0.013038 0.007528 0.000000 0.000000 0.015055 0.000000 0.000000 0.000000 0.013081 0.00000 0.00000 0.00000 Chapman, E.G. Costantino, D.A. Rabe, J.L. Moon, S.L. Wilusz, J. Nix, J.C. Kieft, J.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 76.698 76.698 76.448 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 Mg 2 24.305 MAGNESIUM ION 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 MG N 115 N O N 116 N P N 117 N O N 118 N O N 119 N O N 120 N C N 121 R C N 122 N O N 123 S C N 124 N O N 125 R C N 126 N O N 127 R C N 128 N N N 129 N C N 130 N O N 131 N N N 132 N C N 133 N O N 134 N C N 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 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 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 N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N doub N 151 N sing N 152 N sing US Science SCIEAS 0038 0036-8075 344 307 310 10.1126/science.1250897 24744377 The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. 2014 10.2210/pdb4pqv/pdb pdb_00004pqv 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CMOS 2013-09-27 TAURUS-1 Rosenbaum-Rock sagitally focused Si(111) SINGLE WAVELENGTH M x-ray 1 1.0972 1.0 4.2.2 ALS 1.0972 SYNCHROTRON ALS BEAMLINE 4.2.2 22095.186 XRN1-resistant flaviviral RNA U2G, G-U pair insertion 1 syn polymer 24.305 MAGNESIUM ION 9 syn non-polymer 18.015 water 7 nat water no no GGGUCAGAUCGGCGAAAGUCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU GGGUCAGAUCGGCGAAAGUCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU 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 1 2.94 58.13 VAPOR DIFFUSION, SITTING DROP 7.5 drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 2 uL 10% MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine, 80 mM sodium chloride, 20 mM magnesium chloride (Nucleic Acid Mini-Screen kit, Hampton Research), well: 20-35% MPD, crystals appeared within 2-3 days and grew to full size over 1-2 weeks. To obtain derivatized crystals for phasing, 5 uL 4 mM iridium (III) hexammine in RNase-free water was added directly to crystallization drops and well solutions <35% MPD were replaced with 35% MPD. Wells were then re-sealed and allowed to re-equilibrate for at least 2 days, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 15.721 1 19 A 3 A 40 2.174 A_G3:C40_A 1 -1.973 -0.404 0.496 -0.309 -4.693 1 19 A 23 A 39 -1.097 A_C23:G39_A 2 -8.478 0.307 0.526 -0.616 8.694 3 23 A 24 A 4 60.777 A_A24:U4_A 3 -1.868 0.267 -0.608 -3.294 2.914 1 19 A 25 A 37 -3.839 A_C25:G37_A 4 -16.239 0.208 0.276 -0.204 8.783 1 20 A 26 A 36 -0.638 A_U26:A36_A 5 -24.847 -0.179 -0.554 -0.231 0.491 1 28 A 27 A 35 3.529 A_U27:G35_A 6 -20.504 2.230 0.216 -0.808 0.107 1 19 A 28 A 34 -0.550 A_C28:G34_A 7 -12.334 0.102 0.226 -0.441 -8.147 A 17 A 14 -56.245 A_A17:G14_A 8 -18.741 -8.168 1.091 -4.882 -3.679 1 19 A 18 A 13 -0.026 A_G18:C13_A 9 -7.974 -0.219 -0.302 -0.205 4.781 1 28 A 19 A 12 3.725 A_U19:G12_A 10 -8.794 2.285 -0.046 -0.026 -1.720 1 A 20 A 11 6.798 A_C20:G11_A 11 -16.407 0.182 0.356 0.480 29.904 1 19 A 21 A 10 -9.534 A_G21:C10_A 12 9.931 -0.246 0.175 0.119 28.332 1 20 A 42 A 9 -1.771 A_A42:U9_A 13 -10.192 0.661 0.659 -0.245 8.403 1 20 A 43 A 8 -0.035 A_U43:A8_A 14 -29.590 0.212 -0.415 0.133 -8.770 1 19 A 44 A 7 1.866 A_C44:G7_A 15 -10.454 -0.294 1.121 0.049 -5.782 1 20 A 45 A 6 4.130 A_U45:A6_A 16 -21.182 -0.474 0.427 0.154 -2.109 1 19 A 46 A 5 -7.901 A_G46:C5_A 17 -12.006 0.193 -0.159 -0.587 -2.989 3 23 A 47 A 49 -65.595 A_U47:A49_A 18 -9.508 -0.226 0.319 3.047 5.263 1 19 A 53 A 67 -3.873 A_C53:G67_A 19 -9.144 -0.319 -0.297 -0.471 7.914 1 19 A 54 A 66 -3.593 A_C54:G66_A 20 -15.760 -0.081 -0.456 -0.284 -4.887 1 19 A 55 A 65 -1.246 A_C55:G65_A 21 0.118 0.257 0.071 -0.064 0.851 1 20 A 56 A 64 3.083 A_A56:U64_A 22 -6.059 0.038 0.312 -0.161 -9.863 1 19 A 57 A 63 2.864 A_G57:C63_A 23 -10.603 -0.348 0.029 -0.317 2.834 10 11 A 58 A 62 -5.020 A_G58:A62_A 24 4.968 6.396 0.169 -4.419 3.638 54.562 A A 3 23 7.347 A A 40 39 3.599 6.712 -1.984 -0.858 AA_G3C23:G39C40_AA 1 -5.183 5.674 53.950 -1.388 1.816 2.905 -4.763 A A 23 24 -20.246 A A 39 4 3.485 1.610 0.352 0.024 AA_C23A24:U4G39_AA 2 1.691 21.268 -4.152 -14.166 18.822 2.204 57.449 A A 24 25 10.748 A A 4 37 2.827 10.277 -0.547 -3.728 AA_A24C25:G37U4_AA 3 -3.777 3.949 56.483 -4.312 0.410 2.157 30.894 A A 25 26 20.322 A A 37 36 3.039 10.596 -0.840 -1.800 AA_C25U26:A36G37_AA 4 3.192 -6.122 28.890 -5.069 2.087 3.291 44.195 A A 26 27 14.950 A A 36 35 3.562 11.129 0.058 -0.639 AA_U26U27:G35A36_AA 5 -3.255 4.373 42.720 -1.961 -0.402 3.219 31.280 A A 27 28 0.792 A A 35 34 3.227 0.425 0.340 -1.503 AA_U27C28:G34G35_AA 6 5.263 -9.806 30.842 -2.868 0.358 2.860 57.603 A A 17 18 19.767 A A 14 13 3.504 18.751 4.583 -2.086 AA_A17G18:C13G14_AA 7 1.998 -2.106 54.680 -3.180 -4.648 2.927 42.154 A A 18 19 6.124 A A 13 12 3.116 4.396 0.488 -1.545 AA_G18U19:G12C13_AA 8 -1.566 2.181 41.907 -2.568 -0.828 2.299 23.999 A A 19 20 21.025 A A 12 11 3.258 8.554 -0.793 -2.086 AA_U19C20:G11G12_AA 9 0.500 -1.229 22.438 -7.446 2.050 0.850 20.625 A A 20 21 43.504 A A 11 10 2.424 14.129 -1.416 -1.539 AA_C20G21:C10G11_AA 10 -2.038 6.275 14.925 -7.908 3.434 3.391 52.720 A A 21 42 4.722 A A 10 9 3.196 4.171 -1.472 0.083 AA_G21A42:U9C10_AA 11 -9.257 10.481 51.802 -0.182 1.046 3.442 28.377 A A 42 43 12.238 A A 9 8 3.709 5.925 0.122 -0.740 AA_A42U43:A8U9_AA 12 5.080 -10.493 27.304 -3.031 1.056 2.454 33.492 A A 43 44 14.839 A A 8 7 3.512 8.219 0.145 -2.468 AA_U43C44:G7A8_AA 13 -13.747 24.819 29.511 -5.602 -2.456 2.669 31.200 A A 44 45 10.426 A A 7 6 3.003 5.556 -0.111 -1.345 AA_C44U45:A6G7_AA 14 4.968 -9.322 30.318 -3.431 1.038 2.809 34.909 A A 45 46 16.130 A A 6 5 3.270 9.559 -0.517 -1.242 AA_U45G46:C5A6_AA 15 0.872 -1.471 33.603 -3.443 0.986 2.583 49.521 A A 46 47 6.415 A A 5 49 3.034 5.364 -0.555 -4.407 AA_G46U47:A49C5_AA 16 -1.239 1.482 49.233 -5.603 0.583 2.713 36.049 A A 53 