0.008592 0.004960 0.000000 0.000000 0.009921 0.000000 0.000000 0.000000 0.017307 0.00000 0.00000 0.00000 Numata, T. Schneekloth, J.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 116.390 116.390 57.780 677859.217 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C16 H19 N3 O 269.342 ~{N},~{N}-dimethyl-2-[(1-methyl-9~{H}-pyrido[3,4-b]indol-7-yl)oxy]ethanamine non-polymer 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 C5 H11 O7 P 214.110 ANY 5'-MONOPHOSPHATE NUCLEOTIDE 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE RNA linking 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 C N 39 N N N 40 N C Y 41 N C N 42 N C Y 43 N C Y 44 N C Y 45 N C Y 46 N C Y 47 N C Y 48 N C Y 49 N C N 50 N C N 51 N C Y 52 N C Y 53 N C Y 54 N C Y 55 N N Y 56 N N N 57 N O 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 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 O N 154 N P N 155 N O N 156 N O N 157 N O N 158 N C N 159 R C N 160 N O N 161 S C N 162 N O N 163 R C N 164 N O N 165 R C N 166 N N N 167 N C N 168 N O N 169 N N N 170 N C N 171 N O N 172 N C N 173 N C 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 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 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 Y 41 N doub Y 42 N sing Y 43 N doub Y 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 Y 51 N doub Y 52 N sing Y 53 N doub Y 54 N sing Y 55 N sing Y 56 N doub Y 57 N sing Y 58 N doub Y 59 N sing Y 60 N sing Y 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N doub 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 sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub 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 N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing Y 141 N sing Y 142 N sing Y 143 N doub N 144 N sing Y 145 N sing N 146 N sing Y 147 N doub N 148 N doub 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 doub 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 doub N 186 N sing N 187 N sing N 188 N sing N 189 N doub N 190 N sing N 191 N doub N 192 N sing N 193 N sing US Biorxiv 2692-8205 10.1101/2024.02.23.581746 38903087 Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression. 2024 0000-0002-3960-4405 0000-0003-1671-3243 0000-0002-5027-2763 0000-0002-4244-8829 0000-0001-7459-783X 10.2210/pdb8yan/pdb pdb_00008yan 100 1 N PIXEL 2020-04-06 DECTRIS PILATUS 6M SINGLE WAVELENGTH M x-ray 1 1.0 1.0 BL45XU SPring-8 1.0 SYNCHROTRON SPRING-8 BEAMLINE BL45XU N means abasic site of the RNA 10224.107 RNA (33-MER) 1 syn polymer 269.342 ~{N},~{N}-dimethyl-2-[(1-methyl-9~{H}-pyrido[3,4-b]indol-7-yl)oxy]ethanamine 1 syn non-polymer 18.015 water 5 nat water no no CUGGGUCGCAGU(N)(N)(N)CCCAGUUAACAAAACAAG CUGGGUCGCAGUNNNCCCAGUUAACAAAACAAG 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 1 5.53 77.74 VAPOR DIFFUSION, HANGING DROP 5.6 0.1M potassium sodium tartrate, 0.1M sodium citrate (pH 5.6), 2.6M ammonium sulfate 293 1.951 1 19 A 1 A 20 -3.918 A_C1:G20_A 1 -12.305 -0.030 -0.143 -0.213 -0.777 1 20 A 2 A 19 -3.758 A_U2:A19_A 2 -21.175 0.319 0.171 -0.282 -6.128 1 19 A 3 A 18 -2.707 A_G3:C18_A 3 -10.034 0.154 0.057 -0.058 -3.619 1 19 A 4 A 17 -0.168 A_G4:C17_A 4 -14.421 0.184 0.219 -0.028 -7.878 1 19 A 5 A 16 0.921 A_G5:C16_A 5 -15.510 -0.141 0.087 0.066 -28.693 3 23 A 6 A 28 -70.655 A_U6:A28_A 6 -17.470 -0.415 1.711 3.431 -20.414 A 7 