0.018093 0.000000 0.000000 0.000000 0.009845 0.000000 0.000000 0.000000 0.008960 0.00000 0.00000 0.00000 Colussi, T.M. Costantino, D.A. Hammond, J.A. Ruehle, G.M. Nix, J.C. Kieft, J.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 55.270 101.570 111.610 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C10 H13 N5 O9 P2 409.186 n ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE 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 H18 Ir N6 3 294.400 IRIDIUM HEXAMMINE ION non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer C10 H26 N4 202.340 SPERMINE 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 S P N 39 N O N 40 N O N 41 N P N 42 N O N 43 N O N 44 N O N 45 N O N 46 N C N 47 R C N 48 N O N 49 R C N 50 N O N 51 R C N 52 N O N 53 R C Y 54 N N Y 55 N C Y 56 N N Y 57 N C Y 58 N C N 59 N N Y 60 N N Y 61 N C Y 62 N N Y 63 N C 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 H N 74 N H N 75 N H N 76 N H N 77 N O N 78 N P N 79 N O N 80 N O N 81 N O N 82 N C N 83 R C N 84 N O N 85 S C N 86 N O N 87 R C N 88 N O N 89 R C N 90 N N N 91 N C N 92 N O N 93 N N N 94 N C N 95 N N N 96 N C N 97 N C 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 H N 112 N O N 113 N P N 114 N O N 115 N O N 116 N O N 117 N C N 118 R C N 119 N O N 120 S C N 121 N O N 122 R C N 123 N O N 124 R C Y 125 N N Y 126 N C Y 127 N N Y 128 N C N 129 N C N 130 N O N 131 N N N 132 N C N 133 N N N 134 N N Y 135 N C N 136 N H N 137 N H N 138 N H N 139 N H 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 O N 151 N H N 152 N H N 153 N IR N 154 N N N 155 N N N 156 N N N 157 N N N 158 N N N 159 N N N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N MG N 179 N N N 180 N C N 181 N C N 182 N C N 183 N N N 184 N C N 185 N C N 186 N C N 187 N C N 188 N N N 189 N C N 190 N C N 191 N C N 192 N N N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N O N 220 N P N 221 N O N 222 N O N 223 N O N 224 N C N 225 R C N 226 N O N 227 S C N 228 N O N 229 R C N 230 N O N 231 R C N 232 N N N 233 N C N 234 N O N 235 N N N 236 N C N 237 N O N 238 N C N 239 N C N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 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 doub N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub 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 sing Y 67 N sing Y 68 N sing Y 69 N doub N 70 N sing Y 71 N sing Y 72 N sing Y 73 N doub N 74 N sing Y 75 N doub N 76 N sing N 77 N sing Y 78 N sing Y 79 N doub N 80 N sing Y 81 N sing N 82 N sing N 83 N sing N 84 N doub 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 N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub 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 sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing Y 142 N sing Y 143 N sing Y 144 N doub N 145 N sing Y 146 N sing N 147 N sing Y 148 N doub N 149 N doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub 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 sing 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 sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N doub N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N doub N 250 N sing N 251 N sing N 252 N sing N 253 N doub N 254 N sing N 255 N doub N 256 N sing N 257 N sing UK Nature NATUAS 0006 1476-4687 511 366 369 10.1038/nature13378 24909993 The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. 2014 UK J.Mol.Biol. JMOBAK 0070 1089-8638 399 450 463 10.1016/j.jmb.2010.04.016 20398674 Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA. 2010 UK Rna RNARFU 2122 1469-9001 15 294 307 10.1261/rna.1360709 19144910 Comparison and functional implications of the 3D architectures of viral tRNA-like structures. 