1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0001-7780-5278 Jones, C.P. 0000-0003-4549-1619 Ferre-D'Amare, A.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 90.00 90.00 90.00 1.00 1.00 1.00 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer K 1 39.098 POTASSIUM ION non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer C20 H24 N2 O2 324.417 Quinine (3alpha,8alpha,9R)-6'-methoxycinchonan-9-ol non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N O N 112 N H N 113 N H N 114 N K N 115 N MG N 116 N O N 117 R C N 118 S C N 119 S N N 120 N C N 121 N C N 122 N C N 123 R C N 124 N C N 125 N C N 126 S C N 127 N C Y 128 N C Y 129 N C Y 130 N C Y 131 N N Y 132 N C Y 133 N C Y 134 N C Y 135 N C Y 136 N C Y 137 N C N 138 N O N 139 N C N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N O N 165 N P N 166 N O N 167 N O N 168 N O N 169 N C N 170 R C N 171 N O N 172 S C N 173 N O N 174 R C N 175 N O N 176 R C N 177 N N N 178 N C N 179 N O N 180 N N N 181 N C N 182 N O N 183 N C N 184 N C N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing Y 132 N doub Y 133 N sing Y 134 N sing N 135 N sing N 136 N sing Y 137 N doub Y 138 N doub Y 139 N sing Y 140 N sing Y 141 N sing Y 142 N doub Y 143 N doub Y 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N doub N 196 N sing N 197 N sing N 198 N sing N 199 N doub N 200 N sing N 201 N doub N 202 N sing N 203 N sing To Be Published 0353 Symmetric scaffolds enable de novo modelling of RNA by cryoEM 0000-0001-7780-5278 0000-0003-4549-1619 10.2210/pdb9ndv/pdb pdb_00009ndv 9NDV 882884 2.92 FSC 0.143 CUT-OFF POINT REL 2025-02-18 RCSB 2026-03-04 2026-03-04 Scaffold attached to quinine-I aptamer (Tonic) local refinement of aptamer 7.4 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 Scaffold attached to quinine-I aptamer (Tonic) local refinement of aptamer 0 RECOMBINANT COMPLEX 32630 synthetic construct 905931 in vitro transcription vector pT7-TP(deltai) PARTICLE 1 1 SINGLE PARTICLE 45.09 GATAN K3 BIOQUANTUM (6k x 4k) 300 FIELD EMISSION GUN SPOT SCAN TFS KRIOS BRIGHT FIELD 2000 800 1 PARTICLE SELECTION 1 IMAGE ACQUISITION 1 MASKING CTF CORRECTION 1 LAYERLINE INDEXING DIFFRACTION INDEXING MODEL FITTING MODEL REFINEMENT OTHER INITIAL EULER ASSIGNMENT 1 FINAL EULER ASSIGNMENT 1 CLASSIFICATION 1 RECONSTRUCTION 1 NO NO NO YES ETHANE 9NDV 53433.723 RNA (67-MER) 1 syn polymer 324.417 Quinine 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 39.098 POTASSIUM ION 2 syn non-polymer 18.015 water 17 nat water no no GGGCCACUGUUUCACUGUUGCGCUACAUCUCCGGACGACUCUAUACCGCGUGGAUAUGGCACGCAACUUCAAGACGGGCA