2022-10-12 OBS PDBe PDBe PDBe 2016-10-05 2016-11-23 2017-01-18 2022-10-12 2022-10-12 National Institutes of Health GM082251 United States Cryo-EM reconstruction of the maedi-visna virus (MVV) intasome Ballandras-Colas A Maskell D Pye VE Locke J Swuec S Kotecha A Costa A Cherepanov P Ballandras-Colas A Maskell DP Serrao E Locke J Swuec P Jonsson SR Kotecha A Cook NJ Pye VE Taylor IA Andresdottir V Engelman AN Costa A Cherepanov P A supramolecular assembly mediates lentiviral DNA integration. Science US 355 93 95 2017 28059770 doi:10.1126/science.aah7002 1095-9203 0038 SCIEAS EMD-4138 associated EM volume
Cryo-EM reconstruction of the MVV intasome
 5m0q FULLOVERLAP MVV intasome MVV intasome 0 1 2 3 0.5 intergrase 1 1 Maedi visna virus (strain KV1772) Escherichia coli vDNA 1 2 3 Visna lentivirus (strain 1514) integrase Maedi visna virus KV1772 0.032368825999999996 16 Escherichia coli LEVO WIENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGIDHWQVDYTHYEDKIILVWVE TNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNGPAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTL KNTLEKLIPMFNAFESALAGTLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQEKIRFCYYRTRKRGHPGEWQGP TQVLWGGDGAIVVKDRGTDRYLVIANKDVKFIPPPKEIQKE 3.4.23.- vDNA, non-transferred strand Visna lentivirus (strain 1514) 0.006456145999999999 2 (DG)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DA)(DT)(DC)(DC)(DG)(DC)(DT)(DC)(DC)(DG)(DG)(DT) (DG) DNA vDNA, transferred strand Visna lentivirus (strain 1514) 0.0058157619999999995 2 (DC)(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DG)(DA)(DT)(DC)(DT)(DC)(DG)(DC)(DA) DNA singleParticle particle 0.3 6.5 1.0 NaCl sodium chroloride 3.0 CaCl2 calcium chloride 25.0 bis-tris Ted Pella, lacey carbon grids coated with ultrathin carbon COPPER 400 CARBON CONTINUOUS 2.0 GLOW DISCHARGE ETHANE 100 293 FEI VITROBOT MARK IV
To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s followed by plunging into liquid ethane..
FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 1651 1.0 1 253785 CTFFIND 4 RELION 1.4
Initial model was generated in EMAN2 using e2initialmodel.py from 2D class averages of particles stained with uranyl formate.
 1 C2 4.94 FSC 0.143 CUT-OFF RELION 1.4 94283 RANDOM ASSIGNMENT RELION 1.4 PROJECTION MATCHING RELION 1.4 3 84595.0 RELION 1.4 emd_4138.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.088338904 0.18512976 0.00044352724 0.004510368 1.35 1.35 1.35 0.03 EMDB FLEXIBLE FIT REAL emd_4138_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.075744145 0.16862665 0.0001557803 0.0048510125 1.35 1.35 1.35 EMDB emd_4138_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.01208165 0.051774345 7.969258e-05 0.002047399 1.35 1.35 1.35 EMDB emd_4138_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.009793107 0.050018147 8.158349e-05 0.0020542378 1.35 1.35 1.35 EMDB