0.032338 0.000000 0.000000 0.000000 0.018835 0.000000 0.000000 0.000000 0.012743 0.00000 0.00000 0.00000 Kondo, J. Morishita, E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 30.923 53.093 78.476 C9 H12 Br N2 O9 P 403.077 n 5-BROMO-URIDINE-5'-MONOPHOSPHATE RNA linking 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 K 1 39.098 POTASSIUM ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N P N 2 N O 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 N 14 N N N 15 N C N 16 N O N 17 N N N 18 N C N 19 N O N 20 N C N 21 N C N 22 N BR N 23 N H 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 O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 R C N 46 N O N 47 R C Y 48 N N Y 49 N C Y 50 N N Y 51 N C Y 52 N C N 53 N N Y 54 N N Y 55 N C Y 56 N N Y 57 N C N 58 N H 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 O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 R C N 83 N O N 84 R C N 85 N N N 86 N C N 87 N O N 88 N N N 89 N C N 90 N N N 91 N C N 92 N C N 93 N H N 94 N H N 95 N H N 96 N H 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 O N 108 N P N 109 N O N 110 N O N 111 N O N 112 N C N 113 R C N 114 N O N 115 S C N 116 N O N 117 R C N 118 N O N 119 R C Y 120 N N Y 121 N C Y 122 N N Y 123 N C N 124 N C N 125 N O N 126 N N N 127 N C N 128 N N N 129 N N Y 130 N C N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H 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 K N 146 N O N 147 N P N 148 N O N 149 N O N 150 N O N 151 N C N 152 R C N 153 N O N 154 S C N 155 N O N 156 R C N 157 N O N 158 R C N 159 N N N 160 N C N 161 N O N 162 N N N 163 N C N 164 N O N 165 N C N 166 N C 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 H N 179 N H N 1 N doub N 2 N sing N 3 N sing 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 N 25 N sing N 26 N sing N 27 N doub N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing N 42 N sing 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 Y 60 N sing Y 61 N sing Y 62 N doub N 63 N sing Y 64 N sing Y 65 N sing Y 66 N doub N 67 N sing Y 68 N doub N 69 N sing N 70 N sing Y 71 N sing Y 72 N doub N 73 N sing Y 74 N sing N 75 N sing N 76 N sing N 77 N doub N 78 N sing 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 N 100 N sing N 101 N doub N 102 N sing N 103 N doub 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 sing N 111 N sing N 112 N sing N 113 N doub 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 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 Y 135 N sing Y 136 N sing Y 137 N doub N 138 N sing Y 139 N sing N 140 N sing Y 141 N doub N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N doub N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub 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 sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N doub N 184 N sing N 185 N sing DE Small Sci 2688-4046 6 e202600007 e202600007 10.1002/smsc.202600007 42006585 AI-Augmented Iterative Screening of Libraries Against RNA Targets (AISLAR) Boosts Discovery of SAR-Tractable RNA Binders and Rational Analog Design. 