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Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins
by single particle (icosahedral) reconstruction, at 24 A resolution
#1: Surface view with section colored by density value, Surface level: 1.98, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1.98, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-2r6p, Surface level: 1.98, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-2r6p, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1418 |
|---|---|
| Title | Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins |
| Map | This is a map of Fab 1A1D-2 complexed with Dengue virus |
| Sample | Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus |
| Authors | Lok SM |
| Date | Deposition: 2007-09-07, Header release: 2007-09-07, Map release: 2008-01-02, Last update: 2012-10-10 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.98, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1.98, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2r6p, Surface level: 1.98, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-2r6p, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Nat. Struct. Mol. Biol., Vol. 15, Issue 3, Page 312-7, Year 2008 |
|---|---|
| Title | Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. |
| Authors | Shee-Mei Lok, Victor Kostyuchenko, Grant E Nybakken, Heather A Holdaway, Anthony J Battisti, Soila Sukupolvi-Petty, Dagmar Sedlak, Daved H Fremont, Paul R Chipman, John T Roehrig, Michael S Diamond, Richard J Kuhn, Michael G Rossmann Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, USA. |
| Keywords |  Antibodies, Monoclonal (chemistry), Antibodies, Viral (chemistry), Binding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Dengue Virus (chemistry), Membrane Glycoproteins (chemistry), Neutralization Tests, Temperature |
| Links | DOI: 10.1038/nsmb.1382, PubMed: 18264114 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1418.map ( map file in CCP4 format, 95552 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 789.12 A , B = 789.12 A , C = 789.12 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.74 A , Y = 2.74 A , Z = 2.74 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a map of Fab 1A1D-2 complexed with Dengue virus | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus |
|---|---|
| Oligomeric State | The Fab molecule binds to two of the three E proteins in the icosahedral assymmetric unit |
| Number of Components | 2 |
| Component #1: virus - DENV | |
| Scientific name | Dengue virus 2 |
| Common Name | DENV |
| Scientific Name of Species | Dengue virus 2 (NCBI Taxonomy: 11060) |
| Common Name of Species | DENV |
| Enveloped | Yes |
| Empty | No |
| Class | VIRION |
| Isolate | SEROTYPE |
| Natural Source | Host Category: VERTEBRATES Host Species: Homo sapiens (NCBI Taxonomy: 9606) |
| Shell | Name Element: envelope T Number: 3 Diameter: 240 A |
| Component #2: protein - 1A1D-2 | |
| Scientific name | Fab fragment of MAb 1A1D-2 |
| Common Name | 1A1D-2 |
| Theoretical Mass | 50 MDa |
| Experimental Mass | 50 MDa |
| Oligomeric Details | heterodimer |
| Number of Copies | 2 |
| Scientific Name of Species | Mus musculus (NCBI Taxonomy: 10090)
|
| Common Name of Species | House mouse |
| Recombinant expression | No |
| Natural Source | Cell: hybridoma |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 0.6 mg/ml |
|---|---|
| Specimen Support Details | 400 mesh copper grid |
| Specimen State | particle |
| Buffer | Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA pH: 7.6 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Instrument | HOMEMADE PLUNGER |
| Method | A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope. |
| Details | Vitrification instrument: Guillotine-style plunge freezeing device |
| Imaging | |
| Microscope | FEI/PHILIPS CM200T |
| Date | 2007-03-21 |
| Details | low dose |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 24 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, Calibrated: 51040 X |
| Astigmatism | live FFT |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2270 nm - 3370 nm |
| Specimen Holder | |
| Holder | Eucentric ( GATAN LIQUID NITROGEN ) |
| Temperature | 98 Kelvin |
| Camera | |
| Detector | Kodak SO163 |
| Image Acquisition | |
| Sampling Size | 7 microns |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | projection matching |
| Software | spider,XMIPP |
| CTF Correction | each particle |
| Resolution By Author | 24 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 2885 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Refinement Protocol | rigid body |
| Software | EMFIT |
| Details | Protocol: Rigid body |
| Fitted Coordinate | |
| PDB entry ID | |
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