CCGUAAAUGUCCUCGGGCGUCGUCCGGAGGCCACACGAAAGUGUGGAGUGACCAGUGGCCCCACCCUGAAGGUAAACUUG UAGCGC GGGCCACUGUUUCACUGUUGCGCUACAUCUCCGGACGACUCUAUACCGCGUGGAUAUGGCACGCAACUUCAAGACGGGCA CCGUAAAUGUCCUCGGGCGUCGUCCGGAGGCCACACGAAAGUGUGGAGUGACCAGUGGCCCCACCCUGAAGGUAAACUUG UAGCGC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n -5.441 1 19 A 36 A 102 0.095 A_C36:G102_A 1 4.928 0.211 -0.273 -0.173 4.479 1 19 A 37 A 101 -8.775 A_G37:C101_A 2 -3.909 -0.036 0.884 -0.464 2.602 1 20 A 38 A 100 2.956 A_A38:U100_A 3 -3.598 -0.068 0.758 -0.396 1.197 1 19 A 39 A 99 -1.475 A_C39:G99_A 4 -6.533 0.192 0.583 -0.284 -0.665 A 40 A 98 -11.987 A_U40:C98_A 5 -11.664 1.253 0.352 -1.214 0.454 1 19 A 41 A 97 -0.933 A_C41:G97_A 6 -9.333 0.251 0.174 -0.158 -13.620 2 27 A 42 A 96 -168.176 A_U42:G96_A 7 8.793 -0.206 -0.102 1.104 -6.030 1 19 A 70 A 95 2.027 A_C70:G95_A 8 -1.807 0.386 -0.385 0.192 -49.424 A 71 A 43 158.860 A_A71:A43_A 9 -15.795 -1.985 0.860 -1.055 12.876 2 21 A 72 A 44 177.063 A_A72:U44_A 10 1.494 0.203 -0.753 1.040 -36.441 5 A 46 A 65 72.623 A_C46:A65_A 11 -10.712 5.968 -1.701 0.664 12.082 1 19 A 48 A 64 2.598 A_G48:C64_A 12 7.792 -0.113 1.115 -0.181 4.698 1 19 A 49 A 63 10.139 A_C49:G63_A 13 -36.766 1.865 0.672 -0.700 1.774 1 19 A 50 A 62 -0.473 A_G50:C62_A 14 -0.353 -0.080 0.495 -0.162 2.811 1 20 A 51 A 61 -8.592 A_U51:A61_A 15 -7.473 -0.254 0.733 -0.076 8.418 1 19 A 52 A 60 -0.130 A_G52:C60_A 16 -1.986 -0.239 -0.723 -0.277 -5.176 1 19 A 73 A 94 1.170 A_G73:C94_A 17 3.882 -0.171 -0.280 -0.171 6.863 1 20 A 74 A 93 6.059 A_A74:U93_A 18 3.709 -0.612 -0.141 -0.052 0.373 1 19 A 76 A 92 2.230 A_G76:C92_A 19 -7.209 -0.231 -0.505 -0.122 -1.078 1 19 A 77 A 91 0.316 A_G77:C91_A 20 2.945 -0.219 -0.604 -0.176 -17.695 1 19 A 79 A 89 -6.502 A_C79:G89_A 21 5.230 0.205 -0.733 -0.350 -5.320 1 20 A 80 A 88 -3.313 A_A80:U88_A 22 6.330 0.044 0.364 0.044 -6.726 1 19 A 81 A 59 2.357 A_C81:G59_A 23 4.450 0.152 0.263 -0.076 -7.733 1 19 A 82 A 58 3.097 A_C82:G58_A 24 5.446 0.174 1.278 -0.358 9.242 A 83 A 85 113.759 A_G83:A85_A 25 57.320 4.039 0.151 3.037 1.745 39.485 A A 36 37 28.135 A A 102 101 2.783 18.228 0.010 -1.551 AA_C36G37:C101G102_AA 1 -7.119 10.988 34.464 -3.894 -0.639 3.042 35.540 A A 37 38 2.426 A A 101 100 3.140 1.479 0.265 -1.801 AA_G37A38:U100C101_AA 2 -2.298 3.769 35.438 -3.156 -0.751 3.141 30.783 A A 38 39 4.383 A A 100 99 3.293 2.324 -0.674 -1.837 AA_A38C39:G99U100_AA 3 0.339 -0.638 30.695 -3.908 1.336 2.941 38.287 A A 39 40 4.673 A A 99 98 3.094 3.062 -0.749 -1.619 AA_C39U40:C98G99_AA 4 0.977 -1.492 38.157 -2.824 1.256 2.728 36.217 A A 