A 29 -43.977 A_C7:A29_A 7 18.468 4.662 2.285 -0.068 -4.328 1 19 A 11 A 30 1.187 A_G11:C30_A 8 -24.276 -0.567 0.341 -0.172 18.333 6 10 A 8 A 31 -65.755 A_G8:A31_A 9 13.120 3.952 -0.132 -4.244 8.820 10 A 10 A 32 -22.769 A_A10:A32_A 10 -14.565 6.475 -0.304 -4.363 -2.365 1 19 A 9 A 33 -3.570 A_C9:G33_A 11 -8.318 0.272 -0.203 -0.098 2.792 39.885 A A 1 2 14.006 A A 20 19 3.221 9.470 0.534 -1.485 AA_C1U2:A19G20_AA 1 -0.410 0.607 38.787 -3.196 -0.827 2.851 31.816 A A 2 3 14.006 A A 19 18 3.338 7.607 -0.294 -1.670 AA_U2G3:C18A19_AA 2 0.533 -0.981 30.912 -4.381 0.630 2.870 30.350 A A 3 4 9.608 A A 18 17 3.144 5.007 0.548 -1.552 AA_G3G4:C17C18_AA 3 1.103 -2.117 29.923 -3.898 -0.841 3.176 33.206 A A 4 5 7.007 A A 17 16 3.381 3.988 0.477 -1.823 AA_G4G5:C16C17_AA 4 3.524 -6.192 32.789 -3.865 -0.240 -2.500 25.610 A A 5 6 19.526 A A 16 28 1.174 8.166 -6.782 -1.202 AA_G5U6:A28C16_AA 5 11.835 -28.296 21.249 -2.196 14.555 3.908 51.754 A A 6 7 -0.986 A A 28 29 3.873 -0.860 2.743 -1.574 AA_U6C7:A29A28_AA 6 0.234 -0.268 51.747 -1.734 -3.124 0.655 179.579 A A 7 11 -49.139 A A 29 30 0.568 -98.237 0.776 -1.825 AA_C7G11:C30A29_AA 7 -149.363 74.713 139.814 -0.853 -0.478 0.798 -172.042 A A 11 8 5.099 A A 30 31 2.574 -10.062 -2.895 2.898 AA_G11G8:A31C30_AA 8 -164.386 -83.301 -117.196 -1.423 -1.921 4.873 -156.227 A A 8 10 -22.274 A A 31 32 -1.561 39.659 -6.227 2.731 AA_G8A10:A32A31_AA 9 150.553 84.554 -23.973 -1.743 -1.862 -3.371 -58.543 A A 10 9 1.687 A A 32 33 -3.373 -1.649 1.258 0.914 AA_A10C9:G33A32_AA 10 1.156 1.182 -58.511 -1.023 1.224 repository Initial release 1 0 2024-09-11 Japan Japan Society for the Promotion of Science (JSPS) 20K21281 Japan Japan Society for the Promotion of Science (JSPS) 20H02916 tomoyuki.numata94@agr.kyushu-u.ac.jp 0000-0002-4244-8829 Tomoyuki Numata principal investigator/group leader N PDBJ N PDBJ 2024-02-09 REL REL A1LYL A1LYL SUBJECT OF INVESTIGATION A1LYL ~{N},~{N}-dimethyl-2-[(1-methyl-9~{H}-pyrido[3,4-b]indol-7-yl)oxy]ethanamine HOH water 119072 Caldanaerobacter subterraneus subsp. tengcongensis sample 1 33 Y 6E1S PDB experimental model LIG 1 2 A1LYL A1LYL 101 A HOH 4 3 HOH HOH 201 A HOH 1 3 HOH HOH 202 A HOH 2 3 HOH HOH 203 A HOH 5 3 HOH HOH 204 A HOH 3 3 HOH HOH 205 A C 1 n 1 C 1 A U 2 n 2 U 2 A G 3 n 3 G 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A C 7 n 7 C 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A A 10 n 10 A 10 A G 11 n 11 G 11 A U 12 n 12 U 12 A N 13 n 13 N 13 A N 14 n 14 N 14 A N 15 n 15 N 15 A C 16 n 16 C 16 A C 17 n 17 C 17 A C 18 n 18 C 18 A A 19 n 19 A 19 A G 20 n 20 G 20 A U 21 n 21 U 21 A U 22 n 22 U 22 A A 23 n 23 A 23 A A 24 n 24 A 24 A C 25 n 25 C 25 A A 26 n 26 A 26 A A 27 n 27 A 27 A A 28 n 28 A 28 A A 29 n 29 A 29 A C 30 n 30 C 30 A A 31 n 31 A 31 A A 32 n 32 A 32 A G 33 n 33 G 33 A 3.1224 -1.5187 -1.3045 0.7379 0.6429 0.5508 0.5114 0.5199 -1.6633 -0.7764 0.1036 0.3717 0.4465 -0.3556 -0.4467 1.3938 -0.0279 -0.4175 0.6535 -0.2494 0.9120 refined 53.1733 -16.0544 -2.6816 X-RAY DIFFRACTION 6.2599 -7.7766 -7.3305 9.6219 9.0087 8.9018 0.8323 0.8706 -0.5290 -0.6989 -0.4590 -0.7968 -0.5145 -0.4538 -0.4169 1.0540 -0.0064 -0.2821 0.6370 -0.1863 0.8518 refined 52.9467 -11.1726 -6.8806 X-RAY DIFFRACTION 4.1771 1.6205 -0.7051 3.8793 3.7240 6.6046 0.3414 0.1017 -0.8230 0.0498 -0.1540 0.2525 0.6710 -0.8576 -0.1601 1.0609 -0.0182 -0.2476 0.6402 -0.0319 0.6647 