+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2143 | |||||||||
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Title | Highly Conserved Protective Epitopes on Influenza B Viruses | |||||||||
Map data | Reconstruction of Influenza hemagglutinin (B/Florida/4/2006) complexed to neutralizing antibody (Fab CR8033) | |||||||||
Sample |
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Keywords | Influenza hemagglutinin (B/Florida/4/2006) / neutralizing antibody (Fab CR8033) / negative stained / single particle analysis | |||||||||
Biological species | Influenza B virus (B/Florida/4/2006) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.0 Å | |||||||||
Authors | Khayat R / Lee JH / Dreyfus C / Laursen NS / Wilson IA / Ward AB | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2143.map.gz | 14.2 MB | EMDB map data format | |
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Header (meta data) | emd-2143-v30.xml emd-2143.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_2143.png | 33.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2143 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2143 | HTTPS FTP |
-Validation report
Summary document | emd_2143_validation.pdf.gz | 210.6 KB | Display | EMDB validaton report |
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Full document | emd_2143_full_validation.pdf.gz | 209.7 KB | Display | |
Data in XML | emd_2143_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2143 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2143 | HTTPS FTP |
-Related structure data
Related structure data | 2144C 2145C 2146C 2147C 2148C 2149C 2150C 4fqhC 4fqiC 4fqjC 4fqkC 4fqlC 4fqmC 4fqvC 4fqyC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2143.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Influenza hemagglutinin (B/Florida/4/2006) complexed to neutralizing antibody (Fab CR8033) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Influenza hemagglutinin (B/Florida/4/2006), neutralizing antibody...
Entire | Name: Influenza hemagglutinin (B/Florida/4/2006), neutralizing antibody (Fab CR8033), negative stained, single particle analysis |
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Components |
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-Supramolecule #1000: Influenza hemagglutinin (B/Florida/4/2006), neutralizing antibody...
Supramolecule | Name: Influenza hemagglutinin (B/Florida/4/2006), neutralizing antibody (Fab CR8033), negative stained, single particle analysis type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Trimer of hemagglutinin bound to 3 Fabs / Number unique components: 2 |
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Molecular weight | Experimental: 282 KDa / Theoretical: 282 KDa / Method: Amino acid sequence |
-Macromolecule #1: Influenza hemagglutinin (B/Florida/4/2006)
Macromolecule | Name: Influenza hemagglutinin (B/Florida/4/2006) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Influenza B virus (B/Florida/4/2006) / synonym: Influenza |
Molecular weight | Experimental: 49 KDa / Theoretical: 49 KDa |
Recombinant expression | Organism: Sf9 / Recombinant plasmid: pDCE198 |
-Macromolecule #2: neutralizing antibody (Fab CR8033)
Macromolecule | Name: neutralizing antibody (Fab CR8033) / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Oligomeric state: 3 monomers / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 45 KDa / Theoretical: 45 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 / Details: 20 mM HEPES 8.0, 50mM NaCl |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on Nano-W for 30 seconds |
Grid | Details: 400 mesh gold grid with thin carbon support, glow discharged in amylamine atmosphere |
Vitrification | Cryogen name: NONE / Chamber humidity: 18 % / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Details | Weak beam illumination |
Date | Jan 12, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 10.9 µm / Number real images: 220 / Average electron dose: 16 e/Å2 / Od range: 1.4 / Bits/pixel: 16 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected using DoG Picker and processed using a combination of EMAN2 and Sparx. |
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CTF correction | Details: Each Particle |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, and, Sparx / Number images used: 11195 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Molrep, Chimera |
Details | Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Molrep, Chimera |
Details | Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |