1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0002-2735-0049 Mertinkus, K.R. 0000-0001-6859-6849 Oxenfarth, A. 0000-0001-5693-7909 Schwalbe, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 R C N 122 N O N 123 R C N 124 N N N 125 N C N 126 N O N 127 N N N 128 N C N 129 N O N 130 N C N 131 N C 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 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 doub 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 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 doub N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N doub N 149 N sing N 150 N sing US J.Am.Chem.Soc. JACSAT 1520-5126 146 30139 30154 10.1021/jacs.4c08406 39442924 Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2. 2024 0000-0003-0788-8447 0000-0003-2254-7560 0000-0001-5693-7909 10.2210/pdb9fo8/pdb pdb_00009fo8 10.13018/BMR51138 9285.499 RNA (29-MER) 1 syn polymer no no GGCACAUCUAGGUUUCGUCCGGGUGUGCC GGCACAUCUAGGUUUCGUCCGGGUGUGCC 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 1.309 1 19 A 1 A 29 15.098 A_G1:C29_A 1 26.729 -0.076 0.615 -0.057 -13.673 1 19 A 2 A 28 0.452 A_G2:C28_A 2 -4.456 0.763 -0.774 -0.212 0.068 1 19 A 3 A 27 5.578 A_C3:G27_A 3 -7.810 0.281 -0.215 0.010 -12.921 1 20 A 4 A 26 8.346 A_A4:U26_A 4 -8.113 -0.708 -1.103 -0.074 0.576 1 19 A 5 A 25 -2.768 A_C5:G25_A 5 -14.161 0.174 -0.136 -0.204 -4.953 1 20 A 6 A 24 -10.657 A_A6:U24_A 6 -5.004 -0.451 -0.299 -0.162 -6.275 1 28 A 7 A 23 -21.561 A_U7:G23_A 7 -6.394 2.570 0.338 -0.715 0.504 1 19 A 8 A 22 0.102 A_C8:G22_A 8 -0.766 0.570 -0.256 -0.262 -5.033 1 28 A 9 A 21 25.425 A_U9:G21_A 9 -9.174 2.404 -0.606 -0.137 15.324 1 19 A 11 A 20 -5.612 A_G11:C20_A 10 -2.807 -0.528 -0.225 -0.287 -15.718 1 19 A 12 A 19 -28.698 A_G12:C19_A 11 -33.944 0.402 1.210 -0.713 8.884 2 A 13 A 17 165.279 A_U13:G17_A 12 8.509 -0.343 -0.875 -1.926 2.217 32.043 A A 1 2 36.866 A A 29 28 4.615 18.256 -0.677 -1.217 AA_G1G2:C28C29_AA 1 14.556 -29.394 22.100 -6.315 4.502 3.462 22.018 A A 2 3 7.759 A A 28 27 3.661 2.954 0.603 -1.042 AA_G2C3:G27C28_AA 2 -0.941 2.473 21.801 -3.970 -1.974 5.128 28.144 A A 3 4 -24.163 A A 27 26 5.115 -11.418 0.033 -1.113 AA_C3A4:U26G27_AA 3 1.561 -3.303 25.720 2.098 0.532 3.283 34.293 A A 4 5 4.542 A A 26 25 3.311 2.669 -0.434 -0.622 AA_A4C5:G25U26_AA 4 -4.225 7.190 33.938 -1.479 0.063 3.846 31.293 A A 5 6 5.747 A A 25 24 3.980 3.091 -0.884 -1.863 AA_C5A6:U24G25_AA 5 -2.939 5.464 31.008 -4.157 0.971 3.261 46.977 A A 6 7 11.244 A A 24 23 3.600 8.913 -0.807 -1.694 AA_A6U7:G23U24_AA 6 -1.558 1.965 46.146 -2.904 0.876 3.629 29.039 A A 7 8 -1.120 A A 23 22 3.353 -0.555 1.380 -1.669 AA_U7C8:G22G23_AA 7 7.790 -15.721 27.991 -3.196 -0.889 5.192 32.961 A A 8 9 10.679 A A 22 21 4.954 5.977 1.943 0.069 AA_C8U9:G21G22_AA 8 7.427 -13.269 31.588 -1.492 -1.420 4.598 40.110 A A 9 11 -6.383 A A 21 20 3.615 -4.343 -6.313 1.312 AA_U9G11:C20G21_AA 9 -7.969 11.713 39.111 2.544 8.048 5.282 46.305 A A 11 12 7.282 A A 20 19 5.466 5.711 -0.887 -1.592 AA_G11G12:C19C20_AA 10 -2.598 3.312 45.902 -2.825 0.764 3.137 -102.680 A A 12 13 -2.240 A A 19 17 2.986 3.491 -1.073 -2.090 AA_G12U13:G17C19_AA 11 15.755 10.110 -101.760 1.290 -0.470 citation repository Initial release Database references 1 0 2024-11-06 1 1 2024-11-13 _citation.journal_volume _citation.page_first _citation.page_last Germany German Research Foundation (DFG) 161793742 Germany German Research Foundation (DFG) 495006306 H.S. schwalbe@nmr.uni-frankfurt.de 0000-0001-5693-7909 Harald Schwalbe J. principal investigator/group leader N PDBE Y PDBE 2024-06-11 REL REL 2901879 Severe acute respiratory syndrome coronavirus sample 1 29 N structures with the lowest energy 200 10 isotropic 1 2D 1H-1H NOESY isotropic 1 2D 1H-1H NOESY xfilter isotropic 1 2D 1H-13C HSQC isotropic 1 2D 1H-13C HSQC aromatic isotropic 2 2D IPAP 1H-13C HSQC isotropic 2 2D IPAP 1H-13C HSQC aromatic anisotropic 2 2D IPAP 1H-13C HSQC anisotropic 2 2D IPAP 1H-13C HSQC aromatic 0.51 mM [U-100% 13C; U-100% 15N] 50 mM natural abundance 25 mM natural abundance 0.2 mM [U-100% 13C; U-100% 15N] 50 mM