2009 10.2210/pdb4p5j/pdb pdb_00004p5j 100 1 CMOS 2013-10-21 RDI CMOS_8M Rosenbaum-Rock Si(111) sagitally focused monochromator SINGLE WAVELENGTH M x-ray 1 1.0972 1.0 4.2.2 ALS 1.0972 SYNCHROTRON ALS BEAMLINE 4.2.2 27593.316 Turnip yellow mosaic virus mRNA for the coat protein 1 syn polymer 24.305 MAGNESIUM ION 2 syn non-polymer 294.400 IRIDIUM HEXAMMINE ION 12 syn non-polymer 202.340 SPERMINE 1 syn non-polymer 18.015 water 126 nat water no yes UUAGCUCGCCAGUUAGCGAGGUCUGUCUCGACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCG GAACC(A23) UUAGCUCGCCAGUUAGCGAGGUCUGUCUCGACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCG GAACCA 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 1 2.84 56.76 VAPOR DIFFUSION, SITTING DROP 7.5 This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room temperature. After cooling, Spermidine was added to 0.5 mM. The reaction was centrifuged for 10 minutes at 13000 x g and then used in sitting-drop vapor diffusion crystallization at 4?C. 1 ?L of RNA solution was combined with 2 ?L of 10% MPD, 40 mM Na-Cacodylate pH 6.0, 12 mM Spermine, 80 mM NaCl, and 20 mM MgCl2. The well solution was 20-35% MPD. Crystals appeared and grew to full size over the course of 1-2 days. 277.15 -7.577 1 19 A 2 A 74 -1.992 A_G2:C74_A 1 -5.705 0.047 -0.454 -0.167 20.267 A 32 A 26 159.736 A_C32:U26_A 2 -11.904 1.425 -0.509 -4.552 -4.082 1 19 A 33 A 25 3.451 A_G33:C25_A 3 -10.801 -0.544 0.290 -0.175 4.091 1 20 A 34 A 24 1.044 A_A34:U24_A 4 -10.690 -0.335 0.206 -0.198 4.442 1 19 A 35 A 23 -1.403 A_C35:G23_A 5 -11.608 0.630 0.097 -0.310 3.564 1 20 A 36 A 22 -0.447 A_A36:U22_A 6 -12.961 -0.001 0.127 -0.260 -1.738 1 19 A 37 A 21 -3.293 A_G37:C21_A 7 -13.814 -0.357 0.126 -0.375 -8.553 1 20 A 38 A 20 -0.715 A_A38:U20_A 8 -18.129 0.040 -0.027 -0.109 1.016 1 28 A 39 A 19 -4.210 A_U39:G19_A 9 -12.385 2.214 0.128 -0.628 -5.815 1 19 A 3 A 18 0.997 A_C3:G18_A 10 -10.421 0.107 0.121 -0.179 -8.591 1 20 A 4 A 17 1.543 A_U4:A17_A 11 -8.080 0.126 0.181 -0.148 1.358 1 19 A 5 A 16 -0.333 A_C5:G16_A 12 -10.509 0.238 0.060 -0.114 1.396 1 19 A 6 A 15 -0.930 A_G6:C15_A 13 -8.745 -0.145 0.189 -0.117 7.866 1 19 A 7 A 14 -0.066 A_C7:G14_A 14 -9.586 0.220 0.057 -0.209 13.023 2 15 A 8 A 52 178.881 A_C8:C52_A 15 36.275 1.714 0.141 1.536 -18.919 10 11 A 9 A 48 -3.130 A_A9:G48_A 16 11.398 -6.824 0.252 -4.451 -1.412 4 24 A 51 A 47 -99.833 A_A51:U47_A 17 1.528 -4.111 0.237 -1.972 5.993 1 19 A 54 A 46 1.029 A_C54:G46_A 18 -10.333 0.208 0.149 -0.213 6.301 1 19 A 55 A 45 -0.242 A_C55:G45_A 19 -12.443 0.006 -0.101 -0.082 4.102 1 19 A 56 A 44 0.079 A_C56:G44_A 20 -8.539 0.347 0.106 -0.134 0.185 1 19 A 57 A 43 -2.062 A_G57:C43_A 21 -7.899 -0.119 -0.129 -0.078 9.026 1 19 A 58 A 72 -4.008 A_C58:G72_A 22 -7.634 0.287 0.060 -0.175 5.047 1 19 A 59 A 71 2.019 A_C59:G71_A 23 -22.420 0.251 0.295 -0.260 -5.996 1 19 A 60 A 70 -2.478 A_C60:G70_A 24 -12.674 0.280 0.454 -0.158 -7.351 1 20 A 76 A 69 8.204 A_U76:A69_A 25 -0.087 -0.004 0.190 -0.215 1.397 1 19 A 77 A 68 -0.649 A_C77:G68_A 26 -14.115 0.210 0.058 -0.157 0.546 1 19 A 78 A 67 2.152 A_G78:C67_A 27 -12.071 -0.312 0.341 -0.170 2.602 1 19 A 79 A 66 -1.896 A_G79:C66_A 28 -14.544 0.027 0.158 -0.197 -3.422 1 20 A 80 A 65 0.229 A_A80:U65_A 29 -21.936 -0.089 -0.026 -0.139 -7.895 1 20 A 81 A 64 2.229 A_A81:U64_A 30 -10.081 0.075 0.294 -0.043 -7.828 2 15 A 83 A 63 -177.492 A_C83:C63_A 31 -6.595 -2.033 -0.341 -1.234 -27.199 1 19 A 10 A 49 0.771 A_G10:C49_A 32 -20.643 -0.173 -0.135 -0.083 3.054 130.572 A A 32 33 -2.862 A A 26 25 3.055 -5.199 0.909 -0.302 AA_C32G33:C25U26_AA 1 -1.786 0.983 130.512 -0.131 -0.513 2.975 34.018 A A 33 34 4.032 A A 25 24 3.045 2.355 -0.289 -1.130 AA_G33A34:U24C25_AA 2 -2.351 4.024 33.859 -2.278 0.149 2.928 36.007 A A 34 35 9.960 A A 24 23 3.234 6.129 -0.004 -1.592 AA_A34C35:G23U24_AA 3 0.030 -0.049 35.498 -3.402 0.011 2.248 29.596 A A 35 36 23.045 A A 23 22 3.114 11.475 -0.121 -1.665 AA_C35A36:U22G23_AA 4 -0.641 1.287 27.319 -5.335 0.122 2.780 34.359 A A 36 37 15.634 A A 22 21 3.251 9.129 -0.294 -1.427 AA_A36G37:C21U22_AA 5 -1.264 2.165 33.136 -3.758 0.312 3.153 35.273 A A 37 38 11.425 A A 21 20 3.425 6.874 0.410 -1.231 AA_G37A38:U20C21_AA 6 2.902 -4.823 34.500 -3.069 -0.239 2.727 39.794 A A 38 39 10.720 A A 20 19 3.001 7.255 0.051 -1.290 AA_A38U39:G19U20_AA 7 2.358 -3.484 39.085 -2.638 0.166 2.951 48.947 A A 39 3 9.257 A A 19 18 3.175 7.642 -2.106 -1.211 AA_U39C3:G18G19_AA 8 0.279 -0.338 48.382 -2.007 2.562 2.724 30.911 A A 3 4 15.417 A A 18 17 3.233 8.125 -0.445 -1.549 AA_C3U4:A17G18_AA 9 0.164 -0.312 29.849 -4.366 0.864 2.948 29.232 A A 4 5 3.385 A A 17 16 3.044 1.706 0.078 -1.543 AA_U4C5:G16A17_AA 10 2.212 -4.389 29.101 -3.398 0.285 2.579 31.422 A A 5 6 16.650 A A 16 15 3.149 8.899 0.153 -1.610 AA_C5G6:C15G16_AA 11 -0.291 0.544 30.164 -4.464 -0.332 3.230 33.644 A A 6 7 -0.849 A A 15 14 3.190 -0.491 0.458 -1.432 AA_G6C7:G14C15_AA 12 1.836 -3.173 33.592 -2.395 -0.498 2.542 -57.744 A A 7 8 4.923 A A 14 52 2.619 -4.745 0.602 -1.434 AA_C7C8:C52G14_AA 13 -4.812 -4.993 -57.381 1.686 0.419 -0.996 -7.127 A A 9 51 -9.863 A A 48 47 2.902 0.926 -2.013 -0.134 AA_A9A51:U47G48_AA 14 -6.725 -71.595 -2.173 -0.449 -27.277 2.961 89.360 A A 51 54 2.699 A A 47 46 3.091 3.794 1.873 -2.124 AA_A51C54:G46U47_AA 15 -3.371 2.398 89.246 -1.583 -1.396 2.835 32.214 A A 54 55 7.723 A A 46 45 3.111 4.273 -0.649 -2.083 AA_C54C55:G45G46_AA 16 -1.065 1.925 31.920 -4.449 0.996 3.032 31.129 A A 55 56 8.838 A A 45 44 3.313 4.719 -0.434 -1.824 AA_C55C56:G44G45_AA 17 -2.910 5.450 30.643 -4.281 0.264 3.010 32.207 A A 56 57 9.989 A A 44 43 3.362 5.515 0.176 -1.808 AA_C56G57:C43G44_AA 18 -0.495 0.896 31.740 -4.225 -0.404 2.977 39.303 A A 57 58 0.734 A A 43 72 3.020 0.493 0.272 -1.284 AA_G57C58:G72C43_AA 19 -2.943 4.379 39.195 -1.962 -0.726 2.727 38.123 A A 58 59 15.719 A A 72 71 3.115 10.151 1.000 -1.214 AA_C58C59:G71G72_AA 20 1.177 -1.823 36.777 -3.028 -1.395 2.909 36.308 A A 59 60 12.291 A A 71 70 3.329 7.604 -0.032 -1.717 AA_C59C60:G70G71_AA 21 1.273 -2.057 35.507 -3.781 0.222 1.665 36.601 A A 60 76 20.098 A A 70 69 2.855 12.376 -0.737 -2.949 AA_C60U76:A69G70_AA 22 2.874 -4.668 34.396 -5.911 1.456 3.230 29.300 A A 76 77 -9.055 A A 69 68 3.070 -4.557 -0.873 -0.895 AA_U76C77:G68A69_AA 23 -2.390 4.748 28.854 -0.815 1.225 1.983 30.804 A A 77 78 25.092 A A 68 67 3.013 12.914 -0.265 -1.885 AA_C77G78:C67G68_AA 24 -2.918 5.670 27.876 -5.575 0.041 2.791 35.720 A A 78 79 13.084 A A 67 66 3.125 7.962 -0.356 -1.221 AA_G78G79:C66C67_AA 25 -0.317 0.521 34.849 -3.045 0.538 3.173 35.167 A A 79 80 9.126 A A 66 65 3.377 5.486 0.144 -1.098 AA_G79A80:U65C66_AA 26 3.016 -5.016 34.622 -2.644 0.215 3.379 32.130 A A 80 81 2.480 A A 65 64 3.313 1.367 0.956 -0.839 AA_A80A81:U64U65_AA 27 4.814 -8.732 31.748 -1.767 -0.840 0.477 -163.456 A A 81 83 66.690 A A 64 63 -0.672 -128.191 6.554 -2.690 AA_A81C83:C63U64_AA 28 -87.609 -45.578 -95.580 1.328 3.332 citation pdbx_audit_support pdbx_database_status pdbx_entity_src_syn pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list pdbx_validate_close_contact pdbx_audit_support chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle refine_hist struct_conn struct_conn_type repository Initial release Database references Database references Database references Advisory Author supporting evidence Database references Derived calculations Other Source and taxonomy Author supporting evidence Data collection Database references Derived calculations Refinement description 1 0 2014-06-04 1 1 2014-06-25 1 2 2014-07-30 1 3 2014-10-01 1 4 2017-09-06 1 5 2019-11-20 1 6 2023-12-27 _citation.journal_id_CSD _pdbx_audit_support.funding_organization _pdbx_database_status.pdb_format_compatible _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_struct_assembly.oligomeric_details _pdbx_struct_oper_list.symmetry_operation _pdbx_audit_support.funding_organization _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id United States Howard Hughes Medical Institute (HHMI) United States National Institutes of Health/National Cancer Institute (NIH/NCI) P30CA046934 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM081346 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM097333 United States Department of Energy (DOE, United States) DE-AC02-05CH11231 N RCSB Y RCSB 2014-03-17 REL REL MG MAGNESIUM ION IRI IRIDIUM HEXAMMINE ION SPM SPERMINE HOH water RNA was prepared by in vitro transcription with T7 RNA polymerase 12154 Turnip yellow mosaic virus sample 1 86 MG 1 2 MG MG 101 A MG 1 2 MG MG 102 A