1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Barbault, F. Huynh-Dinh, T. Paoletti, J. Lancelot, G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking US J.Biomol.Struct.Dyn. JBSDD6 0646 0739-1102 19 649 658 11843626 A new peculiar DNA structure: NMR solution structure of a DNA kissing complex. 2002 10.2210/pdb1jua/pdb pdb_00001jua 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 dSL1 stable dimer 7091.574 5'-D(*CP*TP*TP*GP*CP*TP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' 2 syn polymer no no (DC)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DA)(DG)(DC)(DG)(DC)(DG)(DC)(DA)(DC)(DG)(DG)(DC) (DA)(DA)(DG) CTTGCTGAAGCGCGCACGGCAAG A,B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n -0.459 1 19 A 1 A 23 -0.869 A_DC1:DG23_A 1 -6.666 -0.317 -0.770 -0.212 -0.792 1 20 A 2 A 22 -18.829 A_DT2:DA22_A 2 -10.596 0.375 -0.670 -0.141 5.682 1 20 A 3 A 21 -19.687 A_DT3:DA21_A 3 -9.867 0.679 -1.103 -0.239 -4.781 1 19 A 4 A 20 -2.240 A_DG4:DC20_A 4 -0.289 0.549 -1.387 -0.417 4.618 1 19 A 5 A 19 -1.845 A_DC5:DG19_A 5 -3.574 -0.595 -1.796 -0.600 2.687 1 28 A 6 A 18 2.804 A_DT6:DG18_A 6 -1.396 2.048 -0.682 -0.224 1.063 1 19 A 7 A 17 1.194 A_DG7:DC17_A 7 -8.478 0.034 0.111 -0.055 26.687 1 B 9 A 16 33.659 B_DA9:DA16_A 8 50.625 -1.134 1.658 0.116 4.426 1 19 B 10 A 15 3.049 B_DG10:DC15_A 9 19.771 0.487 1.574 -0.605 1.288 1 19 B 11 A 14 -0.314 B_DC11:DG14_A 10 19.524 -0.313 -1.207 -0.197 3.171 1 19 B 12 A 13 -0.206 B_DG12:DC13_A 11 23.743 -0.073 -0.815 -0.104 -3.556 1 19 B 13 A 12 -0.471 B_DC13:DG12_A 12 23.769 0.110 -0.782 -0.105 -1.082 1 19 B 14 A 11 -0.471 B_DG14:DC11_A 13 19.691 0.432 -1.217 -0.189 -6.793 1 19 B 15 A 10 3.300 B_DC15:DG10_A 14 21.097 -0.418 1.544 -0.553 -0.283 1 19 B 1 B 23 -1.255 B_DC1:DG23_B 15 -6.174 -0.372 -0.889 -0.232 -0.823 1 20 B 2 B 22 -19.182 B_DT2:DA22_B 16 -10.473 0.370 -0.674 -0.131 5.779 1 20 B 3 B 21 -20.066 B_DT3:DA21_B 17 -9.946 0.686 -1.110 -0.231 -5.002 1 19 B 4 B 20 -2.202 B_DG4:DC20_B 18 -0.330 0.578 -1.398 -0.410 5.294 1 19 B 5 B 19 -1.786 B_DC5:DG19_B 19 -2.758 -0.589 -1.802 -0.580 3.231 1 28 B 6 B 18 4.346 B_DT6:DG18_B 20 -2.841 2.167 -0.678 -0.258 0.866 1 19 B 7 B 17 0.321 B_DG7:DC17_B 21 -5.473 0.087 -0.366 -0.090 3.605 42.025 A A 1 2 -0.084 A A 23 22 3.611 -0.060 -0.774 0.212 AA_DC1DT2:DA22DG23_AA 1 0.292 -0.407 42.024 0.303 1.112 2.891 36.987 A A 2 3 -5.760 A A 22 21 2.839 -3.644 0.114 -0.682 AA_DT2DT3:DA21DA22_AA 2 3.182 -5.030 36.680 -0.643 0.197 4.320 35.981 A A 3 4 -6.450 A A 21 20 4.268 -3.977 1.161 -0.617 AA_DT3DG4:DC20DA21_AA 3 0.326 -0.528 35.766 -0.253 -1.818 2.817 36.201 A A 4 5 9.122 A A 20 19 2.882 5.642 0.085 -0.201 AA_DG4DC5:DG19DC20_AA 4 2.606 -4.214 35.681 -1.020 0.185 3.768 43.234 A A 5 6 5.777 A A 19 18 3.799 4.247 0.455 0.230 AA_DC5DT6:DG18DG19_AA 5 -2.798 3.806 42.948 -0.170 -0.935 4.084 27.864 A A 6 7 -12.433 A A 18 17 4.012 -5.941 -0.154 -0.755 AA_DT6DG7:DC17DG18_AA 6 -1.371 2.869 27.202 0.211 -0.090 2.751 67.004 A B 7 9 31.074 A A 17 16 3.210 33.067 -2.127 -0.611 AB_DG7DA9:DA16DC17_AA 7 -5.821 5.470 58.853 -1.836 1.701 4.254 51.630 B B 9 10 44.146 A A 16 15 4.781 34.888 -1.773 1.894 BB_DA9DG10:DC15DA16_AA 8 12.732 -16.111 36.521 -1.760 3.472 1.718 24.134 B B 10 11 49.672 A A 15 14 4.812 17.687 -0.115 -1.313 BB_DG10DC11:DG14DC15_AA 9 9.343 -26.240 13.572 -10.419 4.119 0.664 26.074 B B 11 12 66.841 A A 14 13 4.163 23.690 -0.749 -1.163 BB_DC11DG12:DC13DG14_AA 10 -4.882 13.773 9.810 -9.609 0.211 -0.535 34.765 B B 12 13 70.317 A A 13 12 3.917 32.675 0.016 -2.040 BB_DG12DC13:DG12DC13_AA 11 -0.079 0.170 12.038 -7.338 -0.036 0.655 26.295 B B 13 14 66.736 A A 12 11 4.141 23.834 0.757 -1.171 BB_DC13DG14:DC11DG12_AA 12 5.272 -14.763 9.851 -9.495 -0.132 1.797 23.294 B B 14 15 49.419 A A 11 10 5.005 16.957 0.166 -1.298 BB_DG14DC15:DG10DC11_AA 13 -9.379 27.334 12.990 -11.039 -4.739 3.644 42.281 B B 1 2 -0.416 B B 23 22 3.643 -0.300 -0.791 0.216 BB_DC1DT2:DA22DG23_BB 14 -0.134 0.186 42.280 0.334 1.081 2.880 36.969 B B 2 3 -6.609 B B 22 21 2.822 -4.178 0.122 -0.682 BB_DT2DT3:DA21DA22_BB 15 3.197 -5.058 36.606 -0.583 0.186 4.377 36.652 B B 3 4 -9.275 B B 21 20 4.325 -5.809 1.204 -0.609 BB_DT3DG4:DC20DA21_BB 16 0.311 -0.497 36.203 0.098 -1.858 2.838 36.007 B B 4 5 7.545 B B 20 19 2.885 4.648 0.060 -0.167 BB_DG4DC5:DG19DC20_BB 17 2.674 -4.340 35.619 -0.852 0.237 3.839 44.004 B B 5 6 2.775 B B 19 18 3.870 2.077 0.550 0.278 BB_DC5DT6:DG18DG19_BB 18 -2.708 3.618 43.878 0.140 -1.035 4.114 28.702 B B 6 7 -9.450 B B 18 17 4.094 -4.665 -0.410 -0.480 BB_DT6DG7:DC17DG18_BB 19 0.237 -0.481 28.327 0.359 0.895 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2004-01-20 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name Solution structure of HIV-1Lai mutated SL1 hairpin NMR solution structure of a DNA kissing complex Dimer initiation sequence of HIV-1Lai genomic RNA : NMR solution structure of the extended duplex RCSB Y RCSB 2001-08-24 REL This structure was determined using standard 2D homonuclear techniques. back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy 13 13 2D NOESY 2D NOESY DQF-COSY 50mM NaCl 5.8 ambient 278 K 50mM NaCl 5.8 ambient 300 K Simulated annealing Relaxation matrix refinement Chemical shifts