natural abundance 25 mM natural abundance 0.2 mM [U-100% 13C; U-100% 15N] 50 mM natural abundance 25 mM natural abundance 10 mg/mL natural abundance Sample was stored at 277K. Measurments were performed between 278-313K. 25 mM 13C15N 6.2 pH 1 Pa 277 K simulated annealing water refinement na 1 lowest energy 0.51 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 95% H2O/5% D2O 13C15N 95% H2O/5% D2O solution 0.2 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 95% H2O/5% D2O RDC ref 95% H2O/5% D2O solution 0.2 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 50 mM potassium chloride, 25 mM potassium phosphate, 10 mg/mL Pf1 phage, 95% H2O/5% D2O RDC cross 95% H2O/5% D2O solution Lee W, Tonelli M, Markley JL chemical shift assignment NMRFAM-SPARKY 3.190 Brunger, Adams, Clore, Gros, Nilges and Read structure calculation CNS Linge, O'Donoghue and Nilges refinement ARIA Bruker Biospin processing TopSpin 4.1.4 800 Bruker AVANCE III 600 Bruker AVANCE NEO G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A A 4 n 4 A 4 A C 5 n 5 C 5 A A 6 n 6 A 6 A U 7 n 7 U 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A A 10 n 10 A 10 A G 11 n 11 G 11 A G 12 n 12 G 12 A U 13 n 13 U 13 A U 14 n 14 U 14 A U 15 n 15 U 15 A C 16 n 16 C 16 A G 17 n 17 G 17 A U 18 n 18 U 18 A C 19 n 19 C 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A G 22 n 22 G 22 A G 23 n 23 G 23 A U 24 n 24 U 24 A G 25 n 25 G 25 A U 26 n 26 U 26 A G 27 n 27 G 27 A C 28 n 28 C 28 A C 29 n 29 C 29 A author_and_software_defined_assembly 1 monomeric not applicable SAXS 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 1_555 x,y,z identity operation 0.0 0.0 0.0 10 A A HO2' OP2 U C 18 19 1.51 1 A C 19 0.058 SIDE CHAIN 1 A G 21 0.064 SIDE CHAIN 3 A U 18 0.070 SIDE CHAIN 9 A C 19 0.061 SIDE CHAIN 10 8.70 1.20 119.70 128.40 A A A C3' O3' P U U C 18 18 19 Y N 5_SL5b_GC of the 5_SL5 RNA 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 29 A N3 C 29 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 29 A O2 C 29 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 29 A N4 C 29 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 28 A N3 C 28 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 28 A O2 C 28 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 28 A N4 C 28 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 27 A N1 G 27 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 27 A O6 G 27 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 27 A N2 G 27 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 26 A N3 U 26 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 26 A O4 U 26 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 25 A N1 G 25 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 25 A O6 G 25 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 25 A N2 G 25 1_555 hydrog WATSON-CRICK A A 6 A N1 A 6 1_555 A U 24 A N3 U 24 1_555 hydrog WATSON-CRICK A A 6 A N6 A 6 1_555 A U 24 A O4 U 24 1_555 hydrog TYPE_28_PAIR A U 7 A N3 U 7 1_555 A G 23 A O6 G 23 1_555 hydrog TYPE_28_PAIR A U 7 A O2 U 7 1_555 A G 23 A N1 G 23 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 22 A O6 G 22 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 22 A N2 G 22 1_555 hydrog TYPE_28_PAIR A U 9 A N3 U 9 1_555 A G 21 A O6 G 21 1_555 hydrog TYPE_28_PAIR A U 9 A O2 U 9 1_555 A G 21 A N1 G 21 1_555 hydrog TYPE_11_PAIR A A 10 A N6 A 10 1_555 A G 21 A N3 G 21 1_555 hydrog TYPE_11_PAIR A A 10 A N7 A 10 1_555 A G 21 A N2 G 21 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 20 A N4 C 20 1_555 hydrog WATSON-CRICK A G 12 A N1 G 12 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 12 A N2 G 12 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 12 A O6 G 12 1_555 A C 19 A N4 C 19 1_555 hydrog U-G MISPAIR A U 13 A O4 U 13 1_555 A G 17 A N1 G 17 1_555 hydrog U-C MISPAIR A U 18 A O2 U 18 1_555 A C 20 A N4 C 20 1_555 hydrog U-G MISPAIR A U 18 A O2 U 18 1_555 A G 21 A N2 G 21 1_555 RNA Sars-Cov-2, 5_SL5, 5_SL5b, UUUCGU, repetetive structure motif, RNA 9FO8 PDB 1 1 9FO8 1 29 9FO8 1 29 9FO8 A 1 1 29