40 41 11.195 A A 98 97 3.086 6.898 0.245 -1.683 AA_U40C41:G97C98_AA 5 5.004 -8.121 35.233 -3.581 0.240 -0.225 -177.555 A A 41 42 74.947 A A 97 96 -0.918 -149.160 3.195 -1.092 AA_C41U42:G96G97_AA 6 -93.645 -47.053 -101.879 0.374 1.706 -2.107 -177.124 A A 42 70 29.008 A A 96 95 -1.944 -57.884 -2.000 2.912 AA_U42C70:G95G96_AA 7 -158.840 -79.600 -149.484 -1.549 -0.746 0.604 -41.717 A A 70 71 -1.614 A A 95 43 2.598 1.082 2.656 1.634 AA_C70A71:A43G95_AA 8 24.266 36.183 -34.176 -2.356 5.119 1.695 54.204 A A 71 72 -2.504 A A 43 44 4.623 -1.861 0.297 2.143 AA_A71A72:U44A43_AA 9 -49.327 66.384 23.130 2.515 -4.647 2.843 48.018 A A 48 49 20.022 A A 64 63 3.161 15.844 2.991 -2.522 AA_G48C49:G63C64_AA 10 12.424 -15.700 43.821 -4.307 -2.729 1.084 38.977 A A 49 50 38.031 A A 63 62 2.508 23.718 -0.547 -1.548 AA_C49G50:C62G63_AA 11 1.139 -1.827 31.134 -4.091 0.905 3.513 19.574 A A 50 51 -4.277 A A 62 61 3.257 -1.451 -1.349 -2.357 AA_G50U51:A61C62_AA 12 -1.490 4.391 19.465 -6.199 3.215 2.345 32.710 A A 51 52 13.804 A A 61 60 2.848 7.693 0.065 -1.833 AA_U51G52:C60A61_AA 13 3.159 -5.668 31.663 -4.329 0.324 2.819 32.508 A A 73 74 7.795 A A 94 93 3.049 4.351 0.041 -1.553 AA_G73A74:U93C94_AA 14 -0.767 1.375 32.214 -3.459 -0.195 3.447 54.530 A A 74 76 24.959 A A 93 92 5.487 21.727 -1.998 -1.250 AA_A74G76:C92U93_AA 15 21.360 -24.537 45.775 -3.351 4.134 2.543 24.402 A A 76 77 16.557 A A 92 91 3.309 6.903 0.873 -2.115 AA_G76G77:C91C92_AA 16 -1.155 2.771 23.392 -6.976 -2.395 2.370 36.557 A A 79 80 10.536 A A 89 88 2.793 6.531 0.488 -1.319 AA_C79A80:U88G89_AA 17 -7.488 12.079 35.225 -2.828 -1.609 3.329 50.493 A A 80 81 1.029 A A 88 59 3.183 0.877 2.215 -1.154 AA_A80C81:G59U88_AA 18 4.251 -4.989 50.319 -1.415 -2.296 3.190 29.028 A A 81 82 1.896 A A 59 58 3.301 0.944 -0.042 -1.867 AA_C81C82:G58G59_AA 19 -5.511 11.061 28.496 -3.933 -1.130 -0.442 -45.714 A A 82 83 -59.091 A A 58 85 2.220 37.813 -2.931 3.002 AA_C82G83:A85G58_AA 20 15.189 23.737 -21.173 -5.135 -3.263 repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release 1 0 2026-03-04 1 0 2026-03-04 1 0 1 2026-03-04 1 0 1 2026-03-04 1 0 2 2026-03-04 1 0 2026-03-04 1 0 1 2026-03-04 1 0 2026-03-04 United States National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) adrian.ferre@nih.gov 0000-0003-4549-1619 Adrian Ferre-D'Amare principal investigator/group leader Scaffold attached to quinine-I aptamer (Tonic) local refinement of aptamer N RCSB Y RCSB 2025-02-18 REL QI9 QI9 SUBJECT OF INVESTIGATION QI9 Quinine MG MAGNESIUM ION K POTASSIUM ION HOH water 32630 synthetic construct sample 1 166 Y N QI9 