back-calculation refinement 9 lowest energy 2.7mM oligonucleotide 10 mM phosphate buffer 50 mM NaCl 90% H2O/10% D2O 2.7mM oligonucleotide 10 mM phosphate buffer 50 mM NaCl 100% D2O collection VNMR processing VNMR Brunger structure solution CNS 1.0 Lancelot iterative matrix relaxation RELAZ 1.0 Wijmenga refinement NUCHEMICS 600 Varian INOVA CYT 1 n 1 DC 1 A THY 2 n 2 DT 2 A THY 3 n 3 DT 3 A GUA 4 n 4 DG 4 A CYT 5 n 5 DC 5 A THY 6 n 6 DT 6 A GUA 7 n 7 DG 7 A ADE 8 n 8 DA 8 A ADE 9 n 9 DA 9 A GUA 10 n 10 DG 10 A CYT 11 n 11 DC 11 A GUA 12 n 12 DG 12 A CYT 13 n 13 DC 13 A GUA 14 n 14 DG 14 A CYT 15 n 15 DC 15 A ADE 16 n 16 DA 16 A CYT 17 n 17 DC 17 A GUA 18 n 18 DG 18 A GUA 19 n 19 DG 19 A CYT 20 n 20 DC 20 A ADE 21 n 21 DA 21 A ADE 22 n 22 DA 22 A GUA 23 n 23 DG 23 A CYT 1 n 1 DC 1 B THY 2 n 2 DT 2 B THY 3 n 3 DT 3 B GUA 4 n 4 DG 4 B CYT 5 n 5 DC 5 B THY 6 n 6 DT 6 B GUA 7 n 7 DG 7 B ADE 8 n 8 DA 8 B ADE 9 n 9 DA 9 B GUA 10 n 10 DG 10 B CYT 11 n 11 DC 11 B GUA 12 n 12 DG 12 B CYT 13 n 13 DC 13 B GUA 14 n 14 DG 14 B CYT 15 n 15 DC 15 B ADE 16 n 16 DA 16 B CYT 17 n 17 DC 17 B GUA 18 n 18 DG 18 B GUA 19 n 19 DG 19 B CYT 20 n 20 DC 20 B ADE 21 n 21 DA 21 B ADE 22 n 22 DA 22 B GUA 23 n 23 DG 23 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A A O4 H61 DT DA 2 22 1.58 1 B B O4 H61 DT DA 2 22 1.58 2 B B O4 H61 DT DA 2 22 1.58 3 A A O4 H61 DT DA 2 22 1.59 4 A A O4 H61 DT DA 2 22 1.58 5 A A O4 H61 DT DA 2 22 1.58 6 B B O4 H61 DT DA 2 22 1.58 6 A A O4 H61 DT DA 2 22 1.58 7 B B O4 H61 DT DA 2 22 1.58 7 A A O4 H61 DT DA 2 22 1.58 9 A A H1 H41 DG DC 7 17 0.91 9 B B H1 H41 DG DC 7 17 0.93 9 B B H41 H1 DC DG 1 23 1.01 9 A A H41 H1 DC DG 1 23 1.01 9 A B H41 H1 DC DG 13 12 1.02 9 A B H1 H41 DG DC 12 13 1.03 9 B B H1 H41 DG DC 4 20 1.12 9 A A H1 H41 DG DC 4 20 1.13 9 A B H41 H1 DC DG 11 14 1.19 9 A B H1 H41 DG DC 14 11 1.22 9 A B H61 H61 DA DA 9 16 1.27 9 A B H61 H61 DA DA 16 9 1.27 9 A A H3 H61 DT DA 3 21 1.28 9 B B H3 H61 DT DA 3 21 1.28 9 B B H41 H1 DC DG 5 19 1.29 9 A A H41 H1 DC DG 5 19 1.30 9 A B N3 H21 DC DG 13 12 1.36 9 A B H21 N3 DG DC 12 13 1.36 9 B B N3 H21 DC DG 1 23 1.37 9 A A N3 H21 DC DG 1 23 1.37 9 A A H21 N3 DG DC 4 20 1.39 9 A A H21 N3 DG DC 7 17 1.39 9 B B H21 N3 DG DC 4 20 1.39 9 B B H21 N3 DG DC 7 17 1.39 9 A B H21 N3 DG DC 10 15 1.41 9 A B N3 H21 DC DG 15 10 1.43 9 B B N3 H21 DC DG 5 19 1.44 9 A A N3 H21 DC DG 5 19 1.44 9 A B N3 H21 DC DG 11 14 1.50 9 A B H21 N3 DG DC 14 11 1.50 9 B B H41 N1 DC DG 1 23 1.51 9 A A H41 N1 DC DG 1 23 1.51 9 A B H41 N1 DC DG 13 12 1.52 9 A A N1 H41 DG DC 7 17 1.52 9 A B N1 H41 DG DC 12 13 1.52 9 B B N1 