0.014021 0.000000 0.000000 0.000000 0.014021 0.000000 0.000000 0.000000 0.011974 0.00000 0.00000 0.00000 3.54356 2.42580 25.62398 1.50364 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0.51345 0.48472 24.73122 6.32584 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.41153 2.53737 2.59044 63.03566 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.01032 2.96436 19.97189 1.75589 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.38062 1.54875 3.38349 72.32734 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.49882 3.47563 15.80542 1.70748 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.51135 5.44231 1.42069 35.72801 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 0000-0002-0586-0742 Chen, H.-A. 0009-0000-7822-2066 Scheitl, C.P.M. 0000-0002-4548-2299 Hoebartner, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 71.323 71.323 83.512 424823.066 C11 H16 N5 O7 P 361.248 n 6-HYDRO-1-METHYLADENOSINE-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 C5 H5 N5 O 151.126 GUANINE non-polymer H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer Na 1 22.990 SODIUM ION non-polymer C10 H16 N3 O8 P 337.223 n O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H15 N2 O9 P 338.208 n O2'-METHYLURIDINE 5'-MONOPHOSPHATE RNA linking 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 Y 14 N N Y 15 N C Y 16 N N Y 17 N C N 18 N C N 19 N N N 20 N N N 21 N C N 22 N C N 23 N N Y 24 N C 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 H N 39 N H N 40 N H N 41 N O N 42 N P 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 S 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 H N 78 N O N 79 N P N 80 N O N 81 N O N 82 N O N 83 N C N 84 R C N 85 N O N 86 S C N 87 N O N 88 R C N 89 N O N 90 R C N 91 N N N 92 N C N 93 N O N 94 N N N 95 N C N 96 N N N 97 N C N 98 N C 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 H N 113 N O N 114 N P N 115 N O N 116 N O N 117 N O N 118 N C N 119 R C N 120 N O N 121 S C N 122 N O N 123 R C N 124 N O N 125 R C Y 126 N N Y 127 N C Y 128 N N Y 129 N C N 130 N C N 131 N O N 132 N N N 133 N C N 134 N N N 135 N N Y 136 N C 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 H Y 151 N N Y 152 N C Y 153 N N Y 154 N C N 155 N C N 156 N O N 157 N N N 158 N C N 159 N N N 160 N N Y 161 N C N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N O N 168 N H N 169 N H N 170 N MG N 171 N NA N 172 N N N 173 N C N 174 N N N 175 N C N 176 N C N 177 N C N 178 N O N 179 N N N 180 R C N 181 R C N 182 N O N 183 N C N 184 R C N 185 R C N 186 N O N 187 N O N 188 N C N 189 N O N 190 N P N 191 N O N 192 N O N 193 N O 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 N N 211 N C N 212 N N N 213 N C N 214 N C N 215 N C N 216 N O N 217 N O N 218 R C N 219 R C N 220 N O N 221 N C N 222 R C N 223 R C N 224 N O N 225 N O N 226 N C N 227 N O N 228 N P N 229 N O N 230 N O N 231 N O N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H 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 