IRI 1 3 IRI IRI 103 A IRI 1 3 IRI IRI 104 A IRI 1 3 IRI IRI 105 A IRI 1 3 IRI IRI 106 A IRI 1 3 IRI IRI 107 A IRI 1 3 IRI IRI 108 A IRI 1 3 IRI IRI 109 A IRI 1 3 IRI IRI 110 A IRI 1 3 IRI IRI 111 A IRI 1 3 IRI IRI 112 A IRI 1 3 IRI IRI 113 A IRI 1 3 IRI IRI 114 A SPM 1 4 SPM SPM 115 A HOH 16 5 HOH HOH 201 A HOH 40 5 HOH HOH 202 A HOH 61 5 HOH HOH 203 A HOH 15 5 HOH HOH 204 A HOH 62 5 HOH HOH 205 A HOH 43 5 HOH HOH 206 A HOH 72 5 HOH HOH 207 A HOH 58 5 HOH HOH 208 A HOH 46 5 HOH HOH 209 A HOH 112 5 HOH HOH 210 A HOH 19 5 HOH HOH 211 A HOH 53 5 HOH HOH 212 A HOH 29 5 HOH HOH 213 A HOH 45 5 HOH HOH 214 A HOH 48 5 HOH HOH 215 A HOH 22 5 HOH HOH 216 A HOH 49 5 HOH HOH 217 A HOH 44 5 HOH HOH 218 A HOH 31 5 HOH HOH 219 A HOH 57 5 HOH HOH 220 A HOH 120 5 HOH HOH 221 A HOH 54 5 HOH HOH 222 A HOH 123 5 HOH HOH 223 A HOH 1 5 HOH HOH 224 A HOH 2 5 HOH HOH 225 A HOH 3 5 HOH HOH 226 A HOH 4 5 HOH HOH 227 A HOH 5 5 HOH HOH 228 A HOH 6 5 HOH HOH 229 A HOH 7 5 HOH HOH 230 A HOH 8 5 HOH HOH 231 A HOH 9 5 HOH HOH 232 A HOH 10 5 HOH HOH 233 A HOH 11 5 HOH HOH 234 A HOH 12 5 HOH HOH 235 A HOH 13 5 HOH HOH 236 A HOH 14 5 HOH HOH 237 A HOH 17 5 HOH HOH 238 A HOH 18 5 HOH HOH 239 A HOH 20 5 HOH HOH 240 A HOH 21 5 HOH HOH 241 A HOH 23 5 HOH HOH 242 A HOH 24 5 HOH HOH 243 A HOH 25 5 HOH HOH 244 A HOH 26 5 HOH HOH 245 A HOH 27 5 HOH HOH 246 A HOH 28 5 HOH HOH 247 A HOH 30 5 HOH HOH 248 A HOH 32 5 HOH HOH 249 A HOH 33 5 HOH HOH 250 A HOH 34 5 HOH HOH 251 A HOH 35 5 HOH HOH 252 A HOH 36 5 HOH HOH 253 A HOH 37 5 HOH HOH 254 A HOH 38 5 HOH HOH 255 A HOH 39 5 HOH HOH 256 A HOH 41 5 HOH HOH 257 A HOH 42 5 HOH HOH 258 A HOH 47 5 HOH HOH 259 A HOH 50 5 HOH HOH 260 A HOH 51 5 HOH HOH 261 A HOH 52 5 HOH HOH 262 A HOH 55 5 HOH HOH 263 A HOH 56 5 HOH HOH 264 A HOH 59 5 HOH HOH 265 A HOH 60 5 HOH HOH 266 A HOH 63 5 HOH HOH 267 A HOH 64 5 HOH HOH 268 A HOH 65 5 HOH HOH 269 A HOH 66 5 HOH HOH 270 A HOH 67 5 HOH HOH 271 A HOH 68 5 HOH HOH 272 A HOH 69 5 HOH HOH 273 A HOH 70 5 HOH HOH 274 A HOH 71 5 HOH HOH 275 A HOH 73 5 HOH HOH 276 A HOH 74 5 HOH HOH 277 A HOH 75 5 HOH HOH 278 A HOH 76 5 HOH HOH 279 A HOH 77 5 HOH HOH 280 A HOH 78 5 HOH HOH 281 A HOH 79 5 HOH HOH 282 A HOH 80 5 HOH HOH 283 A HOH 81 5 HOH HOH 284 A HOH 82 5 HOH HOH 285 A HOH 83 5 HOH HOH 286 A HOH 84 5 HOH HOH 287 A HOH 85 5 HOH HOH 288 A HOH 86 5 HOH HOH 289 A HOH 87 5 HOH HOH 290 A HOH 88 5 HOH HOH 291 A HOH 89 5 HOH HOH 292 A HOH 90 5 HOH HOH 293 A HOH 91 5 HOH HOH 294 A HOH 92 5 HOH HOH 295 A HOH 93 5 HOH HOH 296 A HOH 94 5 HOH HOH 297 A HOH 95 5 HOH HOH 298 A HOH 96 5 HOH HOH 299 A HOH 97 5 HOH HOH 300 A HOH 98 5 HOH HOH 301 A HOH 99 5 HOH HOH 302 A HOH 100 5 HOH HOH 303 A HOH 101 5 HOH HOH 304 A HOH 102 5 HOH HOH 305 A HOH 103 5 HOH HOH 306 A HOH 104 5 HOH HOH 307 A HOH 105 5 HOH HOH 308 A HOH 106 5 HOH HOH 309 A HOH 107 5 HOH HOH 310 A HOH 108 5 HOH HOH 311 A HOH 109 5 HOH HOH 312 A HOH 110 5 HOH HOH 313 A HOH 111 5 HOH HOH 314 A HOH 113 5 HOH HOH 315 A HOH 114 5 HOH HOH 316 A HOH 115 5 HOH HOH 317 A HOH 116 5 HOH HOH 318 A HOH 117 5 HOH HOH 319 A HOH 118 5 HOH HOH 320 A HOH 119 5 HOH HOH 321 A HOH 121 5 HOH HOH 322 A HOH 122 5 HOH HOH 323 A HOH 124 5 HOH HOH 324 A HOH 125 5 HOH HOH 325 A HOH 126 5 HOH HOH 326 A n 1 -1 A n 2 0 A A 1 n 3 A 1 A G 2 n 4 G 2 A C 3 n 5 C 3 A U 4 n 6 U 4 A C 5 n 7 C 5 A G 6 n 8 G 6 A C 7 n 9 C 7 A C 8 n 10 C 8 A A 9 n 11 A 9 A G 10 n 12 G 10 A U 11 n 13 U 11 A U 12 n 14 U 12 A A 13 n 15 A 13 A G 14 n 16 G 14 A C 15 n 17 C 15 A G 16 n 18 G 16 A A 17 n 19 A 17 A G 18 n 20 G 18 A G 19 n 21 G 19 A U 20 n 22 U 20 A C 21 n 23 C 21 A U 22 n 24 U 22 A G 23 n 25 G 23 A U 24 n 26 U 24 A C 25 n 27 C 25 A U 26 n 28 U 26 A C 27 n 29 C 27 A G 28 n 30 G 28 A A 29 n 31 A 29 A C 30 n 32 C 30 A A 31 n 33 A 31 A C 32 n 34 C 32 A G 33 n 35 G 33 A A 34 n 36 A 34 A C 35 n 37 C 35 A A 36 n 38 A 36 A G 37 n 39 G 37 A A 38 n 40 A 38 A U 39 n 41 U 39 A A 40 n 42 A 40 A A 41 n 43 A 41 A U 42 n 44 U 42 A C 43 n 45 C 43 A G 44 n 46 G 44 A G 45 n 47 G 45 A G 46 n 48 G 46 A U 47 n 49 U 47 A G 48 n 50 G 48 A C 49 n 51 C 49 A A 50 n 52 A 50 A A 51 