H41 DG DC 7 17 1.52 9 B B N1 H41 DG DC 4 20 1.55 9 A A N1 H41 DG DC 4 20 1.55 9 A B O6 N1 DG DA 14 8 2.05 9 A B N1 O6 DA DG 8 14 2.12 9 A B N2 N3 DG DC 10 15 2.18 9 A B N3 N2 DC DG 15 10 2.19 10 A A O4 H61 DT DA 2 22 1.58 11 B B O4 H61 DT DA 2 22 1.58 12 B B O4 H61 DT DA 2 22 1.58 9 A DC 11 0.081 SIDE CHAIN 9 A DG 12 0.067 SIDE CHAIN 9 A DC 13 0.112 SIDE CHAIN 9 B DC 11 0.084 SIDE CHAIN 9 B DG 12 0.069 SIDE CHAIN 9 B DC 13 0.112 SIDE CHAIN 9 2.29 0.30 108.30 110.59 A A A O4' C1' N9 DG DG DG 12 12 12 N 9 2.72 0.30 108.30 111.02 A A A O4' C1' N1 DC DC DC 13 13 13 N 9 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DC DC DC 15 15 15 N 9 2.33 0.30 108.30 110.63 B B B O4' C1' N9 DG DG DG 12 12 12 N 9 2.71 0.30 108.30 111.01 B B B O4' C1' N1 DC DC DC 13 13 13 N 9 2.11 0.30 108.30 110.41 B B B O4' C1' N1 DC DC DC 15 15 15 N Solution Structure of the Deoxyribose HIV-1Lai Initiation Sequence Stable Dimer 1 N N 1 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 23 A N1 DG 23 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 23 A O6 DG 23 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 23 A N2 DG 23 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 A DA 22 A N1 DA 22 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 A DA 22 A N6 DA 22 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 A DA 21 A N1 DA 21 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 A DA 21 A N6 DA 21 1_555 hydrog DT-DA PAIR A DT 3 A N3 DT 3 1_555 A DA 22 A N1 DA 22 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 20 A N3 DC 20 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 20 A O2 DC 20 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 20 A N4 DC 20 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 19 A N1 DG 19 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 19 A O6 DG 19 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 19 A N2 DG 19 1_555 hydrog TYPE_28_PAIR A DT 6 A N3 DT 6 1_555 A DG 18 A O6 DG 18 1_555 hydrog TYPE_28_PAIR A DT 6 A O2 DT 6 1_555 A DG 18 A N1 DG 18 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 A DC 17 A N3 DC 17 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 A DC 17 A O2 DC 17 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 A DC 17 A N4 DC 17 1_555 hydrog DA-DC MISPAIR A DA 8 A N3 DA 8 1_555 B DC 15 B N4 DC 15 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 15 B N3 DC 15 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 15 B O2 DC 15 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 15 B N4 DC 15 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 14 B N1 DG 14 