54 19.573 A A 67 66 3.360 11.899 0.427 -1.490 AA_C53C54:G66G67_AA 17 0.601 -0.989 34.085 -4.022 -0.609 2.956 28.721 A A 54 55 17.782 A A 66 65 3.667 8.635 -0.689 -2.062 AA_C54C55:G65G66_AA 18 -5.490 11.306 26.873 -6.190 0.095 2.563 31.653 A A 55 56 13.769 A A 65 64 3.045 7.443 0.750 -1.791 AA_C55A56:U64G65_AA 19 0.463 -0.857 30.784 -4.479 -1.300 3.296 31.059 A A 56 57 10.324 A A 64 63 3.641 5.488 0.316 -1.751 AA_A56G57:C63U64_AA 20 3.677 -6.917 30.365 -4.401 0.166 3.025 64.072 A A 57 58 4.252 A A 63 62 3.057 4.508 -0.649 -0.597 AA_G57G58:A62C63_AA 21 -1.372 1.294 63.917 -0.743 0.557 software chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Refinement description Data collection Database references Derived calculations 1 0 2014-04-30 1 1 2017-11-22 1 2 2024-02-28 _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2014-03-04 REL REL MG MAGNESIUM ION HOH water RNA was prepared by in vitro transcription with T7 polymerase 11079 Murray Valley encephalitis virus sample MG 1 2 MG MG 101 A MG 1 2 MG MG 102 A MG 1 2 MG MG 103 A MG 1 2 MG MG 104 A MG 1 2 MG MG 105 A MG 1 2 MG MG 106 A MG 1 2 MG MG 107 A MG 1 2 MG MG 108 A MG 1 2 MG MG 109 A HOH 1 3 HOH HOH 201 A HOH 2 3 HOH HOH 202 A HOH 3 3 HOH HOH 203 A HOH 4 3 HOH HOH 204 A HOH 5 3 HOH HOH 205 A HOH 6 3 HOH HOH 206 A HOH 13 3 HOH HOH 207 A G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A C 5 n 5 C 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A A 8 n 8 A 8 A U 9 n 9 U 9 A C 10 n 10 C 10 A G 11 n 11 G 11 A G 12 n 12 G 12 A C 13 n 13 C 13 A G 14 n 14 G 14 A A 15 n 15 A 15 A A 16 n 16 A 16 A A 17 n 17 A 17 A G 18 n 18 G 18 A U 19 n 19 U 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A C 22 n 22 C 22 A C 23 n 23 C 23 A A 24 n 24 A 24 A C 25 n 25 C 25 A U 26 n 26 U 26 A U 27 n 27 U 27 A C 28 n 28 C 28 A G 29 n 29 G 29 A C 30 n 30 C 30 A C 31 n 31 C 31 A G 32 n 32 G 32 A A 33 n 33 A 33 A G 34 n 34 G 34 A G 35 n 35 G 35 A A 36 n 36 A 36 A G 37 n 37 G 37 A U 38 n 38 U 38 A G 39 n 39 G 39 A C 40 n 40 C 40 A A 41 n 41 A 41 A A 42 n 42 A 42 A U 43 n 43 U 43 A C 44 n 44 C 44 A U 45 n 45 U 45 A G 46 n 46 G 46 A U 47 n 47 U 47 A G 48 n 48 G 48 A A 49 n 49 A 49 A G 50 n 50 G 50 A G 51 n 51 G 51 A C 52 n 52 C 52 A C 53 n 53 C 53 A C 54 n 54 C 54 A C 55 n 55 C 55 A A 56 n 56 A 56 A G 57 n 57 G 57 A G 58 n 58 G 58 A A 59 n 59 A 59 A G 60 n 60 G 60 A G 61 n 61 G 61 A A 62 n 62 A 62 A C 63 n 63 C 63 A U 64 n 64 U 64 A G 65 n 65 G 65 A G 66 n 66 G 66 A G 67 n 67 G 67 A U 68 n 68 U 68 A author_defined_assembly 1 monomeric A C 5 A OP2 C 5 1_555 A MG 102 C MG MG 1_555 A C 23 A OP2 C 23 1_555 92.8 A C 5 A OP2 C 5 1_555 A MG 102 C MG MG 1_555 A HOH 201 K O HOH 1_555 87.8 A C 23 A OP2 C 23 1_555 A MG 102 C MG MG 1_555 A HOH 201 K O HOH 1_555 135.0 A C 5 A OP2 C 5 1_555 A MG 102 C MG MG 1_555 A HOH 202 K O HOH 1_555 154.9 A C 23 A OP2 C 23 1_555 A MG 102 C MG MG 1_555 A HOH 202 K O HOH 1_555 90.0 A HOH 201 K O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 