1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0003-3250-3043 Leopold, D. 0000-0001-6859-6849 Oxenfarth, A. 0000-0002-2096-4873 Thomasen, F.E. 0000-0002-4697-4658 Kuemmerer, F. Schnieders, R. 0000-0001-6769-7277 Pinter, G. 0000-0001-5892-5661 Wacker, A. 0000-0002-5582-3931 Jonker, H.R.A. 0000-0001-6443-7656 Fuertig, B. 0000-0002-5420-2826 Richter, C. 0000-0002-4750-6039 Lindorff-Larsen, K. 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 UK Rna RNARFU 2122 1469-9001 32 1199 1212 10.1261/rna.081067.126 42215280 Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops. 2026 10.2210/pdb9sy8/pdb pdb_00009sy8 10.13018/BMR35020 4540.787 RNA hairpin with GAAG tetraloop 1 syn polymer no no GGCACGAAGGUGCC GGCACGAAGGUGCC A polyribonucleotide n n n n n n n n n n n n n n 3.940 1 19 A 1 A 14 -7.514 A_G1:C14_A 1 2.650 -0.806 0.201 -0.281 6.254 1 19 A 2 A 13 -2.156 A_G2:C13_A 2 -11.112 -0.231 0.095 -0.266 -1.728 1 19 A 3 A 12 1.242 A_C3:G12_A 3 -10.723 0.226 0.146 -0.080 -1.158 1 20 A 4 A 11 0.146 A_A4:U11_A 4 -2.690 -0.606 0.478 -0.258 18.366 1 19 A 5 A 10 -3.741 A_C5:G10_A 5 -16.152 -0.157 0.273 -0.176 3.253 32.858 A A 1 2 17.567 A A 14 13 3.686 9.794 0.325 -0.932 AA_G1G2:C13C14_AA 1 -0.288 0.516 31.401 -3.470 -0.628 2.965 40.318 A A 2 3 28.402 A A 13 12 3.594 18.863 0.474 -0.476 AA_G2C3:G12C13_AA 2 -1.820 2.740 35.751 -2.968 -0.908 4.524 33.073 A A 3 4 -11.705 A A 12 11 4.424 -6.615 0.167 -1.059 AA_C3A4:U11G12_AA 3 -2.312 4.090 32.342 -0.314 -0.834 3.314 33.672 A A 4 5 -12.944 A A 11 10 3.063 -7.439 0.131 -1.492 AA_A4C5:G10U11_AA 4 1.068 -1.858 32.846 -1.378 -0.055 citation citation_author repository Initial release Database references 1 0 2026-06-24 1 1 2026-07-29 _citation.journal_volume _citation.page_first _citation.page_last _citation.title _citation_author.identifier_ORCID Germany German Research Foundation (DFG) SCHW701/32-1 Denmark Lundbeckfonden R155-2015-2666 Denmark Novo Nordisk Foundation NNF18OC0032608 schwalbe@nmr.uni-frankfurt.de 0000-0001-5693-7909 Harald Schwalbe principal investigator/group leader lindorff@bio.ku.dk 0000-0002-4750-6039 Kresten Lindorff-Larsen principal investigator/group leader Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GAAG ARIA structure N PDBE Y PDBE 2025-10-10 REL REL 14mer RNA hairpin with GAAG tetraloop 2086595 synthetic RNA sample 1 14 N structures with the lowest energy 200 20 isotropic 6 2D 1H-1H NOESY isotropic 4 2D 1H-13C HSQC anisotropic 4 2D 1H-13C HSQC isotropic 4 2D 1H-15N HSQC anisotropic 4 2D 1H-15N HSQC isotropic 2 3D qHCP isotropic 2 2D qHCP isotropic 6 2D P-FIDS isotropic 1 3D HCC-TOCSY-CCH-E.COSY isotropic 6 2D HNN-COSY isotropic 2 2D gamma HCCH isotropic 2 2D gamma HCNCH isotropic 1 2D gamma HCP isotropic 6 2D 1H-13C HSQC isotropic 6 2D 1H-15N HSQC isotropic 1 2D HCN isotropic 1 3D forward directed HCCH-TOCSY isotropic 6 2D 1H-1H NOESY 1.24 mM [U-13C; U-15N] 50 mM natural abundance 50 uM natural abundance 0.64 mM [U-13C; U-15N] 50 mM natural abundance 50 uM natural abundance 1.3 mM natural abundance 50 mM natural abundance 50 uM natural abundance 1.26 mM natural abundance 50 mM natural abundance 50 uM natural abundance 0.2 mM [U-13C; U-15N] 50 mM natural abundance 50 uM natural abundance 0.2 mM [U-13C; U-15N] 50 mM natural abundance 50 uM natural abundance 20 mg/mL natural abundance 50 mM condition 6.4 pH 1 atm 298 K simulated annealing 1 closest to the average 1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 95% H2O/5% D2O 13C15N in H2O 95% H2O/5% D2O solution 0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 