n 53 A 51 A C 52 n 54 C 52 A U 53 n 55 U 53 A C 54 n 56 C 54 A C 55 n 57 C 55 A C 56 n 58 C 56 A G 57 n 59 G 57 A C 58 n 60 C 58 A C 59 n 61 C 59 A C 60 n 62 C 60 A C 61 n 63 C 61 A U 62 n 64 U 62 A C 63 n 65 C 63 A U 64 n 66 U 64 A U 65 n 67 U 65 A C 66 n 68 C 66 A C 67 n 69 C 67 A G 68 n 70 G 68 A A 69 n 71 A 69 A G 70 n 72 G 70 A G 71 n 73 G 71 A G 72 n 74 G 72 A U 73 n 75 U 73 A C 74 n 76 C 74 A A 75 n 77 A 75 A U 76 n 78 U 76 A C 77 n 79 C 77 A G 78 n 80 G 78 A G 79 n 81 G 79 A A 80 n 82 A 80 A A 81 n 83 A 81 A C 82 n 84 C 82 A C 83 n 85 C 83 A A23 84 n 86 A23 84 A author_and_software_defined_assembly PISA 1 monomeric 4020 -40 14100 A A 40 A OP2 A 42 1_555 A MG 102 C MG MG 1_555 A HOH 225 Q O HOH 1_555 90.7 A A 40 A OP2 A 42 1_555 A MG 102 C MG MG 1_555 A HOH 228 Q O HOH 1_555 80.8 A HOH 225 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 228 Q O HOH 1_555 78.2 A A 40 A OP2 A 42 1_555 A MG 102 C MG MG 1_555 A HOH 244 Q O HOH 1_555 81.3 A HOH 225 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 244 Q O HOH 1_555 152.8 A HOH 228 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 244 Q O HOH 1_555 74.9 A A 40 A OP2 A 42 1_555 A MG 102 C MG MG 1_555 A HOH 252 Q O HOH 1_555 156.8 A HOH 225 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 252 Q O HOH 1_555 76.7 A HOH 228 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 252 Q O HOH 1_555 77.6 A HOH 244 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 252 Q O HOH 1_555 101.0 A A 40 A OP2 A 42 1_555 A MG 102 C MG MG 1_555 A HOH 273 Q O HOH 1_555 111.7 A HOH 225 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 273 Q O HOH 1_555 90.7 A HOH 228 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 273 Q O HOH 1_555 163.6 A HOH 244 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 273 Q O HOH 1_555 116.4 A HOH 252 Q O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 273 Q O HOH 1_555 88.2 A HOH 224 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 226 Q O HOH 1_555 88.2 A HOH 224 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 227 Q O HOH 1_555 88.8 A HOH 226 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 227 Q O HOH 1_555 174.8 A HOH 224 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 229 Q O HOH 1_555 172.6 A HOH 226 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 229 Q O HOH 1_555 87.6 A HOH 227 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 229 Q O HOH 1_555 95.9 A HOH 224 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 236 Q O HOH 1_555 92.8 A HOH 226 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 236 Q O HOH 1_555 93.1 A HOH 227 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 236 Q O HOH 1_555 82.9 A HOH 229 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 236 Q O HOH 1_555 93.4 A HOH 224 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 237 Q O HOH 1_555 94.2 A HOH 226 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 237 Q O HOH 1_555 91.5 A HOH 227 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 237 Q O HOH 1_555 92.9 A HOH 229 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 237 Q O HOH 1_555 79.9 A HOH 236 Q O HOH 1_555 A MG 101 B MG MG 1_555 A HOH 237 Q O HOH 1_555 171.7 A A23 84 modified residue A A23 86 A 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 HOH 219 Q HOH 1 A U -1 A U 1 1 Y 1 A U 0 A U 2 1 Y 1 A A O6 O G HOH 23 324 2.14 1 A A O2 N3 U IRI 26 104 2.17 1 A A N1 O IRI HOH 104 311 2.19 1 A G 48 0.049 SIDE CHAIN 1 -4.48 0.70 118.00 113.52 A A A N3 C4 N4 C C C 5 5 5 N 1 -5.11 0.80 109.40 104.29 A A A O5' C5' C4' A A A 9 9 9 N 1 -2.75 0.40 110.80 108.05 A A A C4 C5 N7 G G G 10 10 10 N 1 4.88 0.70 108.50 113.38 A A A O4' C1' N1 U U U 12 12 12 N 1 2.89 0.40 106.40 109.29 A A A C8 N9 C4 G G G 14 14 14 N 1 -4.17 0.50 113.10 108.93 A A A N7 C8 N9 G G G 16 16 16 N 1 3.51 0.40 106.40 109.91 A A A C8 N9 C4 G G G 16 16 16 N 1 4.20 0.60 119.90 124.10 A A A N1 C6 O6 G G G 16 16 16 N 1 -4.62 0.60 128.60 123.98 A A A C5 C6 O6 G G G 16 16 16 N 1 -4.65 0.60 128.60 123.95 A A A C5 C6 O6 G G G 23 23 23 N 