202 K O HOH 1_555 107.5 A C 5 A OP2 C 5 1_555 A MG 102 C MG MG 1_555 A HOH 203 K O HOH 1_555 78.5 A C 23 A OP2 C 23 1_555 A MG 102 C MG MG 1_555 A HOH 203 K O HOH 1_555 155.7 A HOH 201 K O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 203 K O HOH 1_555 67.9 A HOH 202 K O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 203 K O HOH 1_555 88.8 A C 5 A OP2 C 5 1_555 A MG 102 C MG MG 1_555 A HOH 207 K O HOH 1_555 64.1 A C 23 A OP2 C 23 1_555 A MG 102 C MG MG 1_555 A HOH 207 K O HOH 1_555 92.8 A HOH 201 K O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 207 K O HOH 1_555 126.8 A HOH 202 K O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 207 K O HOH 1_555 90.9 A HOH 203 K O HOH 1_555 A MG 102 C MG MG 1_555 A HOH 207 K O HOH 1_555 63.0 A A 16 A OP1 A 16 1_555 A MG 104 E MG MG 1_555 A HOH 204 K O HOH 1_555 165.5 A A 16 A OP1 A 16 1_555 A MG 104 E MG MG 1_555 A HOH 205 K O HOH 1_555 117.5 A HOH 204 K O HOH 1_555 A MG 104 E MG MG 1_555 A HOH 205 K O HOH 1_555 75.7 A A 16 A OP1 A 16 1_555 A MG 104 E MG MG 1_555 A HOH 206 K O HOH 1_555 142.4 A HOH 204 K O HOH 1_555 A MG 104 E MG MG 1_555 A HOH 206 K O HOH 1_555 50.6 A HOH 205 K O HOH 1_555 A MG 104 E MG MG 1_555 A HOH 206 K O HOH 1_555 48.7 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 A O O HOH HOH 205 206 2.14 1 A A O O HOH HOH 204 206 2.19 1 4.30 0.70 108.50 112.80 A A A O4' C1' N9 G G G 21 21 21 N 1 -2.47 0.40 120.30 117.83 A A A C6 N1 C2 C C C 31 31 31 N 1 4.61 0.60 123.90 128.51 A A A N1 C2 N3 G G G 32 32 32 N 1 -4.10 0.50 111.90 107.80 A A A C2 N3 C4 G G G 32 32 32 N 1 -4.12 0.60 130.40 126.28 A A A C6 C5 N7 G G G 32 32 32 N 1 -8.02 0.90 116.20 108.18 A A A N1 C2 N2 G G G 32 32 32 N 1 -3.62 0.50 104.30 100.68 A A A C5 N7 C8 G G G 48 48 48 N 1 4.23 0.50 113.10 117.33 A A A N7 C8 N9 G G G 48 48 48 N 1 -4.48 0.40 106.40 101.92 A A A C8 N9 C4 G G G 48 48 48 N 1 2.56 0.40 105.40 107.96 A A A N9 C4 C5 G G G 48 48 48 N 0.2835 0.2303 0.2357 2.463 50.140 824 8418 9.91 85.47 0.35 RANDOM 1 1.39 SAD 38.25 0.90 1.11 ML FLAT BULK SOLVENT MODEL 2.463 50.140 7 1482 9 1466 0 0.006 1641 1.247 2560 14.545 813 0.050 340 0.007 68 0.6652 0.4780 2.5422 24 180 13.00 0.4572 0.4380 2.6331 63 611 40.00 0.3844 0.3632 2.7385 142 1344 91.00 0.3826 0.3357 2.8631 165 1450 100.00 0.3750 0.3115 3.0141 165 1495 100.00 0.2777 0.2623 3.2029 166 1478 100.00 0.2881 0.2303 3.4501 166 1483 100.00 0.2516 0.2166 3.7972 159 1507 100.00 0.2710 0.2010 4.3464 164 1481 100.00 0.2577 0.2051 5.4749 165 1510 100.00 0.2714 0.2051 50.1505 163 1477 99.00 2.45 50.14 4PQV 9499 1 2.45 1 data collection Blu-Ice Ice model building PHENIX refinement PHENIX (phenix.refine: 1.8.4_1496) data reduction d*TREK data scaling d*TREK phasing PHENIX Crystal structure of an Xrn1-resistant RNA from the 3' untranslated region of a flavivirus (Murray Valley Encephalitis virus) 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N metalc 2.215 A C 5 A