2024-07-10 REL PDBe PDBe PDBe 2019-06-05 2019-06-12 2020-02-05 2024-07-10 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM082251 United States The Francis Crick Institute FC001061 United Kingdom SIVrcm intasome in complex with dolutegravir Cherepanov P Nans A Cook N retroviral integrase, lentivirus, strand transfer inhibior, protein-DNA complex, RECOMBINATION Cook NJ Li W Berta D Badaoui M Ballandras-Colas A Nans A Kotecha A Rosta E Engelman AN Cherepanov P Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Science US 367 806 810 2020 32001525 doi:10.1126/science.aay4919 1095-9203 0038 SCIEAS 6rwn FULLOVERLAP SIVrcm intasome in complex with dolutegravir SIVrcm intasome in complex with dolutegravir 0 1 2 3 Pol protein 1 1 Simian immunodeficiency virus DNA 1 2 3 Simian immunodeficiency virus Pol protein Simian immunodeficiency virus 0.032732182 12 Escherichia coli LEVO GFLDGIEKAQEEHEKYHNNWRAMAEDFQIPQVVAKEIVAQCPKCQVKGEAMHGQVDASPKTWQMDCTHLEGKVIIVAVHV ASGYIEAEVLPAETGKETAHFLLKLAARWPVKHLHTDNGDNFTSSAVQAVCWWAQIEHTFGVPYNPQSQGVVESMNHQLK TIITQIRDQAEKIETAVQMAVLIHNFKRKGGIGGYSAGERIIDIIASDLQTTKLQNQISKIQNFRVYFREGRDQQWKGPA TLIWKGEGAVVIQDGQDLKVVPRRKCKIIKDYGRKDVDSETSMEGRQEKD E1ANT8 DNA (5'-D(*AP*AP*CP*TP*GP*GP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*TP*CP*TP*TP*AP*GP*C)-3') Simian immunodeficiency virus 0.010134540999999999 2 (DA)(DA)(DC)(DT)(DG)(DG)(DT)(DA)(DG)(DA)(DG)(DA)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DT) (DA)(DG)(DC)(DC)(DT)(DT)(DC)(DT)(DA)(DG)(DA)(DA)(DC) DNA DNA (5'-D(P*GP*CP*TP*AP*AP*GP*AP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*CP*CP*A)-3') Simian immunodeficiency virus 0.009223995 2 (DG)(DT)(DT)(DC)(DT)(DA)(DG)(DA)(DA)(DG)(DG)(DC)(DT)(DA)(DA)(DG)(DA)(DA)(DA)(DA) (DA)(DT)(DC)(DT)(DC)(DT)(DA)(DC)(DC)(DA) DNA ZINC ION 6.5409e-05 8 ZN CHLORIDE ION 3.5453e-05 2 CL (4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide 0.000419379 2 DLU MAGNESIUM ION 2.4305e-05 4 MG water 1.8015e-05 8 HOH singleParticle particle 7.0 0.35 NaCl sodium chloride 0.025 Hepes 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 0.005 MgSO4 magnesium sulfate ETHANE 95 295 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.6 3.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-30 1 6838 50.4 1
ab initio, as implemented in CryoSPARC
 C2 3.1 FSC 0.143 CUT-OFF cryoSPARC 2 18302 RANDOM ASSIGNMENT cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 12 RELION 2.1 emd_10043.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 496.8 496.8 496.8 90.0 90.0 90.0 X Y Z -3.603641 6.915492 0.0013935855 0.18609895 1.38 1.38 1.38 0.3 AUTHOR Map sharpened with B factor -110 2B4J PDB experimental model 1EX4 PDB experimental model 1K6Y PDB experimental model RIGID BODY FIT REAL emd_10043_msk_1.map emd_10043_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 496.8 496.8 496.8 90.0 90.0 90.0 X Y Z -0.54521465 1.9739817 0.00023452348 0.04148641 1.38 1.38 1.38 AUTHOR Unsharpened CryoSPARC map emd_10043_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 496.8 496.8 496.8 90.0 90.0 90.0 X Y Z -1.3741342 3.4012923 0.00023447235 0.05379182 1.38 1.38 1.38 AUTHOR Locally filtered autosharpened CryoSPARC map emd_10043_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 496.8 496.8 496.8 90.0 90.0 90.0 X Y Z -0.6840058 2.3466396 0.0013925403 0.083220765 1.38 1.38 1.38 AUTHOR Half map B emd_10043_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 496.8 496.8 496.8 90.0 90.0 90.0 X Y Z -0.7193294 2.242569 0.0013946309 0.08318247 1.38 1.38 1.38 AUTHOR Half map A