1 -5.97 0.90 105.70 99.73 A A A O5' P OP2 U U U 42 42 42 N 1 -4.02 0.60 127.00 122.98 A A A C2 N3 C4 U U U 42 42 42 N 1 9.03 1.50 119.60 128.63 A A A OP1 P OP2 G G G 48 48 48 N 1 4.99 0.50 111.90 116.89 A A A C2 N3 C4 G G G 48 48 48 N 1 -3.19 0.50 128.60 125.41 A A A N3 C4 C5 G G G 48 48 48 N 1 -3.05 0.50 110.60 107.55 A A A C2 N3 C4 A A A 50 50 50 N 1 3.64 0.60 118.60 122.24 A A A N1 C6 N6 A A A 50 50 50 N 1 2.86 0.40 105.80 108.66 A A A C8 N9 C4 A A A 51 51 51 N 1 6.86 1.10 110.50 117.36 A A A O3' P OP1 A C C 51 52 52 Y 1 6.82 1.10 110.50 117.32 A A A O3' P OP2 C C C 58 59 59 Y 1 -5.31 0.60 118.90 113.59 A A A N1 C2 O2 C C C 60 60 60 N 1 -6.43 0.90 105.70 99.27 A A A O5' P OP2 U U U 62 62 62 N 1 -4.93 0.70 118.00 113.07 A A A N3 C4 N4 C C C 63 63 63 N 1 -11.00 0.90 105.70 94.70 A A A O5' P OP2 G G G 70 70 70 N 1 -6.59 0.90 105.70 99.11 A A A O5' P OP1 G G G 71 71 71 N 1 4.23 0.60 119.90 124.13 A A A N1 C6 O6 G G G 71 71 71 N 1 -4.64 0.60 128.60 123.96 A A A C5 C6 O6 G G G 71 71 71 N 1 4.43 0.60 118.60 123.03 A A A C6 N1 C2 A A A 75 75 75 N 1 -3.37 0.50 129.30 125.93 A A A N1 C2 N3 A A A 75 75 75 N 1 3.62 0.60 121.00 124.62 A A A C6 N1 C2 U U U 76 76 76 N 1 6.20 0.90 109.80 116.00 A A A C5' C4' O4' C C C 77 77 77 N 1 16.71 1.10 110.50 127.21 A A A O3' P OP2 C A23 A23 83 84 84 Y 1 A A N3 C4 A A 51 51 0.036 0.006 1.344 1.380 N 0.2396 0.2057 0.2088 1.9912 28.871 3790 41334 9.17 99.46 0.23 Random 1 FREE R-VALUE 1.34 SAD 27.57 0.90 1.11 ML FLAT BULK SOLVENT MODEL 1.9912 28.871 126 2011 100 1785 0 0.011 2078 1.791 3295 14.148 1042 0.082 420 0.013 84 0.3259 0.3046 2.0164 126 1239 90.00 0.3908 0.2973 2.0430 139 1395 100.00 0.3024 0.2883 2.0709 148 1410 100.00 0.3230 0.2830 2.1005 136 1379 100.00 0.2785 0.2746 2.1319 140 1391 100.00 0.2982 0.2567 2.1652 140 1396 100.00 0.2496 0.2360 2.2007 139 1388 100.00 0.2812 0.2346 2.2386 143 1410 100.00 0.2925 0.2277 2.2793 143 1401 100.00 0.2641 0.2262 2.3231 138 1363 100.00 0.2825 0.2316 2.3705 143 1413 100.00 0.2770 0.2279 2.4220 142 1419 100.00 0.2489 0.2295 2.4783 141 1377 100.00 0.3312 0.2501 2.5403 143 1396 100.00 0.2752 0.2497 2.6089 142 1396 100.00 0.2989 0.2521 2.6856 143 1404 100.00 0.2850 0.2557 2.7722 147 1400 100.00 0.2994 0.2741 2.8712 142 1395 100.00 0.3721 0.2373 2.9861 133 1391 100.00 0.2124 0.2053 3.1218 143 1404 100.00 0.2412 0.1825 3.2862 136 1403 100.00 0.2382 0.1804 3.4918 141 1413 100.00 0.1896 0.1743 3.7608 139 1369 100.00 0.2050 0.1764 4.1383 143 1421 100.00 0.1714 0.1695 4.7349 144 1387 100.00 0.2057 0.1556 5.9568 138 1392 100.00 0.2058 0.2029 28.8736 138 1392 98.00 1.99 66.0 4P5J 41343 2.0 .054 1 21.71 7.45 99.4 .82 1.99 2.03 2.19 1 94.7 refinement PHENIX (phenix.refine: 1.8.4_1496) Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA 1 N N 2 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 4 N N 5 N N covale 1.592 both A C 83 A O3' C 85 1_555 A A23 84 A P A23 86 1_555 metalc 2.013 A A 40 A OP2 A 42 1_555 A MG 102 C MG MG 1_555 metalc 2.033 A MG 101 B MG MG 1_555 A HOH 224 Q O HOH 1_555 metalc 2.129 A MG 101 B MG MG 1_555 A HOH 226 Q O HOH 1_555 metalc 2.021 A MG 101 B MG MG 1_555 A HOH 227 Q O HOH 1_555 metalc 2.332 A MG 101 B MG MG 1_555 A HOH 229 Q O HOH 1_555 metalc 2.103 A MG 101 B MG MG 1_555 A HOH 236 Q O HOH 1_555 metalc 2.197 A MG 101 B MG MG 1_555 A HOH 237 Q O HOH 1_555 metalc 2.249 A MG 102 C MG MG 1_555 A HOH 225 Q O HOH 1_555 metalc 2.376 A MG 102 C MG MG 1_555 A HOH 228 Q O HOH 1_555 metalc 2.123 A MG 102 C MG MG 1_555 A HOH 244 Q O HOH 1_555 metalc 2.238 A MG 102 C MG MG 1_555 A HOH 252 Q O HOH 1_555 metalc 2.144 A MG 102 C MG MG 1_555 A HOH 273 Q O HOH 1_555 hydrog WATSON-CRICK A G 2 A N1 G 4 1_555 A C 74 A N3 C 76 1_555 hydrog WATSON-CRICK A G 2 A N2 G 4 1_555 A C 74 A O2 C 76 1_555 hydrog WATSON-CRICK A G 2 A O6 G 4 1_555 A C 74 A N4 C 76 1_555 hydrog WATSON-CRICK A C 3 A N3 C 5 1_555 A G 18 A N1 G 20 1_555 hydrog WATSON-CRICK A C 3 A N4 C 5 1_555 A G 18 A O6 G 20 1_555 hydrog WATSON-CRICK A C 3 A O2 C 5 1_555 A G 18 A N2 G 20 1_555 hydrog WATSON-CRICK A U 4 A N3 U 6 1_555 A A 17 A N1 A 19 