1 2 QI9 QI9 201 A MG 1 3 MG MG 202 A K 1 4 K K 203 A K 2 4 K K 204 A HOH 11 5 HOH HOH 301 A HOH 15 5 HOH HOH 302 A HOH 13 5 HOH HOH 303 A HOH 14 5 HOH HOH 304 A HOH 7 5 HOH HOH 305 A HOH 20 5 HOH HOH 306 A HOH 1 5 HOH HOH 307 A HOH 21 5 HOH HOH 308 A HOH 24 5 HOH HOH 309 A HOH 19 5 HOH HOH 310 A HOH 17 5 HOH HOH 311 A HOH 10 5 HOH HOH 312 A HOH 8 5 HOH HOH 313 A HOH 18 5 HOH HOH 314 A HOH 23 5 HOH HOH 315 A HOH 16 5 HOH HOH 316 A HOH 9 5 HOH HOH 317 A n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A n 6 6 A n 7 7 A n 8 8 A n 9 9 A n 10 10 A n 11 11 A n 12 12 A n 13 13 A n 14 14 A n 15 15 A n 16 16 A n 17 17 A n 18 18 A n 19 19 A n 20 20 A n 21 21 A n 22 22 A n 23 23 A n 24 24 A n 25 25 A n 26 26 A n 27 27 A n 28 28 A n 29 29 A n 30 30 A n 31 31 A n 32 32 A n 33 33 A n 34 34 A n 35 35 A C 36 n 36 C 36 A G 37 n 37 G 37 A A 38 n 38 A 38 A C 39 n 39 C 39 A U 40 n 40 U 40 A C 41 n 41 C 41 A U 42 n 42 U 42 A A 43 n 43 A 43 A U 44 n 44 U 44 A A 45 n 45 A 45 A C 46 n 46 C 46 A C 47 n 47 C 47 A G 48 n 48 G 48 A C 49 n 49 C 49 A G 50 n 50 G 50 A U 51 n 51 U 51 A G 52 n 52 G 52 A G 53 n 53 G 53 A A 54 n 54 A 54 A U 55 n 55 U 55 A A 56 n 56 A 56 A U 57 n 57 U 57 A G 58 n 58 G 58 A G 59 n 59 G 59 A C 60 n 60 C 60 A A 61 n 61 A 61 A C 62 n 62 C 62 A G 63 n 63 G 63 A C 64 n 64 C 64 A A 65 n 65 A 65 A A 66 n 66 A 66 A C 67 n 67 C 67 A U 68 n 68 U 68 A U 69 n 69 U 69 A C 70 n 70 C 70 A A 71 n 71 A 71 A A 72 n 72 A 72 A G 73 n 73 G 73 A A 74 n 74 A 74 A C 75 n 75 C 75 A G 76 n 76 G 76 A G 77 n 77 G 77 A G 78 n 78 G 78 A C 79 n 79 C 79 A A 80 n 80 A 80 A C 81 n 81 C 81 A C 82 n 82 C 82 A G 83 n 83 G 83 A U 84 n 84 U 84 A A 85 n 85 A 85 A A 86 n 86 A 86 A A 87 n 87 A 87 A U 88 n 88 U 88 A G 89 n 89 G 89 A U 90 n 90 U 90 A C 91 n 91 C 91 A C 92 n 92 C 92 A U 93 n 93 U 93 A C 94 n 94 C 94 A G 95 n 95 G 95 A G 96 n 96 G 96 A G 97 n 97 G 97 A C 98 n 98 C 98 A G 99 n 99 G 99 A U 100 n 100 U 100 A C 101 n 101 C 101 A G 102 n 102 G 102 A n 103 103 A n 104 104 A n 105 105 A n 106 106 A n 107 107 A n 108 108 A n 109 109 A n 110 110 A n 111 111 A n 112 112 A n 113 113 A n 114 114 A n 115 115 A n 116 116 A n 117 117 A n 118 118 A n 119 119 A n 120 120 A n 121 121 A n 122 122 A n 123 123 A n 124 124 A n 125 125 A n 126 126 A n 127 127 A n 128 128 A n 129 129 A n 130 130 A n 131 131 A n 132 132 A n 133 133 A n 134 134 A n 135 135 A n 136 136 A n 137 137 A n 138 138 A n 139 139 A n 140 140 A n 141 141 A n 142 142 A n 143 143 A n 144 144 A n 145 145 A n 146 146 A n 147 147 A n 148 148 A n 149 149 A n 150 150 A n 151 151 A n 152 152 A n 153 153 A n 154 