfluenza hemagglutinin (Wisconsin/1/1966 (H9N2)) in complex with neutralizing IgG antibody fragment(Fab CR9114)
SourceInfluenza A virus (A/turkey/Wisconsin/1/1966(H9N2)) / virus
Homo sapiens / human
Map dataInfluenza hemagglutinin (Wisconsin/1/1966 (H9N2))), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
Methodsingle particle reconstruction, at 14.8 Å resolution
AuthorsKhayat R / Meltagen Z / Ekiert DC / Dreyfus C / Wilson IA / Ward AB
CitationScience, 2012, 337, 1343-1348

Science, 2012, 337, 1343-1348 Yorodumi Papers
Highly conserved protective epitopes on influenza B viruses.
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

DateDeposition: Jun 26, 2012 / Header (metadata) release: Jul 9, 2012 / Map release: Aug 22, 2012 / Last update: Sep 26, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_2149.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.18 Å/pix.
= 348.8 Å
160 pix
2.18 Å/pix.
= 348.8 Å
160 pix
2.18 Å/pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.18 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-9.18911839 - 20.43391991
Average (Standard dev.)0E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
CellA=B=C: 348.80002 Å
α=β=γ: 90 deg.

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-9.18920.434-0.000

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Supplemental data

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Sample components

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Entire Influenza hemagglutinin (Wisconsin/1/1966 (H9N2)) in complex with...

EntireName: Influenza hemagglutinin (Wisconsin/1/1966 (H9N2)) in complex with neutralizing IgG antibody fragment(Fab CR9114)
Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: One hemagglutinin trimer binds 3 Fabs
MassTheoretical: 282 kDa / Experimental: 282 kDa / Measured by: Amino acid sequence

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Component #1: protein, Influenza hemagglutinin (Wisconsin/1/1966 (H9N2)))

ProteinName: Influenza hemagglutinin (Wisconsin/1/1966 (H9N2))) / Oligomeric Details: Trimer / Number of Copies: 3 / Recombinant expression: Yes
MassTheoretical: 49 kDa / Experimental: 49 kDa
SourceSpecies: Influenza A virus (A/turkey/Wisconsin/1/1966(H9N2)) / virus
Source (engineered)Expression System: Sf9 / Vector: pDCE198

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Component #2: protein, IgG Antibody fragment (Fab CR9114)

ProteinName: IgG Antibody fragment (Fab CR9114) / Oligomeric Details: 3 monomers / Recombinant expression: Yes / Number of Copies: 3
MassTheoretical: 45 kDa / Experimental: 45 kDa
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 20 mM HEPES 8.0, 50mM NaCl / pH: 8
Support film400 mesh gold grid with thin carbon support, glow discharged in amylamine atmosphere
StainingGrids with adsorbed protein floated on 2% w/v uranyl formate for 30 seconds.
VitrificationInstrument: NONE / Cryogen name: NONE / Humidity: 18 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: May 3, 2011 / Details: Weak beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 100000 X (nominal), 100000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 1200 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 55 deg.
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 165 / Sampling size: 10.9 microns / Bit depth: 16 / OD range: 1.4

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6629
Details: Particles were selected using DoG Picker and processed using a combination of EMAN2 and Sparx.
Applied symmetry: C3 (3 fold cyclic)
3D reconstructionAlgorithm: Cross-common lines / Software: EMAN2, and, Sparx / CTF correction: Each particle / Resolution: 14.8 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Molrep, Chimera / Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Details: Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
Input PDB model: 4FQH
Modeling #2Software: Molrep, Chimera / Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Details: Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
Input PDB model: 1JSD

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