OP2 C 5 1_555 A MG 102 C MG MG 1_555 metalc 2.988 A G 11 A O6 G 11 1_555 A MG 107 H MG MG 1_555 metalc 2.997 A A 16 A OP1 A 16 1_555 A MG 104 E MG MG 1_555 metalc 1.776 A C 23 A OP2 C 23 1_555 A MG 102 C MG MG 1_555 metalc 2.233 A G 67 A O6 G 67 1_555 A MG 109 J MG MG 1_555 metalc 1.999 A MG 102 C MG MG 1_555 A HOH 201 K O HOH 1_555 metalc 2.088 A MG 102 C MG MG 1_555 A HOH 202 K O HOH 1_555 metalc 2.182 A MG 102 C MG MG 1_555 A HOH 203 K O HOH 1_555 metalc 2.225 A MG 102 C MG MG 1_555 A HOH 207 K O HOH 1_555 metalc 2.249 A MG 104 E MG MG 1_555 A HOH 204 K O HOH 1_555 metalc 2.354 A MG 104 E MG MG 1_555 A HOH 205 K O HOH 1_555 metalc 2.769 A MG 104 E MG MG 1_555 A HOH 206 K O HOH 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 40 A N3 C 40 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 40 A O2 C 40 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 40 A N4 C 40 1_555 hydrog HOOGSTEEN A U 4 A N3 U 4 1_555 A A 24 A N7 A 24 1_555 hydrog HOOGSTEEN A U 4 A O4 U 4 1_555 A A 24 A N6 A 24 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 46 A N1 G 46 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 46 A O6 G 46 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 46 A N2 G 46 1_555 hydrog WATSON-CRICK A A 6 A N1 A 6 1_555 A U 45 A N3 U 45 1_555 hydrog WATSON-CRICK A A 6 A N6 A 6 1_555 A U 45 A O4 U 45 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 A C 44 A N3 C 44 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 A C 44 A O2 C 44 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 A C 44 A N4 C 44 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 A U 43 A N3 U 43 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 A U 43 A O4 U 43 1_555 hydrog WATSON-CRICK A U 9 A N3 U 9 1_555 A A 42 A N1 A 42 1_555 hydrog WATSON-CRICK A U 9 A O4 U 9 1_555 A A 42 A N6 A 42 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 A G 21 A N1 G 21 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 A G 21 A O6 G 21 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 A G 21 A N2 G 21 1_555 hydrog G-C PAIR A G 11 A N1 G 11 1_555 A C 20 A N3 C 20 1_555 hydrog TYPE_28_PAIR A G 12 A N1 G 12 1_555 A U 19 A O2 U 19 1_555 hydrog TYPE_28_PAIR A G 12 A O6 G 12 1_555 A U 19 A N3 U 19 1_555 hydrog WATSON-CRICK A C 13 A N3 C 13 1_555 A G 18 A N1 G 18 1_555 hydrog WATSON-CRICK A C 13 A N4 C 13 1_555 A G 18 A O6 G 18 1_555 hydrog WATSON-CRICK A C 13 A O2 C 13 1_555 A G 18 A N2 G 18 1_555 hydrog G-A MISPAIR A G 14 A N2 G 14 1_555 A A 17 A N7 A 17 1_555 hydrog WATSON-CRICK A C 23 A N3 C 23 1_555 A G 39 A N1 G 39 1_555 hydrog WATSON-CRICK A C 23 A N4 C 23 1_555 A G 39 A O6 G 39 1_555 hydrog WATSON-CRICK A C 23 A O2 C 23 1_555 A G 39 A N2 G 39 1_555 hydrog WATSON-CRICK A C 25 A N3 C 25 1_555 A G 37 A N1 G 37 1_555 hydrog WATSON-CRICK A C 25 A N4 C 25 1_555 A G 37 A O6 G 37 1_555 hydrog WATSON-CRICK A C 25 A O2 C 25 1_555 A G 37 A N2 G 37 1_555 hydrog WATSON-CRICK A U 26 A N3 U 26 