154 A n 155 155 A n 156 156 A n 157 157 A n 158 158 A n 159 159 A n 160 160 A n 161 161 A n 162 162 A n 163 163 A n 164 164 A n 165 165 A n 166 166 A author_defined_assembly 1 monomeric not applicable electron microscopy A U 68 A OP2 U 68 1_555 A MG 202 C MG MG 1_555 A A 71 A OP2 A 71 1_555 138.2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A G 1 A G 1 1 Y 1 A G 2 A G 2 1 Y 1 A G 3 A G 3 1 Y 1 A C 4 A C 4 1 Y 1 A C 5 A C 5 1 Y 1 A A 6 A A 6 1 Y 1 A C 7 A C 7 1 Y 1 A U 8 A U 8 1 Y 1 A G 9 A G 9 1 Y 1 A U 10 A U 10 1 Y 1 A U 11 A U 11 1 Y 1 A U 12 A U 12 1 Y 1 A C 13 A C 13 1 Y 1 A A 14 A A 14 1 Y 1 A C 15 A C 15 1 Y 1 A U 16 A U 16 1 Y 1 A G 17 A G 17 1 Y 1 A U 18 A U 18 1 Y 1 A U 19 A U 19 1 Y 1 A G 20 A G 20 1 Y 1 A C 21 A C 21 1 Y 1 A G 22 A G 22 1 Y 1 A C 23 A C 23 1 Y 1 A U 24 A U 24 1 Y 1 A A 25 A A 25 1 Y 1 A C 26 A C 26 1 Y 1 A A 27 A A 27 1 Y 1 A U 28 A U 28 1 Y 1 A C 29 A C 29 1 Y 1 A U 30 A U 30 1 Y 1 A C 31 A C 31 1 Y 1 A C 32 A C 32 1 Y 1 A G 33 A G 33 1 Y 1 A G 34 A G 34 1 Y 1 A A 35 A A 35 1 Y 1 A U 103 A U 103 1 Y 1 A C 104 A C 104 1 Y 1 A C 105 A C 105 1 Y 1 A G 106 A G 106 1 Y 1 A G 107 A G 107 1 Y 1 A A 108 A A 108 1 Y 1 A G 109 A G 109 1 Y 1 A G 110 A G 110 1 Y 1 A C 111 A C 111 1 Y 1 A C 112 A C 112 1 Y 1 A A 113 A A 113 1 Y 1 A C 114 A C 114 1 Y 1 A A 115 A A 115 1 Y 1 A C 116 A C 116 1 Y 1 A G 117 A G 117 1 Y 1 A A 118 A A 118 1 Y 1 A A 119 A A 119 1 Y 1 A A 120 A A 120 1 Y 1 A G 121 A G 121 1 Y 1 A U 122 A U 122 1 Y 1 A G 123 A G 123 1 Y 1 A U 124 A U 124 1 Y 1 A G 125 A G 125 1 Y 1 A G 126 A G 126 1 Y 1 A A 127 A A 127 1 Y 1 A G 128 A G 128 1 Y 1 A U 129 A U 129 1 Y 1 A G 130 A G 130 1 Y 1 A A 131 A A 131 1 Y 1 A C 132 A C 132 1 Y 1 A C 133 A C 133 1 Y 1 A A 134 A A 134 1 Y 1 A G 135 A G 135 1 Y 1 A U 136 A U 136 1 Y 1 A G 137 A G 137 1 Y 1 A G 138 A G 138 1 Y 1 A C 139 A C 139 1 Y 1 A C 140 A C 140 1 Y 1 A C 141 A C 141 1 Y 1 A C 142 A C 142 1 Y 1 A A 143 A A 143 1 Y 1 A C 144 A C 144 1 Y 1 A C 145 A C 145 1 Y 1 A C 146 A C 146 1 Y 1 A U 147 A U 147 1 Y 1 A G 148 A G 148 1 Y 1 A A 149 A A 149 1 Y 1 A A 150 A A 150 1 Y 1 A G 151 A G 151 1 Y 1 A G 152 A G 152 1 Y 1 A U 153 A U 153 1 Y 1 A A 154 A A 154 1 Y 1 A A 155 A A 155 1 Y 1 A A 156 A A 156 1 Y 1 A C 157 A C 157 1 Y 1 A U 158 A U 158 1 Y 1 A U 159 A U 159 1 Y 1 A G 160 A G 160 1 Y 1 A U 161 A U 161 1 Y 1 A A 162 A A 162 1 Y 1 A G 163 A G 163 1 Y 1 A C 164 A C 164 1 Y 1 A G 165 A G 165 1 Y 1 A C 166 A C 166 1 Y 1 -3.08 0.40 120.30 117.22 A A A C6 N1 C2 C C C 64 64 64 N 1 3.20 0.50 121.00 124.20 A A A C5 C6 N1 C C C 64 64 64 N 1 -5.58 0.90 