2024-07-24 REL PDBe PDBe PDBe 2022-04-28 2022-05-11 2022-05-11 2024-07-24 2022-06-29 EMD-4138 The Francis Crick Institute FC001061 United Kingdom Wellcome Trust FC001061 United Kingdom Medical Research Council (MRC, United Kingdom) FC001061 United Kingdom Cancer Research UK FC001061 United Kingdom MVV cleaved synaptic complex (CSC) intasome at 4.5 A resolution (re-refined) Ballandras-Colas A Maskell D Pye VE Locke J Swuec S Kotecha A Costa A Cherepanov P Integrase, intasome, MVV, nucleoprotein complex, retrovirus, VIRAL PROTEIN 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 7zpp FULLOVERLAP Maedi-visna virus (MVV) intasome Maedi-visna virus (MVV) intasome 0 1 2 3 0.54245 Intergrase 1 1 Visna/maedi virus EV1 KV1772 vDNA 1 2 3 Visna-maedi virus Integrase Visna/maedi virus EV1 KV1772 KV1772 0.032368825999999996 16 Escherichia coli LEVO WIENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGIDHWQVDYTHYEDKIILVWVE TNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNGPAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTL KNTLEKLIPMFNAFESALAGTLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQEKIRFCYYRTRKRGHPGEWQGP TQVLWGGDGAIVVKDRGTDRYLVIANKDVKFIPPPKEIQKE P35956 2.7.7.- 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-maedi virus 0.0058157619999999995 2 (DC)(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DG)(DA)(DT)(DC)(DT)(DC)(DG)(DC)(DA) J04359.1 DNA singleParticle particle 0.3 6.5 1.0 NaCl Sodium Chloride 3.0 CaCl2 Calcium Chloride 25.0 BisTris-HCl
1 M NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl, pH 6.5
 PELCO Ultrathin Carbon with Lacey Carbon CARBON CONTINUOUS GLOW DISCHARGE ETHANE 100 293.15 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..
A 4 ul drop of freshly prepared intasome in 1 M NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 was applied onto glow-discharged lacey carbon grids coated with ultrathin carbon (product 01824, Ted Pella). The grids were incubated for 30 s under 100% humidity in a Vitrobot Mark IV (FEI) at 20 oC. 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 3.5 5.0 GATAN K2 SUMMIT (4k x 4k) 50.0 1 253785
ab-initio in cryoSPARC
 1 C2 FOURIER SPACE 4.5 FSC 0.143 CUT-OFF cryoSPARC 2
Non Uniform Refinement in cryoSPARC-2
128974 PROJECTION MATCHING PROJECTION MATCHING RELION 3.1 cryoSPARC 2 emd_14860.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 428.99997 428.99997 428.99997 90.0 90.0 90.0 X Y Z -0.0017862628 2.0413592 0.0012281933 0.026059164 1.43 1.43 1.43 0.122 AUTHOR deepEMnhancer map 5M0Q PDB experimental model OTHER
5M0Q model was docked to new map (updated relion version and pixel size corrected) in Chimera and refined using phenix.real_space refine and interactively adjusted in coot.
correlation coefficient REAL 100.0 emd_14860_msk_1.map emd_14860_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 428.99997 428.99997 428.99997 90.0 90.0 90.0 X Y Z -5.0856314 6.0379195 0.0051083043 0.07301147 1.43 1.43 1.43 AUTHOR cryosparc local filter map - to which model was fitted and refined against emd_14860_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 428.99997 428.99997 428.99997 90.0 90.0 90.0 X Y Z -0.24504276 1.3082557 0.0020462738 0.045030553 1.43 1.43 1.43 AUTHOR original map - no enhancement emd_14860_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 428.99997 428.99997 428.99997 90.0 90.0 90.0 X Y Z -0.31651217 1.3663691 0.002139969 0.053393226 1.43 1.43 1.43 AUTHOR emd_14860_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 428.99997 428.99997 428.99997 90.0 90.0 90.0 X Y Z -0.3013047 1.3727994 0.0021446936 0.053346537 1.43 1.43 1.43 AUTHOR Half map B