1_555 hydrog WATSON-CRICK A U 4 A O4 U 6 1_555 A A 17 A N6 A 19 1_555 hydrog WATSON-CRICK A C 5 A N3 C 7 1_555 A G 16 A N1 G 18 1_555 hydrog WATSON-CRICK A C 5 A N4 C 7 1_555 A G 16 A O6 G 18 1_555 hydrog WATSON-CRICK A C 5 A O2 C 7 1_555 A G 16 A N2 G 18 1_555 hydrog WATSON-CRICK A G 6 A N1 G 8 1_555 A C 15 A N3 C 17 1_555 hydrog WATSON-CRICK A G 6 A N2 G 8 1_555 A C 15 A O2 C 17 1_555 hydrog WATSON-CRICK A G 6 A O6 G 8 1_555 A C 15 A N4 C 17 1_555 hydrog WATSON-CRICK A C 7 A N3 C 9 1_555 A G 14 A N1 G 16 1_555 hydrog WATSON-CRICK A C 7 A N4 C 9 1_555 A G 14 A O6 G 16 1_555 hydrog WATSON-CRICK A C 7 A O2 C 9 1_555 A G 14 A N2 G 16 1_555 hydrog TYPE_15_PAIR A C 8 A N4 C 10 1_555 A C 52 A O2 C 54 1_555 hydrog TYPE_15_PAIR A C 8 A O2 C 10 1_555 A C 52 A N4 C 54 1_555 hydrog TYPE_11_PAIR A A 9 A N6 A 11 1_555 A G 48 A N3 G 50 1_555 hydrog TYPE_11_PAIR A A 9 A N7 A 11 1_555 A G 48 A N2 G 50 1_555 hydrog WATSON-CRICK A G 10 A N1 G 12 1_555 A C 49 A N3 C 51 1_555 hydrog WATSON-CRICK A G 10 A N2 G 12 1_555 A C 49 A O2 C 51 1_555 hydrog WATSON-CRICK A G 10 A O6 G 12 1_555 A C 49 A N4 C 51 1_555 hydrog TYPE_28_PAIR A G 19 A N1 G 21 1_555 A U 39 A O2 U 41 1_555 hydrog TYPE_28_PAIR A G 19 A O6 G 21 1_555 A U 39 A N3 U 41 1_555 hydrog WATSON-CRICK A U 20 A N3 U 22 1_555 A A 38 A N1 A 40 1_555 hydrog WATSON-CRICK A U 20 A O4 U 22 1_555 A A 38 A N6 A 40 1_555 hydrog WATSON-CRICK A C 21 A N3 C 23 1_555 A G 37 A N1 G 39 1_555 hydrog WATSON-CRICK A C 21 A N4 C 23 1_555 A G 37 A O6 G 39 1_555 hydrog WATSON-CRICK A C 21 A O2 C 23 1_555 A G 37 A N2 G 39 1_555 hydrog WATSON-CRICK A U 22 A N3 U 24 1_555 A A 36 A N1 A 38 1_555 hydrog WATSON-CRICK A U 22 A O4 U 24 1_555 A A 36 A N6 A 38 1_555 hydrog WATSON-CRICK A G 23 A N1 G 25 1_555 A C 35 A N3 C 37 1_555 hydrog WATSON-CRICK A G 23 A N2 G 25 1_555 A C 35 A O2 C 37 1_555 hydrog WATSON-CRICK A G 23 A O6 G 25 1_555 A C 35 A N4 C 37 1_555 hydrog WATSON-CRICK A U 24 A N3 U 26 1_555 A A 34 A N1 A 36 1_555 hydrog WATSON-CRICK A U 24 A O4 U 26 1_555 A A 34 A N6 A 36 1_555 hydrog WATSON-CRICK A C 25 A N3 C 27 1_555 A G 33 A N1 G 35 1_555 hydrog WATSON-CRICK A C 25 A N4 C 27 1_555 A G 33 A O6 G 35 1_555 hydrog WATSON-CRICK A C 25 A O2 C 27 1_555 A G 33 A N2 G 35 1_555 hydrog U-C MISPAIR A U 26 A O4 U 28 1_555 A C 32 A N4 C 34 1_555 hydrog WATSON-CRICK A C 43 A N3 C 45 1_555 A G 57 A N1 G 59 1_555 hydrog WATSON-CRICK A C 43 A N4 C 45 1_555 A G 57 A O6 G 59 1_555 hydrog WATSON-CRICK A C 43 A O2 C 45 1_555 A G 57 A N2 G 59 1_555 hydrog WATSON-CRICK A G 44 A N1 G 46 1_555 A C 56 A N3 C 58 1_555 hydrog WATSON-CRICK A G 44 A N2 G 46 1_555 A C 56 A O2 C 58 1_555 hydrog WATSON-CRICK A G 44 A O6 G 46 1_555 A C 56 A N4 C 58 1_555 hydrog WATSON-CRICK A G 45 A N1 G 47 1_555 A C 55 A N3 C 57 1_555 hydrog WATSON-CRICK A G 45 A N2 G 47 1_555 A C 55 A O2 C 57 1_555 hydrog WATSON-CRICK A G 45 A O6 G 47 1_555 A C 55 A N4 C 57 1_555 hydrog WATSON-CRICK A G 46 A N1 G 48 1_555 A C 54 A N3 C 56 1_555 hydrog WATSON-CRICK A G 46 A N2 G 48 1_555 A C 54 A O2 C 56 1_555 hydrog WATSON-CRICK A G 46 A O6 G 48 1_555 A C 54 A N4 C 56 1_555 hydrog REVERSED HOOGSTEEN A U 47 A N3 U 49 1_555 A A 51 A N7 A 53 1_555 hydrog REVERSED HOOGSTEEN A U 47 A O2 U 49 1_555 A A 51 A N6 A 53 1_555 hydrog WATSON-CRICK A C 58 A N3 C 60 1_555 A G 72 A N1 G 74 1_555 hydrog WATSON-CRICK A C 58 A N4 C 60 1_555 A G 72 A O6 G 74 1_555 hydrog WATSON-CRICK A C 58 A O2 C 60 1_555 A G 72 A N2 G 74 1_555 hydrog WATSON-CRICK A C 59 A N3 C 61 1_555 A G 71 A N1 G 73 1_555 hydrog WATSON-CRICK A C 59 A N4 C 61 1_555 A G 71 A O6 G 73 1_555 hydrog WATSON-CRICK A C 59 A O2 C 61 1_555 A G 71 A N2 G 73 1_555 hydrog WATSON-CRICK A C 60 A N3 C 62 1_555 A G 70 A N1 G 72 1_555 hydrog WATSON-CRICK A C 60 A N4 C 62 1_555 A G 70 A O6 G 72 1_555 hydrog WATSON-CRICK A C 60 A O2 C 62 1_555 A G 70 A N2 G 72 1_555 hydrog C-C MISPAIR A C 61 A O2 C 63 1_555 A C 77 A N4 C 79 1_555 hydrog TYPE_15_PAIR A C 63 A N4 C 65 1_555 A C 83 A O2 C 85 1_555 hydrog TYPE_15_PAIR A C 63 A O2 C 65 1_555 A C 83 A N4 C 85 1_555 hydrog WATSON-CRICK A U 64 