O N 248 N P N 249 N O N 250 N O N 251 N O N 252 N C N 253 R C N 254 N O N 255 S C N 256 N O N 257 R C N 258 N O N 259 R C N 260 N N N 261 N C N 262 N O N 263 N N N 264 N C N 265 N O N 266 N C N 267 N C N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 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 Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing N 30 N sing Y 31 N doub N 32 N doub N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 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 Y 158 N sing Y 159 N sing N 160 N sing Y 161 N doub N 162 N sing Y 163 N sing N 164 N sing Y 165 N doub N 166 N doub 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 doub N 182 N doub 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 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 doub 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 doub N 221 N sing N 222 N sing N 223 N sing N 224 N doub 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 sing N 254 N sing N 255 N sing N 256 N doub N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N doub N 281 N sing N 282 N sing N 283 N sing N 284 N doub N 285 N sing N 286 N doub N 287 N sing N 288 N sing UK Nat Commun 2041-1723 10.1038/s41467-026-75575-8 42469241 A magic methyl effect in the active site of a methyltransferase ribozyme. 2026 US Nat Chem Biol 1552-4469 18 547 555 10.1038/s41589-022-00976-x 35301481 Structure and mechanism of the methyltransferase ribozyme MTR1. 2022 0009-0000-7822-2066 0000-0002-2067-3187 0000-0002-4548-2299 10.2210/pdb9s1d/pdb pdb_00009s1d 100 cold nitrogen stream 1 N PIXEL 2021-06-06 DECTRIS EIGER2 X 16M Si-111 and Si-113 reflection SINGLE WAVELENGTH M x-ray 1 1.0332 1.0 P11 PETRA III, DESY 1.0332 SYNCHROTRON PETRA III, DESY BEAMLINE P11 Chemically synthesized RNA oligonucleotide. N1-methylation of A7 occurred during crystallization process. 4436.710 Chains: A 1 syn polymer Chemically synthesized RNA oligonucleotide. 2'O-methyl modification at position 12 was introduced during solid-phase synthesis. 7655.662 Chains: B 1 syn polymer Chemically synthesized RNA oligonucleotide. 2'O-methyl modification at position 42 was introduced during solid-phase synthesis. 7769.729 Chains: C 1 syn polymer 24.305 MAGNESIUM ION 2 syn non-polymer 22.990 SODIUM ION 2 syn non-polymer 151.126 GUANINE 1 syn non-polymer 18.015 water 45 nat water no yes CCACUG(1MA)GAGCUUC CCACUGAGAGCUUC A polyribonucleotide no yes GGAAGCUCUGA(OMC)CGACCCCCAGCC GGAAGCUCUGACCGACCCCCAGCC B polyribonucleotide no yes GCUGGGACAACUAGACA(OMU)ACAGUG GCUGGGACAACUAGACAUACAGUG C 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 1 2.53 67.16 50-150 um short rod VAPOR DIFFUSION, HANGING DROP 7.5 200 uM RNA in a ratio of A:B:C=1:1:1 in 10 mM HEPES pH7.5, 50 mM potassium chloride, 5 mM magnesium chloride and 240 uM of O6-methylguanine Crystallization cocktail: 100 mM NaCl, 100 mM LiCl, 10 mM MgCl2, 50 mM MES pH 6.4-6.7, 36-42% MPD 