100% D2O 13C15N in D2O 100% D2O solution 1.3 mM RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 100% D2O unlabeled in D2O 100% D2O solution 1.26 mM RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 95% H2O/5% D2O unlabeled in H2O 95% H2O/5% D2O solution 0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 100% D2O Isotropic in D2O 100% D2O solution 0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage, 100% D2O Anisotropic in D2O 100% D2O solution Bruker Biospin processing TopSpin 4.2.0 Bruker Biospin collection TopSpin 4.20 Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG peak picking NMRFAM-SPARKY 1.470 Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG chemical shift assignment NMRFAM-SPARKY 1.470 Zweckstetter and Bax data analysis PALES Brunger, Adams, Clore, Gros, Nilges and Read structure calculation CNS Linge, O'Donoghue and Nilges structure calculation ARIA cryoprobe 600 Bruker AVANCE cryoprobe 600 Bruker AVANCE III HD cryoprobe 700 Bruker AVANCE III HD cryoprobe 800 Bruker AVANCE III cryoprobe 900 Bruker AVANCE NEO cryoprobe 950 Bruker AVANCE III 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 G 6 n 6 G 6 A A 7 n 7 A 7 A A 8 n 8 A 8 A G 9 n 9 G 9 A G 10 n 10 G 10 A U 11 n 11 U 11 A G 12 n 12 G 12 A C 13 n 13 C 13 A C 14 n 14 C 14 A author_and_software_defined_assembly 1 monomeric not applicable NMR Distance Restraints 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 1 A A HO2' O5' A G 8 9 1.52 2 A A HO2' O5' A G 8 9 1.56 3 A A HO2' O5' A G 8 9 1.54 4 A A HO2' O5' A G 8 9 1.53 5 A A HO2' O5' A G 8 9 1.53 6 A A HO2' O5' A G 8 9 1.52 7 A A HO2' O5' A G 8 9 1.53 8 A A HO2' O5' A G 8 9 1.54 9 A A HO2' O5' A G 8 9 1.54 10 A A HO2' O5' A G 8 9 1.53 11 A A HO2' O5' A G 8 9 1.52 12 A A HO2' O5' A G 8 9 1.53 13 A A HO2' O5' A G 8 9 1.51 14 A A HO2' O5' A G 8 9 1.54 15 A A HO2' O5' A G 8 9 1.52 16 A A HO2' O5' A G 8 9 1.51 17 A A HO2' O5' A G 8 9 1.55 18 A A HO2' O5' A G 8 9 1.50 19 A A HO2' O5' A G 8 9 1.56 20 A A HO2' O5' A G 8 9 1.50 1 A A 7 0.074 SIDE CHAIN 2 A A 7 0.085 SIDE CHAIN 3 A A 7 0.081 SIDE CHAIN 4 A C 5 0.060 SIDE CHAIN 4 A A 7 0.078 SIDE CHAIN 5 A A 7 0.072 SIDE CHAIN 6 A A 7 0.081 SIDE CHAIN 7 A A 7 0.078 SIDE CHAIN 8 A A 7 0.073 SIDE CHAIN 9 A A 7 0.073 SIDE CHAIN 10 A A 7 0.076 SIDE CHAIN 11 A A 7 0.082 SIDE CHAIN 12 A A 7 0.073 SIDE CHAIN 13 A A 7 0.078 SIDE CHAIN 14 A A 7 0.076 SIDE CHAIN 15 A A 7 0.078 SIDE CHAIN 16 A A 7 0.081 SIDE CHAIN 17 A A 7 0.081 SIDE CHAIN 18 A A 7 0.079 SIDE CHAIN 19 A A 7 0.078 SIDE CHAIN 20 A A 7 0.074 SIDE CHAIN N Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GAAG ARIA structure 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 14 A N4 C 14 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 13 A N3 C 13 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 13 A O2 C 13 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 13 A N4 C 13 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 12 A N1 G 12 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 12 A O6 G 12 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 12 A N2 G 12 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 11 A N3 U 11 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 11 A O4 U 11 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 10 A N1 G 10 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 10 A O6 G 10 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 10 A N2 G 10 1_555 RNA Model Hairpin, RNA, GAAG, Tetraloop, High Resolution 9SY8 PDB 1 1 9SY8 1 14 9SY8 1 14 9SY8 A 1 1 14