2026 0009-0002-3236-3220 0009-0003-8915-6019 0000-0002-5682-3685 0009-0007-7913-5192 0000-0002-6423-715X 10.2210/pdb9vsn/pdb pdb_00009vsn 100 1 N PIXEL 2021-06-05 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 0.91962 1.0 BL-17A Photon Factory 0.91962 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 7348.248 RNA (5'-R(*UP*UP*GP*GP*AP*AP*AP*CP*AP*UP*(5BU)P*CP*GP*AP*AP*CP*UP*AP*CP*UP*UP*CP*C)-3') 2 syn polymer 39.098 POTASSIUM ION 6 syn non-polymer no yes UUGGAAACAU(5BU)CGAACUACUUCC UUGGAAACAUUCGAACUACUUCC A,B polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n 1 2.19 43.88 VAPOR DIFFUSION, HANGING DROP MPD, MOPS, KCl, Spermine 293 -1.056 1 19 A 3 B 23 9.752 A_G3:C23_B 1 -6.121 -1.256 -0.005 -0.213 -2.378 1 19 A 4 B 22 3.395 A_G4:C22_B 2 -22.640 -0.472 -0.118 -0.228 -24.562 1 20 A 5 B 21 -12.027 A_A5:U21_B 3 -14.701 0.196 -0.901 0.128 17.336 A 8 B 17 2.460 A_C8:U17_B 4 -3.560 -6.176 0.134 -2.403 -1.082 1 A 9 B 16 8.866 A_A9:C16_B 5 -1.565 -2.171 0.147 -0.159 10.399 1 20 A 10 B 15 -5.188 A_U10:A15_B 6 1.873 0.099 -0.056 -0.218 0.342 1 20 A 11 B 14 -5.574 A_5BU11:A14_B 7 -12.267 0.267 -0.290 -0.503 4.927 1 19 A 12 B 13 -0.327 A_C12:G13_B 8 -9.785 0.594 -0.230 -0.590 -5.667 1 19 A 13 B 12 -3.876 A_G13:C12_B 9 -10.177 0.140 -0.416 -0.394 -10.080 1 20 A 14 B 11 -6.397 A_A14:5BU11_B 10 -10.739 -0.299 0.001 -0.459 2.444 1 20 A 15 B 10 11.020 A_A15:U10_B 11 -18.135 -0.570 0.027 -0.138 -12.974 1 A 16 B 9 13.021 A_C16:A9_B 12 -7.107 3.819 0.673 -0.833 -19.057 A 17 B 8 33.076 A_U17:C8_B 13 -12.642 7.127 1.060 -2.569 13.692 A 19 B 7 -36.115 A_C19:A7_B 14 -8.383 -5.142 -0.450 -0.181 5.120 A 20 B 6 -39.861 A_U20:A6_B 15 5.627 0.895 0.278 1.724 12.846 A 21 B 5 12.672 A_U21:A5_B 16 -3.840 -0.746 -0.507 0.758 17.627 1 19 A 22 B 4 -1.087 A_C22:G4_B 17 -11.673 -0.501 -0.598 0.279 0.550 1 19 A 23 B 3 3.472 A_C23:G3_B 18 -12.897 0.220 -0.513 -0.147 2.974 35.611 A A 3 4 11.225 B B 23 22 3.341 6.824 -0.055 -1.648 AA_G3G4:C22C23_BB 1 0.901 -1.481 34.961 -3.662 0.218 2.893 37.960 A A 4 5 20.549 B B 22 21 3.970 13.088 -1.063 -2.166 AA_G4A5:U21C22_BB 2 3.894 -6.113 35.504 -5.147 2.175 3.382 52.665 A A 8 9 15.121 B B 17 16 3.848 13.135 -0.081 -1.046 AA_C8A9:C16U17_BB 3 -14.568 16.772 49.119 -2.163 -1.000 2.923 41.782 A A 9 10 3.786 B B 16 15 3.002 2.698 -0.705 -1.477 AA_A9U10:A15C16_BB 4 -1.203 1.689 41.682 -2.328 0.874 2.704 33.895 A A 10 11 16.229 B B 15 14 3.490 9.325 -0.300 -2.250 AA_U105BU11:A14A15_BB 5 3.915 -6.813 32.394 -5.313 1.124 2.706 36.673 A A 11 12 15.415 B B 14 13 3.109 9.592 0.244 -1.216 AA_5BU11C12:G13A14_BB 6 1.082 -1.739 35.422 -3.123 -0.254 2.694 28.799 A A 12 13 21.909 B B 13 12 3.598 10.640 0.017 -1.794 AA_C12G13:C12G13_BB 7 1.997 -4.111 26.727 -5.985 0.411 2.661 27.374 A A 13 14 19.820 B B 12 11 3.427 9.203 0.507 -1.707 AA_G13A14:5BU11C12_BB 8 -0.477 1.027 25.804 -5.794 -1.184 2.543 36.844 A A 14 15 13.444 B B 11 10 2.891 8.414 1.055 -1.639 AA_A14A15:U105BU11_BB 9 3.550 -5.672 35.732 -3.556 -1.263 3.437 47.991 A A 15 16 8.050 B B 10 9 3.623 6.529 0.805 -1.142 AA_A15C16:A9U10_BB 10 -0.616 0.760 47.567 -1.962 -1.042 3.269 45.655 A A 16 17 