6.4-6.7 293.15 Growth in a thermally controlled cabinet -1.792 1 19 A 2 C 48 1.797 A_C2:G48_C 1 -1.920 -0.498 0.259 0.163 7.302 1 20 A 3 C 47 3.551 A_A3:U47_C 2 -7.876 -0.270 0.470 -0.038 5.386 1 19 A 4 C 46 5.360 A_C4:G46_C 3 -12.837 -0.267 0.114 0.173 1.323 1 20 A 5 C 45 9.829 A_U5:A45_C 4 -13.219 0.122 0.096 0.146 -5.164 1 19 A 6 C 44 3.117 A_G6:C44_C 5 -14.522 -0.344 -0.026 0.017 26.640 5 B 11 C 43 58.885 B_A11:A43_C 6 9.512 -6.286 -0.392 -0.474 -10.499 1 19 B 13 C 38 -1.604 B_C13:G38_C 7 -2.323 -0.160 0.398 0.090 -11.478 1 19 B 14 C 35 1.102 B_G14:C35_C 8 -3.877 -0.147 -0.605 -0.009 -3.434 1 19 B 2 A 14 -4.175 B_G2:C14_A 9 -10.358 0.266 0.116 0.124 -0.894 1 20 B 3 A 13 5.798 B_A3:U13_A 10 -17.598 -0.437 -0.391 0.083 10.036 1 B 4 A 12 14.093 B_A4:U12_A 11 -19.638 -0.082 0.633 0.236 -13.740 1 19 B 5 A 11 4.648 B_G5:C11_A 12 -24.354 0.314 -0.444 0.066 -0.754 1 19 B 6 A 10 -8.112 B_C6:G10_A 13 -16.147 1.613 -0.213 -0.522 -3.185 1 20 B 7 A 9 1.384 B_U7:A9_A 14 -14.272 0.473 -0.188 0.182 0.294 1 19 B 8 A 8 1.631 B_C8:G8_A 15 -9.661 1.195 0.050 -0.078 -11.605 4 24 B 9 C 34 -102.518 B_U9:A34_C 16 -5.642 4.565 -0.700 -2.369 44.584 B 17 C 31 -5.247 B_C17:A31_C 17 -24.169 -2.889 -1.393 0.682 16.276 1 19 B 18 C 30 2.758 B_C18:G30_C 18 -17.651 0.247 -0.329 0.038 8.090 1 19 B 19 C 29 1.106 B_C19:G29_C 19 -12.172 -0.035 -0.312 0.017 4.273 1 19 B 20 C 28 4.968 B_C20:G28_C 20 -6.565 -0.050 -0.163 -0.029 -6.584 1 20 B 21 C 27 8.261 B_A21:U27_C 21 -15.836 -0.220 -0.039 -0.037 -7.863 1 19 B 22 C 26 7.243 B_G22:C26_C 22 -21.209 0.685 -0.067 0.024 -6.358 1 19 B 23 C 25 -3.866 B_C23:G25_C 23 -7.624 0.803 0.306 -0.385 2.111 33.174 A A 2 3 19.288 C C 48 47 2.741 10.798 -0.339 -1.602 AA_C2A3:U47G48_CC 1 -3.813 6.811 31.187 -4.194 0.104 2.858 32.770 A A 3 4 15.001 C C 47 46 3.316 8.366 -0.092 -1.355 AA_A3C4:G46U47_CC 2 2.471 -4.430 31.618 -3.787 0.572 2.815 32.826 A A 4 5 14.284 C C 46 45 3.316 7.994 0.457 -1.671 AA_C4U5:A45G46_CC 3 -0.659 1.178 31.856 -4.263 -0.916 2.558 33.386 A A 5 6 19.501 C C 45 44 3.270 11.002 -0.265 -1.634 AA_U5G6:C44A45_CC 4 1.380 -2.445 31.540 -4.518 0.671 1.600 67.085 A B 6 11 16.089 C C 44 43 3.334 17.490 -3.620 -3.557 AB_G6A11:A43C44_CC 5 15.298 -14.072 63.378 -3.753 3.743 6.561 123.372 B B 11 13 5.857 C C 43 38 6.764 10.301 1.733 -1.535 BB_A11C13:G38A43_CC 6 -13.054 7.422 122.716 -1.056 -1.219 2.521 25.209 B B 13 14 14.169 C C 38 35 3.336 6.033 -0.482 -1.826 BB_C13G14:C35G38_CC 7 7.452 -17.501 23.341 -5.826 3.134 2.455 32.019 B B 2 3 23.948 A A 14 13 3.163 12.833 0.100 -1.143 BB_G2A3:U13C14_AA 8 3.223 -6.014 29.223 -4.158 0.343 2.407 34.207 B B 3 4 16.553 A A 13 12 2.876 9.568 0.464 -0.897 BB_A3A4:U12U13_AA 9 -5.776 9.992 32.382 -2.781 -1.547 2.520 43.721 B B 4 5 27.698 A A 12 11 3.577 19.806 -0.068 -1.415 BB_A4G5:C11U12_AA 10 8.457 -11.827 38.277 -3.798 0.902 2.977 36.891 B B 5 6 6.990 A A 11 10 3.048 4.402 -0.753 -1.046 BB_G5C6:G10C11_AA 11 -4.723 7.500 36.341 -2.207 0.597 2.212 25.410 