1_555 A A 36 A N1 A 36 1_555 hydrog WATSON-CRICK A U 26 A O4 U 26 1_555 A A 36 A N6 A 36 1_555 hydrog TYPE_28_PAIR A U 27 A N3 U 27 1_555 A G 35 A O6 G 35 1_555 hydrog TYPE_28_PAIR A U 27 A O2 U 27 1_555 A G 35 A N1 G 35 1_555 hydrog WATSON-CRICK A C 28 A N3 C 28 1_555 A G 34 A N1 G 34 1_555 hydrog WATSON-CRICK A C 28 A N4 C 28 1_555 A G 34 A O6 G 34 1_555 hydrog WATSON-CRICK A C 28 A O2 C 28 1_555 A G 34 A N2 G 34 1_555 hydrog HOOGSTEEN A U 47 A N3 U 47 1_555 A A 49 A N7 A 49 1_555 hydrog HOOGSTEEN A U 47 A O4 U 47 1_555 A A 49 A N6 A 49 1_555 hydrog WATSON-CRICK A C 53 A N3 C 53 1_555 A G 67 A N1 G 67 1_555 hydrog WATSON-CRICK A C 53 A N4 C 53 1_555 A G 67 A O6 G 67 1_555 hydrog WATSON-CRICK A C 53 A O2 C 53 1_555 A G 67 A N2 G 67 1_555 hydrog WATSON-CRICK A C 54 A N3 C 54 1_555 A G 66 A N1 G 66 1_555 hydrog WATSON-CRICK A C 54 A N4 C 54 1_555 A G 66 A O6 G 66 1_555 hydrog WATSON-CRICK A C 54 A O2 C 54 1_555 A G 66 A N2 G 66 1_555 hydrog WATSON-CRICK A C 55 A N3 C 55 1_555 A G 65 A N1 G 65 1_555 hydrog WATSON-CRICK A C 55 A N4 C 55 1_555 A G 65 A O6 G 65 1_555 hydrog WATSON-CRICK A C 55 A O2 C 55 1_555 A G 65 A N2 G 65 1_555 hydrog WATSON-CRICK A A 56 A N1 A 56 1_555 A U 64 A N3 U 64 1_555 hydrog WATSON-CRICK A A 56 A N6 A 56 1_555 A U 64 A O4 U 64 1_555 hydrog WATSON-CRICK A G 57 A N1 G 57 1_555 A C 63 A N3 C 63 1_555 hydrog WATSON-CRICK A G 57 A N2 G 57 1_555 A C 63 A O2 C 63 1_555 hydrog WATSON-CRICK A G 57 A O6 G 57 1_555 A C 63 A N4 C 63 1_555 hydrog TYPE_11_PAIR A G 58 A N2 G 58 1_555 A A 62 A N7 A 62 1_555 hydrog TYPE_11_PAIR A G 58 A N3 G 58 1_555 A A 62 A N6 A 62 1_555 hydrog G-U MISPAIR A G 66 A N2 G 66 1_555 A U 68 A O4 U 68 1_555 RNA flavivirus, 3' untranslated region, sfRNA, pseudoknot, Type C RNA three-way junction, Xrn1 resistant RNA, xrRNA), resists degradation, exonuclease Xrn1, small flaviviral RNA, RNA KC852196.1 GB 1 10594 KC852196.1 GUGUCAGAUCGCGAAAGCGCCACUUCGCCGAGGAGUGCAAUCUGUGAGGCCCCAGGAGGACUGGGU 10594 10659 4PQV 1 68 KC852196.1 A 1 1 68 1 U engineered mutation G 2 4PQV A KC852196.1 GB 10595 2 1 insertion G 11 4PQV A KC852196.1 GB 11 1 insertion U 19 4PQV A KC852196.1 GB 19 BINDING SITE FOR RESIDUE MG A 102 A MG 102 Software 6 BINDING SITE FOR RESIDUE MG A 103 A MG 103 Software 1 BINDING SITE FOR RESIDUE MG A 104 A MG 104 Software 6 BINDING SITE FOR RESIDUE MG A 105 A MG 105 Software 1 BINDING SITE FOR RESIDUE MG A 107 A MG 107 Software 1 BINDING SITE FOR RESIDUE MG A 108 A MG 108 Software 1 BINDING SITE FOR RESIDUE MG A 109 A MG 109 Software 2 A C 5 A C 5 6 1_555 A C 23 A C 23 6 1_555 A HOH 201 K HOH 6 1_555 A HOH 202 K HOH 6 1_555 A HOH 203 K HOH 6 1_555 A HOH 207 K HOH 6 1_555 A G 51 A G 51 1 1_555 A G 14 A G 14 6 1_555 A A 16 A A 16 6 1_555 A G 58 A G 58 6 5_565 A HOH 204 K HOH 6 1_555 A HOH 205 K HOH 6 1_555 A HOH 206 K HOH 6 1_555 A G 58 A G 58 1 1_555 A G 11 A G 11 1 1_555 A A 59 A A 59 1 5_565 A G 66 A G 66 2 1_555 A G 67 A G 67 2 1_555 154 P 32 2 1