refined 50.6400 -11.8220 -0.3417 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 10 ) X-RAY DIFFRACTION 2 chain 'A' and (resid 11 through 18 ) X-RAY DIFFRACTION 3 chain 'A' and (resid 19 through 33 ) author_defined_assembly 1 monomeric gel filtration 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 201 C HOH 96.87 0.214 0.198 2.25 41.0 570 11405 5 99.92 Random selection 1 FREE R-VALUE MOLECULAR REPLACEMENT GeoStd + Monomer Library + CDL v1.2 2.25 41.0 5 688 20 663 0 0.0016 762 0.3731 1181 0.0191 155 0.0034 31 15.2885 378 0.346 0.333 2.48 138 2630 99.9 2.25 41.0 8YAN 11424 0.999 0.064 0.012 1 32.4 31.2 99.9 3.62 2.25 2.39 1.44 1830 0.589 0.641 1 31.9 99.9 refinement PHENIX 1.17.1-3660 data reduction XDS data scaling XSCALE phasing PHASER 182 hexagonal P 63 2 2 P 6c 2c x,y,z x-y,x,z+1/2 y,-x+y,z+1/2 -y,x-y,z -x+y,-x,z x-y,-y,-z -x,-x+y,-z -x,-y,z+1/2 y,x,-z -y,-x,-z+1/2 -x+y,y,-z+1/2 x,x-y,-z+1/2 N Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1 N N 2 N N 3 N N covale 1.608 both A U 12 A O3' U 12 1_555 A N 13 A P N 13 1_555 covale 1.608 both A N 14 A O3' N 14 1_555 A N 15 A P N 15 1_555 covale 1.607 both A N 15 A O3' N 15 1_555 A C 16 A P C 16 1_555 hydrog WATSON-CRICK A C 1 A N3 C 1 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 1 A N4 C 1 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 1 A O2 C 1 1_555 A G 20 A N2 G 20 1_555 hydrog WATSON-CRICK A U 2 A N3 U 2 1_555 A A 19 A N1 A 19 1_555 hydrog WATSON-CRICK A U 2 A O4 U 2 1_555 A A 19 A N6 A 19 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 18 A N3 C 18 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 18 A O2 C 18 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 18 A N4 C 18 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 17 A N3 C 17 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 17 A O2 C 17 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 17 A N4 C 17 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 16 A N3 C 16 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 16 A O2 C 16 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 16 A N4 C 16 1_555 hydrog TYPE_10_PAIR A G 5 A N2 G 5 1_555 A A 27 A N1 A 27 1_555 hydrog TYPE_10_PAIR A G 5 A N3 G 5 1_555 A A 27 A N6 A 27 1_555 hydrog HOOGSTEEN A U 6 A N3 U 6 1_555 A A 28 A N7 A 28 1_555 hydrog HOOGSTEEN A U 6 A O4 U 6 1_555 A A 28 A N6 A 28 1_555 hydrog C-G PAIR A C 7 A N4 C 7 1_555 A G 11 A N7 G 11 1_555 hydrog C-A MISPAIR A C 7 A O2 C 7 1_555 A A 29 A N6 A 29 1_555 hydrog C-C MISPAIR A C 7 A O2 C 7 1_555 A C 30 A N4 C 30 1_555 hydrog TYPE_10_PAIR A G 8 A N2 G 8 1_555 A A 31 A N1 A 31 1_555 hydrog TYPE_10_PAIR A G 8 A N3 G 8 1_555 A A 31 A N6 A 31 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 33 A N1 G 33 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 33 A O6 G 33 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 33 A N2 G 33 1_555 hydrog A-A MISPAIR A A 10 A N3 A 10 1_555 A A 32 A N6 A 32 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 30 A N3 C 30 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 30 A O2 C 30 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 30 A N4 C 30 1_555 hydrog C-A MISPAIR A C 16 A O2 C 16 1_555 A A 28 A N6 A 28 1_555 hydrog C-A MISPAIR A C 17 A O2 C 17 1_555 A A 26 A N6 A 26 1_555 RNA Riboswitch, RNA 8YAN PDB 1 1 8YAN 1 33 8YAN 1 33 8YAN A 1 1 33 182 P 63 2 2 P 6c 2c