B B 6 7 22.977 A A 10 9 3.188 9.831 0.007 -1.879 BB_C6U7:A9G10_AA 12 2.657 -6.210 23.310 -6.715 0.643 3.053 32.739 B B 7 8 5.585 A A 9 8 3.228 3.143 0.412 -1.667 BB_U7C8:G8A9_AA 13 -0.419 0.744 32.589 -3.478 -0.800 3.038 79.427 B B 8 9 0.550 A C 8 34 3.387 0.702 -3.221 -2.012 BB_C8U9:A34G8_CA 14 9.376 -7.349 78.960 -1.593 2.769 3.637 49.323 B B 17 18 19.810 C C 31 30 4.350 16.156 -0.011 -1.347 BB_C17C18:G30A31_CC 15 -9.889 12.126 45.752 -3.150 -0.926 2.765 32.887 B B 18 19 16.066 C C 30 29 3.403 8.986 -0.162 -1.943 BB_C18C19:G29G30_CC 16 -0.510 0.913 31.664 -4.908 0.202 2.383 29.132 B B 19 20 23.934 C C 29 28 3.395 11.706 -0.419 -1.909 BB_C19C20:G28G29_CC 17 -1.515 3.098 26.681 -6.159 0.528 2.230 32.724 B B 20 21 29.086 C C 28 27 3.411 15.741 0.409 -1.634 BB_C20A21:U27G28_CC 18 -0.694 1.282 28.772 -5.405 -0.836 2.882 39.915 B B 21 22 13.357 C C 27 26 3.255 9.043 0.102 -1.360 BB_A21G22:C26U27_CC 19 1.247 -1.842 38.898 -2.984 -0.012 3.105 31.917 B B 22 23 2.012 C C 26 25 3.143 1.105 -0.287 -1.464 BB_G22C23:G25C26_CC 20 -3.045 5.547 31.757 -2.854 -0.007 citation citation_author repository Initial release Database references 1 0 2026-07-22 1 1 2026-07-29 _citation.pdbx_database_id_PubMed _citation.title Germany German Research Foundation (DFG) European Union European Research Council (ERC) claudia.hoebartner@uni-wuerzburg.de 0000-0002-4548-2299 Claudia Hoebartner principal investigator/group leader N PDBE Y PDBE 2025-07-18 REL REL 1MA 1MA SUBJECT OF INVESTIGATION GUN GUN SUBJECT OF INVESTIGATION OMC OMC SUBJECT OF INVESTIGATION OMU OMU SUBJECT OF INVESTIGATION MG MAGNESIUM ION NA SODIUM ION GUN GUANINE HOH water 32630 synthetic construct sample 1 14 32630 synthetic construct sample 1 24 32630 synthetic construct sample 1 24 Y N 7Q7X search for 1 copy PDB experimental model MG 2 4 MG MG 101 B NA 1 5 NA NA 102 B GUN 101 6 GUN GUN 101 C MG 1 4 MG MG 102 C NA 2 5 NA NA 103 C HOH 7 7 HOH HOH 101 A HOH 40 7 HOH HOH 102 A HOH 38 7 HOH HOH 103 A HOH 24 7 HOH HOH 201 B HOH 11 7 HOH HOH 202 B HOH 20 7 HOH HOH 203 B HOH 30 7 HOH HOH 204 B HOH 28 7 HOH HOH 205 B HOH 13 7 HOH HOH 206 B HOH 27 7 HOH HOH 207 B HOH 17 7 HOH HOH 208 B HOH 29 7 HOH HOH 209 B HOH 31 7 HOH HOH 210 B HOH 19 7 HOH HOH 211 B HOH 9 7 HOH HOH 212 B HOH 2 7 HOH HOH 213 B HOH 35 7 HOH HOH 214 B HOH 3 7 HOH HOH 215 B HOH 39 7 HOH HOH 216 B HOH 36 7 HOH HOH 217 B HOH 41 7 HOH HOH 218 B HOH 34 7 HOH HOH 219 B HOH 23 7 HOH HOH 220 B HOH 37 7 HOH HOH 221 B HOH 45 7 HOH HOH 222 B HOH 5 7 HOH HOH 201 C HOH 16 7 HOH HOH 202 C HOH 4 7 HOH HOH 203 C HOH 33 7 HOH HOH 204 C HOH 26 7 HOH HOH 205 C HOH 43 7 HOH HOH 206 C HOH 10 7 HOH HOH 207 C HOH 22 7 HOH HOH 208 C HOH 6 7 HOH HOH 209 C HOH 15 7 HOH HOH 210 C HOH 8 7 HOH HOH 211 C HOH 18 7 HOH HOH 212 C HOH 32 7 HOH HOH 213 C HOH 44 7 HOH HOH 214 C HOH 21 7 HOH HOH 215 C HOH 14 7 HOH HOH 216 C HOH 42 7 HOH HOH 217 C HOH 25 7 HOH HOH 218 C HOH 1 7 HOH HOH 219 C HOH 12 7 HOH HOH 220 C C 1 n 1 C 1 A C 2 n 2 C 