105.70 100.12 A A A O5' P OP2 A A A 65 65 65 N 1 -4.11 0.60 128.60 124.49 A A A C5 C6 O6 G G G 83 83 83 N 1 10.20 1.50 119.60 129.80 A A A OP1 P OP2 C C C 101 101 101 N 1 -6.79 0.90 105.70 98.91 A A A O5' P OP2 C C C 101 101 101 N 1 3.52 0.50 121.00 124.52 A A A C5 C6 N1 C C C 101 101 101 N 1 7.19 1.10 118.80 125.99 A A A C2 N1 C1' C C C 101 101 101 N N Scaffold attached to quinine-I aptamer (Tonic) local refinement of aptamer 1 N N 2 N N 3 N N 4 N N 4 N N 5 N N metalc 2.035 A U 68 A OP2 U 68 1_555 A MG 202 C MG MG 1_555 metalc 2.313 A A 71 A OP2 A 71 1_555 A MG 202 C MG MG 1_555 hydrog WATSON-CRICK A C 36 A N3 C 36 1_555 A G 102 A N1 G 102 1_555 hydrog WATSON-CRICK A C 36 A N4 C 36 1_555 A G 102 A O6 G 102 1_555 hydrog WATSON-CRICK A C 36 A O2 C 36 1_555 A G 102 A N2 G 102 1_555 hydrog WATSON-CRICK A G 37 A N1 G 37 1_555 A C 101 A N3 C 101 1_555 hydrog WATSON-CRICK A G 37 A N2 G 37 1_555 A C 101 A O2 C 101 1_555 hydrog WATSON-CRICK A G 37 A O6 G 37 1_555 A C 101 A N4 C 101 1_555 hydrog WATSON-CRICK A A 38 A N1 A 38 1_555 A U 100 A N3 U 100 1_555 hydrog WATSON-CRICK A A 38 A N6 A 38 1_555 A U 100 A O4 U 100 1_555 hydrog WATSON-CRICK A C 39 A N3 C 39 1_555 A G 99 A N1 G 99 1_555 hydrog WATSON-CRICK A C 39 A N4 C 39 1_555 A G 99 A O6 G 99 1_555 hydrog WATSON-CRICK A C 39 A O2 C 39 1_555 A G 99 A N2 G 99 1_555 hydrog U-C MISPAIR A U 40 A O4 U 40 1_555 A C 98 A N4 C 98 1_555 hydrog WATSON-CRICK A C 41 A N3 C 41 1_555 A G 97 A N1 G 97 1_555 hydrog WATSON-CRICK A C 41 A N4 C 41 1_555 A G 97 A O6 G 97 1_555 hydrog WATSON-CRICK A C 41 A O2 C 41 1_555 A G 97 A N2 G 97 1_555 hydrog U-U MISPAIR A U 42 A N3 U 42 1_555 A U 68 A O4 U 68 1_555 hydrog TYPE_27_PAIR A U 42 A N3 U 42 1_555 A G 96 A O6 G 96 1_555 hydrog TYPE_27_PAIR A U 42 A O4 U 42 1_555 A G 96 A N1 G 96 1_555 hydrog A-A MISPAIR A A 43 A N1 A 43 1_555 A A 71 A N6 A 71 1_555 hydrog A-G MISPAIR A A 43 A N6 A 43 1_555 A G 95 A O6 G 95 1_555 hydrog REVERSED WATSON-CRICK A U 44 A N3 U 44 1_555 A A 72 A N1 A 72 1_555 hydrog REVERSED WATSON-CRICK A U 44 A O2 U 44 1_555 A A 72 A N6 A 72 1_555 hydrog C-A MISPAIR A C 46 A O2 C 46 1_555 A A 65 A N6 A 65 1_555 hydrog WATSON-CRICK A G 48 A N1 G 48 1_555 A C 64 A N3 C 64 1_555 hydrog WATSON-CRICK A G 48 A N2 G 48 1_555 A C 64 A O2 C 64 1_555 hydrog WATSON-CRICK A G 48 A O6 G 48 1_555 A C 64 A N4 C 64 1_555 hydrog WATSON-CRICK A C 49 A N3 C 49 1_555 A G 63 A N1 G 63 1_555 hydrog WATSON-CRICK A C 49 A N4 C 49 1_555 A G 63 A O6 G 63 1_555 hydrog WATSON-CRICK A C 49 A O2 C 49 1_555 A G 63 A N2 G 63 1_555 hydrog WATSON-CRICK A G 50 A N1 G 50 1_555 