|Entry||Database: EMDB / ID: 1418|
|Title||Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins|
|Sample||Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus|
|Source||Dengue virus 2 / virus / DENV|
Mus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /
|Map data||This is a map of Fab 1A1D-2 complexed with Dengue virus|
|Method||single particle (icosahedral) reconstruction, at 24 Å resolution|
|Citation||Nat. Struct. Mol. Biol., 2008, 15, 312-317|
Nat. Struct. Mol. Biol., 2008, 15, 312-317 Yorodumi Papers
|Validation Report||PDB-ID: 2r6p|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 7, 2007 / Header (metadata) release: Sep 7, 2007 / Map release: Jan 2, 2008 / Last update: Oct 10, 2012|
Downloads & links
|File||emd_1418.map.gz (map file in CCP4 format, 93313 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.74 Å|
CCP4 map header:
-Entire Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
|Entire||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, Dengue virus 2
|Virus||Name: Dengue virus 2 / a.k.a: DENV / Class: VIRION / Enveloped: Yes / Empty: No / Isolate: SEROTYPE|
|Species||Species: Dengue virus 2 / virus / DENV|
|Source (natural)||Host Species: Homo sapiens / human / Host category: VERTEBRATES|
|Shell #1||Name of element: envelope / Diameter: 240 Å / T number(triangulation number): 3|
-Component #2: protein, Fab fragment of MAb 1A1D-2
|Protein||Name: Fab fragment of MAb 1A1D-2 / a.k.a: 1A1D-2 / Oligomeric Details: heterodimer / Recombinant expression: No / Number of Copies: 2|
|Mass||Theoretical: 50 MDa / Experimental: 50 MDa|
|Source||Species: Mus musculus / mammal / House mouse / ハツカネズミ, はつかねずみ /|
|Source (natural)||Cell: hybridoma|
|Sample solution||Specimen conc.: 0.6 mg/ml / Buffer solution: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA / pH: 7.6|
|Support film||400 mesh copper grid|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE|
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
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200T / Date: Mar 21, 2007 / Details: low dose|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 51040 X (calibrated) / Astigmatism: live FFT / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2270 - 3370 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Sampling size: 7 microns|
|Processing||Method: single particle (icosahedral) reconstruction / Number of projections: 2885 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: projection matching / Software: spider,XMIPP / CTF correction: each particle / Resolution: 24 Å / Resolution method: FSC 0.5|
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