2 A A 3 n 3 A 3 A C 4 n 4 C 4 A U 5 n 5 U 5 A G 6 n 6 G 6 A 1MA 7 n 7 1MA 7 A G 8 n 8 G 8 A A 9 n 9 A 9 A G 10 n 10 G 10 A C 11 n 11 C 11 A U 12 n 12 U 12 A U 13 n 13 U 13 A C 14 n 14 C 14 A G 1 n 1 G 1 B G 2 n 2 G 2 B A 3 n 3 A 3 B A 4 n 4 A 4 B G 5 n 5 G 5 B C 6 n 6 C 6 B U 7 n 7 U 7 B C 8 n 8 C 8 B U 9 n 9 U 9 B G 10 n 10 G 10 B A 11 n 11 A 11 B OMC 12 n 12 OMC 12 B C 13 n 13 C 13 B G 14 n 14 G 14 B A 15 n 15 A 15 B C 16 n 16 C 16 B C 17 n 17 C 17 B C 18 n 18 C 18 B C 19 n 19 C 19 B C 20 n 20 C 20 B A 21 n 21 A 21 B G 22 n 22 G 22 B C 23 n 23 C 23 B C 24 n 24 C 24 B G 25 n 1 G 25 C C 26 n 2 C 26 C U 27 n 3 U 27 C G 28 n 4 G 28 C G 29 n 5 G 29 C G 30 n 6 G 30 C A 31 n 7 A 31 C C 32 n 8 C 32 C A 33 n 9 A 33 C A 34 n 10 A 34 C C 35 n 11 C 35 C U 36 n 12 U 36 C A 37 n 13 A 37 C G 38 n 14 G 38 C A 39 n 15 A 39 C C 40 n 16 C 40 C A 41 n 17 A 41 C OMU 42 n 18 OMU 42 C A 43 n 19 A 43 C C 44 n 20 C 44 C A 45 n 21 A 45 C G 46 n 22 G 46 C U 47 n 23 U 47 C G 48 n 24 G 48 C 1.59641992244 1.67545769664 0.960491729552 3.56451931584 1.17173173259 0.745535722809 0.118455355664 0.260724882017 -0.311627276199 -0.237731743779 0.0356448061689 -0.0883943066826 0.29230064591 -0.0900963833593 0.110018429331 0.318956045333 -0.0748165062825 -0.0151336575123 0.202307585073 -0.0636490272973 0.247837939685 refined 29.1686159186 -16.3828363238 -2.89113323894 X-RAY DIFFRACTION 0.674185521993 0.367696363715 0.632705689816 1.08691547608 -0.154536526321 0.876515924261 0.117291887635 -0.451943558784 0.295051160313 0.313676254785 -0.126534852287 0.157439083876 -0.151977470763 -0.386544328762 0.390229171506 0.553361452507 -0.126562964573 -0.032074454871 0.536193803645 -0.289637092522 0.469805690827 refined 15.0520399238 -17.4411765283 1.45283493938 X-RAY DIFFRACTION 1.62817918264 0.582923080757 -0.371157349545 1.57762007181 0.292217436049 1.32555973958 0.380601500117 -0.196016634593 0.15810558664 0.145792293277 -0.332395111635 0.200929723535 -0.0927214020278 -0.350010406366 0.313191919824 0.174227088256 -0.0680527587317 -0.031195707718 0.227114154838 -0.0377052645627 0.196796169293 refined 28.7370251761 -6.79153644328 3.31715974388 X-RAY DIFFRACTION C 25 C C 48 C X-RAY DIFFRACTION 1 (chain 'C' and resid 25 through 101) A 1 A A 14 A X-RAY DIFFRACTION 2 (chain 'A' and resid 1 through 14) B 1 B B 24 B X-RAY DIFFRACTION 3 (chain 'B' and resid 1 through 24) author_defined_assembly 3 trimeric Dissolved crystals were injected into anion exchange HPLC to check the composition. Peak areas were integrated to calculate the ratio of the RNA species. assay for oligomerization 6770 -20 9610 B G 14 B OP1 G 14 1_555 B NA 102 E NA NA 1_555 B A 15 B OP1 A 15 1_555 95.6 C HOH 206 K O HOH 1_555 C MG 102 G MG MG 1_555 C HOH 214 K O HOH 1_555 93.7 C HOH 216 K O HOH 1_555 C NA 103 H NA NA 1_555 C HOH 217 K O HOH 1_555 71.3 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 44.34 Hendrickson-Lattman coefficients were generated in Phenix Resolve based on a non-methylated 7Q7X model, which was used in Phenix Refine as phase restraints (target function: MLHL). Three methyl groups were introduced during following refinements according to the difference map peaks. 