A C 62 A N3 C 62 1_555 hydrog WATSON-CRICK A G 50 A N2 G 50 1_555 A C 62 A O2 C 62 1_555 hydrog WATSON-CRICK A G 50 A O6 G 50 1_555 A C 62 A N4 C 62 1_555 hydrog WATSON-CRICK A U 51 A N3 U 51 1_555 A A 61 A N1 A 61 1_555 hydrog WATSON-CRICK A U 51 A O4 U 51 1_555 A A 61 A N6 A 61 1_555 hydrog WATSON-CRICK A G 52 A N1 G 52 1_555 A C 60 A N3 C 60 1_555 hydrog WATSON-CRICK A G 52 A N2 G 52 1_555 A C 60 A O2 C 60 1_555 hydrog WATSON-CRICK A G 52 A O6 G 52 1_555 A C 60 A N4 C 60 1_555 hydrog U-G MISPAIR A U 55 A O2 U 55 1_555 A G 58 A N2 G 58 1_555 hydrog WATSON-CRICK A G 58 A N1 G 58 1_555 A C 82 A N3 C 82 1_555 hydrog WATSON-CRICK A G 58 A N2 G 58 1_555 A C 82 A O2 C 82 1_555 hydrog WATSON-CRICK A G 58 A O6 G 58 1_555 A C 82 A N4 C 82 1_555 hydrog WATSON-CRICK A G 59 A N1 G 59 1_555 A C 81 A N3 C 81 1_555 hydrog WATSON-CRICK A G 59 A N2 G 59 1_555 A C 81 A O2 C 81 1_555 hydrog WATSON-CRICK A G 59 A O6 G 59 1_555 A C 81 A N4 C 81 1_555 hydrog G-A MISPAIR A G 59 A N2 G 59 1_555 A A 87 A N1 A 87 1_555 hydrog U-C MISPAIR A U 68 A O4 U 68 1_555 A C 70 A N4 C 70 1_555 hydrog WATSON-CRICK A C 70 A N3 C 70 1_555 A G 95 A N1 G 95 1_555 hydrog WATSON-CRICK A C 70 A N4 C 70 1_555 A G 95 A O6 G 95 1_555 hydrog WATSON-CRICK A C 70 A O2 C 70 1_555 A G 95 A N2 G 95 1_555 hydrog WATSON-CRICK A G 73 A N1 G 73 1_555 A C 94 A N3 C 94 1_555 hydrog WATSON-CRICK A G 73 A N2 G 73 1_555 A C 94 A O2 C 94 1_555 hydrog WATSON-CRICK A G 73 A O6 G 73 1_555 A C 94 A N4 C 94 1_555 hydrog WATSON-CRICK A A 74 A N1 A 74 1_555 A U 93 A N3 U 93 1_555 hydrog WATSON-CRICK A A 74 A N6 A 74 1_555 A U 93 A O4 U 93 1_555 hydrog WATSON-CRICK A G 76 A N1 G 76 1_555 A C 92 A N3 C 92 1_555 hydrog WATSON-CRICK A G 76 A N2 G 76 1_555 A C 92 A O2 C 92 1_555 hydrog WATSON-CRICK A G 76 A O6 G 76 1_555 A C 92 A N4 C 92 1_555 hydrog WATSON-CRICK A G 77 A N1 G 77 1_555 A C 91 A N3 C 91 1_555 hydrog WATSON-CRICK A G 77 A N2 G 77 1_555 A C 91 A O2 C 91 1_555 hydrog WATSON-CRICK A G 77 A O6 G 77 1_555 A C 91 A N4 C 91 1_555 hydrog WATSON-CRICK A C 79 A N3 C 79 1_555 A G 89 A N1 G 89 1_555 hydrog WATSON-CRICK A C 79 A N4 C 79 1_555 A G 89 A O6 G 89 1_555 hydrog WATSON-CRICK A C 79 A O2 C 79 1_555 A G 89 A N2 G 89 1_555 hydrog WATSON-CRICK A A 80 A N1 A 80 1_555 A U 88 A N3 U 88 1_555 hydrog WATSON-CRICK A A 80 A N6 A 80 1_555 A U 88 A O4 U 88 1_555 hydrog C-A MISPAIR A C 82 A O2 C 82 1_555 A A 87 A N6 A 87 1_555 hydrog G-A MISPAIR A G 83 A N2 G 83 1_555 A A 85 A N1 A 85 1_555 RNA Synthetic, aptamer, engineering, riboswitch, RNA 9NDV PDB 1 1 9NDV 1 166 9NDV 1 166 9NDV A 1 1 166 1 P 1