A N3 U 66 1_555 A A 81 A N1 A 83 1_555 hydrog WATSON-CRICK A U 64 A O4 U 66 1_555 A A 81 A N6 A 83 1_555 hydrog WATSON-CRICK A U 65 A N3 U 67 1_555 A A 80 A N1 A 82 1_555 hydrog WATSON-CRICK A U 65 A O4 U 67 1_555 A A 80 A N6 A 82 1_555 hydrog WATSON-CRICK A C 66 A N3 C 68 1_555 A G 79 A N1 G 81 1_555 hydrog WATSON-CRICK A C 66 A N4 C 68 1_555 A G 79 A O6 G 81 1_555 hydrog WATSON-CRICK A C 66 A O2 C 68 1_555 A G 79 A N2 G 81 1_555 hydrog WATSON-CRICK A C 67 A N3 C 69 1_555 A G 78 A N1 G 80 1_555 hydrog WATSON-CRICK A C 67 A N4 C 69 1_555 A G 78 A O6 G 80 1_555 hydrog WATSON-CRICK A C 67 A O2 C 69 1_555 A G 78 A N2 G 80 1_555 hydrog WATSON-CRICK A G 68 A N1 G 70 1_555 A C 77 A N3 C 79 1_555 hydrog WATSON-CRICK A G 68 A N2 G 70 1_555 A C 77 A O2 C 79 1_555 hydrog WATSON-CRICK A G 68 A O6 G 70 1_555 A C 77 A N4 C 79 1_555 hydrog WATSON-CRICK A A 69 A N1 A 71 1_555 A U 76 A N3 U 78 1_555 hydrog WATSON-CRICK A A 69 A N6 A 71 1_555 A U 76 A O4 U 78 1_555 hydrog G-A MISPAIR A G 71 A N2 G 73 1_555 A A 75 A N3 A 77 1_555 RNA tRNA-mimic viral RNA Pseudoknot multifunctional, RNA V01418.1 GB 1 610 62226 UUAGCUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCG GAACCA 610 695 4P5J -1 84 62226 A 1 1 86 1 C conflict U 26 4P5J A 62226 GB 637 28 1 C conflict G 28 4P5J A 62226 GB 639 30 binding site for residue MG A 101 A MG 101 Software 6 binding site for residue MG A 102 A MG 102 Software 6 binding site for residue IRI A 103 A IRI 103 Software 11 binding site for residue IRI A 104 A IRI 104 Software 4 binding site for residue IRI A 105 A IRI 105 Software 10 binding site for residue IRI A 106 A IRI 106 Software 6 binding site for residue IRI A 107 A IRI 107 Software 3 binding site for residue IRI A 108 A IRI 108 Software 5 binding site for residue IRI A 109 A IRI 109 Software 6 binding site for residue IRI A 110 A IRI 110 Software 3 binding site for residue IRI A 111 A IRI 111 Software 6 binding site for residue IRI A 112 A IRI 112 Software 3 binding site for residue IRI A 113 A IRI 113 Software 4 binding site for residue IRI A 114 A IRI 114 Software 5 binding site for residue SPM A 115 A SPM 115 Software 5 A HOH 224 Q HOH 6 1_555 A HOH 226 Q HOH 6 1_555 A HOH 227 Q HOH 6 1_555 A HOH 229 Q HOH 6 1_555 A HOH 236 Q HOH 6 1_555 A HOH 237 Q HOH 6 1_555 A A 40 A A 42 6 1_555 A HOH 225 Q HOH 6 1_555 A HOH 228 Q HOH 6 1_555 A HOH 244 Q HOH 6 1_555 A HOH 252 Q HOH 6 1_555 A HOH 273 Q HOH 6 1_555 A G 44 A G 46 11 1_555 A G 45 A G 47 11 1_555 A G 46 A G 48 11 1_555 A A 51 A A 53 11 1_555 A HOH 258 Q HOH 11 1_555 A HOH 272 Q HOH 11 1_555 A HOH 275 Q HOH 11 1_555 A HOH 284 Q HOH 11 1_555 A HOH 286 Q HOH 11 1_555 A HOH 287 Q HOH 11 1_555 A HOH 325 Q HOH 11 1_555 A U 26 A U 28 4 1_555 A C 30 A C 32 4 1_555 A HOH 311 Q HOH 4 1_555 A HOH 319 Q HOH 4 1_555 A C 56 A C 58 10 1_555 A G 57 A G 59 10 1_555 A C 58 A C 60 10 1_555 A G 71 A G 73 10 1_555 A G 72 A G 74 10 1_555 A HOH 248 Q HOH 10 1_555 A HOH 249 Q HOH 10 1_555 A HOH 290 Q HOH 10 1_555 A HOH 291 Q HOH 10 1_555 A HOH 310 Q HOH 10 1_555 A C 5 A C 7 6 2_665 A G 6 A G 8 6 2_665 A G 78 A G 80 6 1_555 A G 79 A G 81 6 1_555 A A23 84 A A23 86 6 1_555 A HOH 309 Q HOH 6 1_555 A G 45 A G 47 3 2_565 A C 60 A C 62 3 1_555 A U 62 A U 64 3 1_555 A U 47 A U 49 5 1_555 A G 48 A G 50 5 1_555 A A 50 A A 52 5 1_555 A HOH 203 Q HOH 5 1_555 A HOH 268 Q HOH 5 1_555 A A 17 A A 19 6 1_555 A G 18 A G 20 6 1_555 A G 19 A G 21 6 1_555 A U 39 A U 41 6 1_555 A HOH 282 Q HOH 6 1_555 A HOH 303 Q HOH 6 1_555 A C 60 A C 62 3 1_555 A C 61 A C 63 3 1_555 A A 75 A A 77 3 1_555 A C 43 A C 45 6 1_555 A G 44 A G 46 6 1_555 A G 57 A G 59 6 1_555 A C 58 A C 60 6 1_555 A C 59 A C 61 6 1_555 A U 73 A U 75 6 1_555 A A 1 A A 3 3 3_655 A G 2 A G 4 3 3_655 A U 22 A U 24 3 1_555 A U 11 A U 13 4 1_555 A U 12 A U 14 4 1_555 A G 28 A G 30 4 3_655 A C 83 A C 85 4 7_555 A G 14 A G 16 5 1_555 A U 39 A U 41 5 1_555 A A 40 A A 42 5 1_555 A A 41 A A 43 5 1_555 A HOH 273 Q HOH 5 1_555 A G 68 A G 70 5 2_665 A G 78 A G 80 5 2_665 A G 79 A G 81 5 1_555 A G 79 A G 81 5 2_665 A A 80 A A 82 5 1_555 23 I 2 2 2