6.156 B B 9 8 3.186 4.719 1.192 -0.984 AA_C16U17:C8A9_BB 11 11.922 -15.553 43.910 -1.685 -0.485 3.019 61.571 A A 19 20 32.976 B B 7 6 4.429 32.074 -2.083 -2.435 AA_C19U20:A6A7_BB 12 -14.076 14.472 51.461 -4.288 1.197 3.474 26.211 A A 20 21 -12.458 B B 6 5 3.607 -5.602 3.080 -0.879 AA_U20U21:A5A6_BB 13 -1.962 4.362 25.542 -0.276 -7.374 2.158 37.761 A A 21 22 22.657 B B 5 4 2.996 14.262 -0.743 -1.929 AA_U21C22:G4A5_BB 14 -5.942 9.440 34.561 -4.501 0.515 3.270 33.789 A A 22 23 14.986 B B 4 3 3.880 8.619 0.061 -1.973 AA_C22C23:G3G4_BB 15 0.438 -0.762 32.699 -4.945 -0.026 repository Initial release 1 0 2026-05-20 Japan Japan Agency for Medical Research and Development (AMED) JP22ama121014 Japan Japan Agency for Medical Research and Development (AMED) JP23ama121014 j.kondo@sophia.ac.jp 0000-0002-5682-3685 Jiro Kondo principal investigator/group leader N PDBJ Y PDBJ 2025-07-09 REL REL K POTASSIUM ION 32630 synthetic construct sample 1 23 N N RNA duplex constructed using Coot Other in silico model K 1 2 K K 101 A K 3 2 K K 102 A K 4 2 K K 103 A K 2 2 K K 101 B K 5 2 K K 102 B K 6 2 K K 103 B U 1 n 1 U 1 A U 2 n 2 U 2 A G 3 n 3 G 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A A 6 n 6 A 6 A A 7 n 7 A 7 A C 8 n 8 C 8 A A 9 n 9 A 9 A U 10 n 10 U 10 A 5BU 11 n 11 5BU 11 A C 12 n 12 C 12 A G 13 n 13 G 13 A A 14 n 14 A 14 A A 15 n 15 A 15 A C 16 n 16 C 16 A U 17 n 17 U 17 A A 18 n 18 A 18 A C 19 n 19 C 19 A U 20 n 20 U 20 A U 21 n 21 U 21 A C 22 n 22 C 22 A C 23 n 23 C 23 A U 1 n 1 U 1 B U 2 n 2 U 2 B G 3 n 3 G 3 B G 4 n 4 G 4 B A 5 n 5 A 5 B A 6 n 6 A 6 B A 7 n 7 A 7 B C 8 n 8 C 8 B A 9 n 9 A 9 B U 10 n 10 U 10 B 5BU 11 n 11 5BU 11 B C 12 n 12 C 12 B G 13 n 13 G 13 B A 14 n 14 A 14 B A 15 n 15 A 15 B C 16 n 16 C 16 B U 17 n 17 U 17 B A 18 n 18 A 18 B C 19 n 19 C 19 B U 20 n 20 U 20 B U 21 n 21 U 21 B C 22 n 22 C 22 B C 23 n 23 C 23 B author_and_software_defined_assembly PISA 2 dimeric none 4770 -24 7870 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 0.2636 0.2189 0.2234 3.10 31.56 441 4452 9.91 98.23 0.32 1 FREE R-VALUE 1.37 MOLECULAR REPLACEMENT 33.57 0.90 1.11 RNA duplex constructed using Coot ML FLAT BULK SOLVENT MODEL 3.10 31.56 0 968 6 962 0 0.006 1072 1.057 1664 11.198 528 0.044 226 0.006 46 0.3692 0.2769 3.55 143 1338 97.00 0.2524 0.2127 4.46 149 1334 99.00 0.2329 0.2018 31.56 149 1339 99.00 3.1 31.56 9VSN 4463 0.994 0.101 0.121 1 7.27 3.4 98.5 0.382 3.10 3.18 314 0.922 0.461 1 0.305 3.18 3.27 316 0.929 0.371 1 0.28 3.27 3.36 325 0.965 0.34 1 0.288 3.36 3.46 310 0.958 0.351 1 0.185 3.46 3.58 286 0.974 0.224 1 0.217 3.58 3.7 279 0.967 0.261 1 0.176 3.70 3.84 294 0.981 0.207 1 0.15 3.84 4.0 254 0.982 0.176 1 0.116 4.00 4.18 245 0.984 0.137 1 0.107 4.18 4.38 265 0.993 0.125 1 0.094 4.38 4.62 218 0.993 0.11 1 0.088 4.62 4.9 223 0.995 0.103 1 0.075 4.90 5.24 218 0.996 0.088 1 0.076 5.24 5.66 187 0.995 0.088 1 0.078 5.66 6.2 185 0.995 0.092 1 0.076 6.20 6.93 147 0.993 0.089 1 0.075 6.93 8.0 144 0.991 0.088 1 0.08 8.00 9.8 117 0.991 0.094 1 0.071 9.80 13.85 90 0.994 0.084 1 0.068 13.85 31.56 46 0.993 0.09 1 refinement PHENIX (1.17.1_3660: ???) data scaling XSCALE phasing PHASER data extraction PDB_EXTRACT N Crystal structure of RNA duplex containing an IRES internal loop 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N covale 1.602 both A U 10 A O3' U 10 1_555 A 5BU 11 A P 5BU 11 1_555 covale 1.607 both A 5BU 11 A O3' 5BU 11 1_555 A C 12 A P C 12 1_555 covale 1.611 both B U 10 B O3' U 10 1_555 B 5BU 11 B P 5BU 11 1_555 covale 1.609 both B 5BU 11 B O3' 5BU 11 1_555 B C 12 B P C 12 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 B C 23 B N3 C 23 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 B C 23 B O2 C 23 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 B C 23 B N4 C 23 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B C 22 B N3 C 22 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B C 22 B O2 C 22 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B C 22 B N4 C 22 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 B U 21 B N3 U 21 1_555 hydrog WATSON-CRICK A A 5 A N6 A 5 1_555 B U 21 B O4 U 21 1_555 hydrog A-U PAIR A A 7 A N6 A 7 1_555 B U 17 B O2 U 17 1_555 hydrog C-U MISPAIR A C 8 A N4 C 8 1_555 B U 17 B O2 U 17 1_555 hydrog A-C MISPAIR A A 9 A N6 A 9 1_555 B C 16 B N3 C 16 1_555 hydrog WATSON-CRICK A U 10 A N3 U 10 1_555 B A 15 B N1 A 15 1_555 hydrog WATSON-CRICK A U 10 A O4 U 10 1_555 B A 15 B N6 A 15 1_555 hydrog WATSON-CRICK A 5BU 11 A N3 5BU 11 1_555 B A 14 B N1 A 14 1_555 hydrog WATSON-CRICK A 5BU 11 A O4 5BU 11 1_555 B A 14 B N6 A 14 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 B G 13 B N1 G 13 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 B G 13 B O6 G 13 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 B G 13 B N2 G 13 1_555 hydrog WATSON-CRICK A G 13 A N1 G 13 1_555 B C 12 B N3 C 12 1_555 hydrog WATSON-CRICK A G 13 A N2 G 13 1_555 B C 12 B O2 C 12 1_555 hydrog WATSON-CRICK A G 13 A O6 G 13 1_555 B C 12 B N4 C 12 1_555 hydrog WATSON-CRICK A A 14 A N1 A 14 1_555 B 5BU 11 B N3 5BU 11 1_555 hydrog WATSON-CRICK A A 14 A N6 A 14 1_555 B 5BU 11 B O4 5BU 11 1_555 hydrog WATSON-CRICK A A 15 A N1 A 15 1_555 B U 10 B N3 U 10 1_555 hydrog WATSON-CRICK A A 15 A N6 A 15 1_555 B U 10 B O4 U 10 1_555 hydrog C-A MISPAIR A C 16 A O2 C 16 1_555 B A 9 B N6 A 9 1_555 hydrog U-C MISPAIR A U 17 A O2 U 17 1_555 B C 8 B N4 C 8 1_555 hydrog TYPE_2_PAIR A A 18 A N6 A 18 1_555 B A 6 B N7 A 6 1_555 hydrog TYPE_2_PAIR A A 18 A N7 A 18 1_555 B A 6 B N6 A 6 1_555 hydrog C-A MISPAIR A C 19 A N4 C 19 1_555 B A 7 B N1 A 7 1_555 hydrog U-A PAIR A U 20 A O4 U 20 1_555 B A 6 B N6 A 6 1_555 hydrog U-A PAIR A U 21 A N3 U 21 1_555 B A 5 B N1 A 5 1_555 hydrog WATSON-CRICK A C 22 A N3 C 22 1_555 B G 4 B N1 G 4 1_555 hydrog WATSON-CRICK A C 22 A N4 C 22 1_555 B G 4 B O6 G 4 1_555 hydrog WATSON-CRICK A C 22 A O2 C 22 1_555 B G 4 B N2 G 4 1_555 hydrog WATSON-CRICK A C 23 A N3 C 23 1_555 B G 3 B N1 G 3 1_555 hydrog WATSON-CRICK A C 23 A N4 C 23 1_555 B G 3 B O6 G 3 1_555 hydrog WATSON-CRICK A C 23 A O2 C 23 1_555 B G 3 B N2 G 3 1_555 RNA IRES, RNA 9VSN PDB 1 1 9VSN 1 23 9VSN 1 23 9VSN A 1 1 23 1 23 9VSN 1 23 9VSN B 1 1 23 19 P 21 21 21