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Electron microscopy of Influenza hemagglutinin (Malaysia/2506/2004) in complex with neutralizing antibody (Fab CR9114
by single particle reconstruction, at 18 A resolution
#1: Surface view with section colored by density value, Surface level: 3.6, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 3.6, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2146 |
|---|---|
| Authors | Khayat R, Lee JH, Ekiert DC, Dreyfus C, Wilson IA, Ward AB |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 3.6, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 3.6, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Map | |||||||||||||||||||||||||
| File |  EMD-2146.map ( map file in CCP4 format, 16386 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 348.80002 A , B = 348.80002 A , C = 348.80002 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.18 A , Y = 2.18 A , Z = 2.18 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis |
|---|---|
| Number of Components | 2 |
| Oligomeric State | One trimer of hemagglutining binds to three Fabs |
| Theoretical Mass | 0.282 MDa |
| Details | The sample was monodisperse |
| Mass-estimation Method | Amino acid sequence |
| Experimental Mass | 0.282 MDa |
| Component #1: protein - Influenza Hemagglutinin | |
| Scientific name | Influenza Hemagglutinin |
| Theoretical Mass | 0.049 MDa |
| Experimental Mass | 0.049 MDa |
| Oligomeric Details | Trimer |
| Number of Copies | 3 |
| Scientific Name of Species | Influenza B virus (B/Malaysia/2506/2004) (NCBI Taxonomy: 464417) |
| Common Name of Species | Influenza |
| Recombinant expression | Yes |
| Engineered Source | Vector: pDCE198 Exp System: Sf9 |
 Experiment | |
| Sample Preparation | |
| Staining | Grids with adsorbed protein floated on 2% w/v uranyl formate for 30 seconds |
|---|---|
| Specimen Conc | 0.1 mg/ml |
| Specimen Support Details | 400 mesh gold grid with thin carbon support, glow discharged in amylamine atmosphere |
| Specimen State | particle |
| Buffer | Details: 20 mM HEPES 8.0, 50mM NaCl pH: 8 |
| Vitrification | |
| Cryogen Name | NONE |
| Humidity | 18 |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Date | 18-JUL-2011 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 120 kV |
| Electron Dose | 16 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 100000 X, Calibrated: 100000 X |
| Astigmatism | Objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 400 nm - 1200 nm |
| Specimen Holder | |
| Holder | ( SIDE ENTRY, EUCENTRIC ) |
| Tilt Angle | 0 degrees - 55 degrees |
| Camera | |
| Detector | Gatan Ultrascan 4000 |
| Image Acquisition | |
| Od Range | 1.4 |
| Number of Digital Images | 200 |
| Sampling Size | 10.9 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Common lines with EMAN2 |
| Software | EMAN2, and, Sparx |
| CTF Correction | Each particle |
| Resolution By Author | 18 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 7128 |
| Details | Particles were selected using DoG Picker and processed using a combination of EMAN2 and Sparx. |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep. |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Target Criteria | Correlation coefficient |
| Software | Molrep, Chimera |
| Model #1 | |
| Refinement Space | REAL |
| Target Criteria | Correlation coefficient |
| Refinement Protocol | rigid body |
| Details | Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep. |
| Software | Molrep, Chimera |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-2146.xml (9.1 KB) | ||
|---|---|---|---|
| Map data | emd_2146.map.gz (12.1 MB) | ||
| Images |  emd_2146.png (29.1 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2146 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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