REL PDBe PDBe PDBe 2007-09-07 2007-09-07 2008-01-02 2012-10-10 Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins Lok SM Lok SM Kostyuchenko V Nybakken GE Holdaway HA Battisti AJ Sukupolvi-Petty S Sedlak D Fremont DH Chipman PR Roehrig JT Diamond MS Kuhn RJ Rossmann MG Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. NAT.STRUCT.MOL.BIOL. 15 312 317 2008 18264114 doi:10.1038/nsmb.1382 2r6p FULLOVERLAP Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus The Fab molecule binds to two of the three E proteins in the icosahedral assymmetric unit 2 Dengue virus 2 Dengue virus 2 Homo sapiens VERTEBRATES envelope 240 3 VIRION SEROTYPE true false DENV Fab fragment of MAb 1A1D-2 Mus musculus House mouse hybridoma 50 50 2 heterodimer false singleParticle particle 0.6 7.6
12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
400 mesh copper grid
 ETHANE HOMEMADE PLUNGER
Vitrification instrument: Guillotine-style plunge freezeing device
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. FEI/PHILIPS CM200T FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 2.27 3.37 50000.0 51040.0 GATAN LIQUID NITROGEN 98 live FFT
low dose
2007-03-21 KODAK SO-163 FILM 7 24 Eucentric
each particle
 I OTHER 24.0 FSC 0.5 CUT-OFF spider,XMIPP 2885 emd_1418.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 -144 -144 -144 288 288 288 789.12 789.12 789.12 90 90 90 X Y Z -4.12769 8.46468 0.00957931 0.995975 2.74 2.74 2.74 1.98 This is a map of Fab 1A1D-2 complexed with Dengue virus
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 1THD 2 R 2 9 RIGID BODY FIT EMFIT
Protocol: Rigid body