2024-11-13 REL PDBe PDBe PDBe 2021-06-28 2021-12-08 2021-12-08 2024-11-13 Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment 166 at the transient P-pocket Singh AK Das K Reverse transcriptase, RT-aptamer complex, RT sliding, P-1 complex, P51, P66, TRANSFERASE Singh AK Martinez SE Gu W Nguyen H Schols D Herdewijn P De Jonghe S Das K Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening. Nat Commun UK 12 7127 7127 2021 34880240 doi:10.1038/s41467-021-27409-y 2041-1723 7ozw FULLOVERLAP HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment 166 at the transient P-pocket HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment 166 at the transient P-pocket 0 1 2 3 Human immunodeficiency virus type 1 BH10 0.1284 HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT 1 1 Human immunodeficiency virus type 1 BH10 HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT 1 2 Human immunodeficiency virus type 1 BH10 Reverse transcriptase/ribonuclease H Human immunodeficiency virus type 1 group M subtype B (isolate BH10) isolate BH10 0.06404739799999999 1 Escherichia coli BL21(DE3) LEVO MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFR ELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA IFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDK WTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVY YDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTE LQAIYLALQDSGLEVNIVTNSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA P03366 2.7.7.49 Reverse transcriptase/ribonuclease H Human immunodeficiency virus type 1 BH10 0.05003948799999999 1 Escherichia coli BL21(DE3) LEVO PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFREL NKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIF QSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYD PSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET WWTEYWQATWIPEWEFVNTPPLVKLWYQ P03366 2.7.7.49 DNA (37-MER) synthetic construct 0.011434332 1 (DT)(DA)(DA)(DT)(DA)(DT)(OMC)(DC)(OMC)(DC)(DC)(DC)(DT)(DT)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DT)(DT)(DG)(DC)(DA)(DC)(DC)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) DNA (1~{R},2~{R})-2-phenyl-~{N}-(1,3-thiazol-2-yl)cyclopropane-1-carboxamide 0.000244312 1 3IR singleParticle particle 0.4 8.0 10.0 NH2C(CH2OH)3HCl Tris-HCl 75.0 NaCl NaCl Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE AIR 0.03 ETHANE 95 281 LEICA EM GP TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 0.5 2.2 2.5 150000.0 NITROGEN FEI FALCON III (4k x 4k) COUNTING 1 660 55.0 50.0 1 856171 5HP1 C1 3.38 FSC 0.143 CUT-OFF RELION 3.1 146670 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_13139.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 125 125 125 0 0 0 125 125 125 121.25 121.25 121.25 90.0 90.0 90.0 X Y Z -0.26864 0.37287086 -0.00012455857 0.019520337 0.97 0.97 0.97 0.0193 AUTHOR 5HP1 PDB experimental model FLEXIBLE FIT Correlation coefficient REAL 140.199999999999989 emd_13139_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 125 125 125 0 0 0 125 125 125 121.25 121.25 121.25 90.0 90.0 90.0 X Y Z -0.05929247 0.10800058 -0.00013288972 0.0076172305 0.97 0.97 0.97 AUTHOR emd_13139_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 125 125 125 0 0 0 125 125 125 121.25 121.25 121.25 90.0 90.0 90.0 X Y Z -0.06376454 0.10978623 -0.00011015295 0.0076133073 0.97 0.97 0.97 AUTHOR