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 14 B O6 DG 14 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 14 B N2 DG 14 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 13 B N3 DC 13 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 13 B O2 DC 13 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 13 B N4 DC 13 1_555 hydrog WATSON-CRICK A DC 13 A N3 DC 13 1_555 B DG 12 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 13 A N4 DC 13 1_555 B DG 12 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 13 A O2 DC 13 1_555 B DG 12 B N2 DG 12 1_555 hydrog WATSON-CRICK A DG 14 A N1 DG 14 1_555 B DC 11 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 14 A N2 DG 14 1_555 B DC 11 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 14 A O6 DG 14 1_555 B DC 11 B N4 DC 11 1_555 hydrog DC-DA MISPAIR A DC 15 A N4 DC 15 1_555 B DA 8 B N3 DA 8 1_555 hydrog WATSON-CRICK A DC 15 A N3 DC 15 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 15 A N4 DC 15 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 15 A O2 DC 15 1_555 B DG 10 B N2 DG 10 1_555 hydrog DA-DA MISPAIR A DA 16 A N1 DA 16 1_555 B DA 9 B N6 DA 9 1_555 hydrog WATSON-CRICK B DC 1 B N3 DC 1 1_555 B DG 23 B N1 DG 23 1_555 hydrog WATSON-CRICK B DC 1 B N4 DC 1 1_555 B DG 23 B O6 DG 23 1_555 hydrog WATSON-CRICK B DC 1 B O2 DC 1 1_555 B DG 23 B N2 DG 23 1_555 hydrog WATSON-CRICK B DT 2 B N3 DT 2 1_555 B DA 22 B N1 DA 22 1_555 hydrog WATSON-CRICK B DT 2 B O4 DT 2 1_555 B DA 22 B N6 DA 22 1_555 hydrog WATSON-CRICK B DT 3 B N3 DT 3 1_555 B DA 21 B N1 DA 21 1_555 hydrog WATSON-CRICK B DT 3 B O4 DT 3 1_555 B DA 21 B N6 DA 21 1_555 hydrog DT-DA PAIR B DT 3 B N3 DT 3 1_555 B DA 22 B N1 DA 22 1_555 hydrog WATSON-CRICK B DG 4 B N1 DG 4 1_555 B DC 20 B N3 DC 20 1_555 hydrog WATSON-CRICK B DG 4 B N2 DG 4 1_555 B DC 20 B O2 DC 20 1_555 hydrog WATSON-CRICK B DG 4 B O6 DG 4 1_555 B DC 20 B N4 DC 20 1_555 hydrog WATSON-CRICK B DC 5 B N3 DC 5 1_555 B DG 19 B N1 DG 19 1_555 hydrog WATSON-CRICK B DC 5 B N4 DC 5 1_555 B DG 19 B O6 DG 19 1_555 hydrog WATSON-CRICK B DC 5 B O2 DC 5 1_555 B DG 19 B N2 DG 19 1_555 hydrog TYPE_28_PAIR B DT 6 B N3 DT 6 1_555 B DG 18 B O6 DG 18 1_555 hydrog TYPE_28_PAIR B DT 6 B O2 DT 6 1_555 B DG 18 B N1 DG 18 1_555 hydrog WATSON-CRICK B DG 7 B N1 DG 7 1_555 B DC 17 B N3 DC 17 1_555 hydrog WATSON-CRICK B DG 7 B N2 DG 7 1_555 B DC 17 B O2 DC 17 1_555 hydrog WATSON-CRICK B DG 7 B O6 DG 7 1_555 B DC 17 B N4 DC 17 1_555 DNA HIV, SL1, DNA, kissing-complex, loop-loop dimer, stable dimer 1JUA PDB 1 1JUA 1 23 1JUA 1 23 1JUA A 1 1 23 1 23 1JUA 1 23 1JUA B 1 1 23