0.2510 0.2201 0.2216 2.60 43.17 347 6700 7047 4.92 99.96 0.3643 1 FREE R-VALUE 1.37 MOLECULAR REPLACEMENT 26.8536 0.9000 1.1000 GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 2.60 43.17 45 1374 15 1314 0 0.0053 1479 0.9398 2297 0.0357 304 0.0049 63 24.5219 916 0.3742 0.3504 2.98 107 2181 100.00 0.2831 0.2259 3.75 119 2195 99.96 0.1822 0.1653 43.17 121 2324 99.92 76.8 2.60 43.17 9S1D 7084 3.0 1 0.044 0.010 0.045 1.04 1 42.9 25.3 100 2.017 2.60 2.72 2.0 837 0.583 0.396 2.039 0.82 1 27 100 data reduction XDS June 30 2024 phasing PHASER 2.8.3 model building Coot 0.9.8.95 refinement PHENIX 1.21.2_5419 data scaling XDS 92 tetragonal P 41 21 2 P 4abw 2nw x,y,z -y+1/2,x+1/2,z+1/4 y+1/2,-x+1/2,z+3/4 x+1/2,-y+1/2,-z+3/4 -x+1/2,y+1/2,-z+1/4 -x,-y,z+1/2 y,x,-z -y,-x,-z+1/2 N Crystal structure of the methyltransferase ribozyme 1 with two 2'O-methylation (MTR1m2) 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N 4 N N 5 N N 7 N N 7 N N 7 N N covale 1.597 both A G 6 A O3' G 6 1_555 A 1MA 7 A P 1MA 7 1_555 covale 1.606 both A 1MA 7 A O3' 1MA 7 1_555 A G 8 A P G 8 1_555 covale 1.606 both B A 11 B O3' A 11 1_555 B OMC 12 B P OMC 12 1_555 covale 1.604 both B OMC 12 B O3' OMC 12 1_555 B C 13 B P C 13 1_555 covale 1.603 both C A 41 C O3' A 17 1_555 C OMU 42 C P OMU 18 1_555 covale 1.601 both C OMU 42 C O3' OMU 18 1_555 C A 43 C P A 19 1_555 metalc 2.928 B G 14 B OP1 G 14 1_555 B NA 102 E NA NA 1_555 metalc 2.933 B A 15 B OP1 A 15 1_555 B NA 102 E NA NA 1_555 metalc 2.149 B MG 101 D MG MG 1_555 B HOH 222 J O HOH 1_555 metalc 1.835 C MG 102 G MG MG 1_555 C HOH 206 K O HOH 1_555 metalc 2.054 C MG 102 G MG MG 1_555 C HOH 214 K O HOH 1_555 metalc 2.328 C NA 103 H NA NA 1_555 C HOH 216 K O HOH 1_555 metalc 2.757 C NA 103 H NA NA 1_555 C HOH 217 K O HOH 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 C G 48 C N1 G 24 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 C G 48 C O6 G 24 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 C G 48 C N2 G 24 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 C U 47 C N3 U 23 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 C U 47 C O4 U 23 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 C G 46 C N1 G 22 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 C G 46 C O6 G 22 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 C G 46 C N2 G 22 1_555 hydrog WATSON-CRICK A U 5 A N3 U 5 1_555 C A 45 C N1 A 21 1_555 hydrog WATSON-CRICK A U 5 A O4 U 5 1_555 C A 45 C N6 A 21 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 C C 44 C N3 C 20 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 C C 44 C O2 C 20 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 C C 44 C N4 C 20 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A A 9 A N1 A 9 1_555 B U 7 B N3 U 7 1_555 hydrog WATSON-CRICK A A 9 A N6 A 9 1_555 B U 7 B O4 U 7 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 B C 6 B N3 C 6 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 B C 6 B O2 C 6 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 B C 6 B N4 C 6 1_555 hydrog WATSON-CRICK A C 11 A N3 C 11 1_555 B G 5 B N1 G 5 1_555 hydrog WATSON-CRICK A C 11 A N4 C 11 1_555 B G 5 B O6 G 5 1_555 hydrog WATSON-CRICK A C 11 A O2 C 11 1_555 B G 5 B N2 G 5 1_555 hydrog U-A PAIR A U 12 A N3 U 12 1_555 B A 4 B N1 A 4 1_555 hydrog WATSON-CRICK A U 13 A N3 U 13 1_555 B A 3 B N1 A 3 1_555 hydrog WATSON-CRICK A U 13 A O4 U 13 1_555 B A 3 B N6 A 3 1_555 hydrog WATSON-CRICK A C 14 A N3 C 14 1_555 B G 2 B N1 G 2 1_555 hydrog WATSON-CRICK A C 14 A N4 C 14 1_555 B G 2 B O6 G 2 1_555 hydrog WATSON-CRICK A C 14 A O2 C 14 1_555 B G 2 B N2 G 2 1_555 hydrog REVERSED HOOGSTEEN B U 9 B N3 U 9 1_555 C A 34 C N7 A 10 1_555 hydrog REVERSED HOOGSTEEN B U 9 B O2 U 9 1_555 C A 34 C N6 A 10 1_555 hydrog A-A MISPAIR B A 11 B N6 A 11 1_555 C A 43 C N3 A 19 1_555 hydrog WATSON-CRICK B C 13 B N3 C 13 1_555 C G 38 C N1 G 14 1_555 hydrog WATSON-CRICK B C 13 B N4 C 13 1_555 C G 38 C O6 G 14 1_555 hydrog WATSON-CRICK B C 13 B O2 C 13 1_555 C G 38 C N2 G 14 1_555 hydrog C-A MISPAIR B C 13 B O2 C 13 1_555 C A 41 C N6 A 17 1_555 hydrog WATSON-CRICK B G 14 B N1 G 14 1_555 C C 35 C N3 C 11 1_555 hydrog WATSON-CRICK B G 14 B N2 G 14 1_555 C C 35 C O2 C 11 1_555 hydrog WATSON-CRICK B G 14 B O6 G 14 1_555 C C 35 C N4 C 11 1_555 hydrog C-A MISPAIR B C 17 B N4 C 17 1_555 C A 31 C N1 A 7 1_555 hydrog WATSON-CRICK B C 18 B N3 C 18 1_555 C G 30 C N1 G 6 1_555 hydrog WATSON-CRICK B C 18 B N4 C 18 1_555 C G 30 C O6 G 6 1_555 hydrog WATSON-CRICK B C 18 B O2 C 18 1_555 C G 30 C N2 G 6 1_555 hydrog WATSON-CRICK B C 19 B N3 C 19 1_555 C G 29 C N1 G 5 1_555 hydrog WATSON-CRICK B C 19 B N4 C 19 1_555 C G 29 C O6 G 5 1_555 hydrog WATSON-CRICK B C 19 B O2 C 19 1_555 C G 29 C N2 G 5 1_555 hydrog WATSON-CRICK B C 20 B N3 C 20 1_555 C G 28 C N1 G 4 1_555 hydrog WATSON-CRICK B C 20 B N4 C 20 1_555 C G 28 C O6 G 4 1_555 hydrog WATSON-CRICK B C 20 B O2 C 20 1_555 C G 28 C N2 G 4 1_555 hydrog WATSON-CRICK B A 21 B N1 A 21 1_555 C U 27 C N3 U 3 1_555 hydrog WATSON-CRICK B A 21 B N6 A 21 1_555 C U 27 C O4 U 3 1_555 hydrog WATSON-CRICK B G 22 B N1 G 22 1_555 C C 26 C N3 C 2 1_555 hydrog WATSON-CRICK B G 22 B N2 G 22 1_555 C C 26 C O2 C 2 1_555 hydrog WATSON-CRICK B G 22 B O6 G 22 1_555 C C 26 C N4 C 2 1_555 hydrog WATSON-CRICK B C 23 B N3 C 23 1_555 C G 25 C N1 G 1 1_555 hydrog WATSON-CRICK B C 23 B N4 C 23 1_555 C G 25 C O6 G 1 1_555 hydrog WATSON-CRICK B C 23 B O2 C 23 1_555 C G 25 C N2 G 1 1_555 RNA Ribozyme, methyltransferase, 2'O-methylation, accelerated catalysis, RNA 9S1D PDB 1 1 9S1D 9S1D PDB 2 1 9S1D 9S1D PDB 3 1 9S1D 1 14 9S1D 1 14 9S1D A 1 1 14 1 24 9S1D 1 24 9S1D B 2 1 24 25 48 9S1D 25 48 9S1D C 3 1 24 92 P 41 21 2 P 4abw 2nw