1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lescrinier, E.M. Tessari, M. van Kuppeveld, F.J. Melchers, W.J. Hilbers, C.W. Heus, H.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 331 759 769 10.1016/S0022-2836(03)00787-3 12909008 Structure of the Pyrimidine-rich Internal Loop in the Poliovirus 3'-UTR: The Importance of Maintaining Pseudo-2-fold Symmetry in RNA Helices Containing Two Adjacent Non-canonical Base-pairs. 2003 10.2210/pdb1n66/pdb pdb_00001n66 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 7034.227 internal loop in the Y-domain of poliovirus 3'UTR 1 syn polymer no no GGACCUCUCGAAAGAGUUGUCC GGACCUCUCGAAAGAGUUGUCC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -9.344 1 19 A 1 A 22 -1.242 A_G1:C22_A 1 -9.935 -0.534 0.009 -0.544 7.895 1 19 A 2 A 21 0.319 A_G2:C21_A 2 -14.217 -0.569 -0.019 -0.587 31.810 1 20 A 3 A 20 -1.764 A_A3:U20_A 3 2.590 -0.102 0.307 -0.095 5.421 1 19 A 4 A 19 0.050 A_C4:G19_A 4 3.687 0.297 -1.112 -0.503 -13.858 A 5 A 18 35.199 A_C5:U18_A 5 18.443 2.534 -0.648 -1.450 -32.016 1 16 A 6 A 17 28.306 A_U6:U17_A 6 -16.736 -2.896 0.208 -1.802 -0.921 1 19 A 7 A 16 14.946 A_C7:G16_A 7 -12.511 1.059 -0.607 -0.324 -0.888 1 20 A 8 A 15 -1.168 A_U8:A15_A 8 8.651 0.525 -0.065 -0.346 13.576 1 19 A 9 A 14 4.461 A_C9:G14_A 9 -14.249 0.197 -1.386 -0.559 1.691 10 A 10 A 13 -14.867 A_G10:A13_A 10 -1.138 6.566 0.087 -5.455 2.764 38.096 A A 1 2 4.676 A A 22 21 2.771 3.043 -0.935 -1.082 AA_G1G2:C21C22_AA 1 -4.275 6.569 37.746 -1.985 0.972 2.637 37.930 A A 2 3 1.433 A A 21 20 2.684 0.931 0.340 -1.172 AA_G2A3:U20C21_AA 2 -1.825 2.809 37.877 -1.899 -0.713 2.772 30.521 A A 3 4 24.808 A A 20 19 3.801 12.443 1.108 -2.114 AA_A3C4:G19U20_AA 3 9.902 -19.742 26.135 -6.706 0.036 3.063 36.194 A A 4 5 16.332 A A 19 18 4.522 9.828 1.774 -1.694 AA_C4C5:U18G19_AA 4 -12.308 20.453 32.691 -4.418 -4.974 -0.424 26.146 A A 5 6 53.292 A A 18 17 3.109 20.895 -0.517 -2.918 AA_C5U6:U17U18_AA 5 -0.150 0.383 15.804 -9.382 1.121 2.066 47.020 A A 6 7 13.585 A A 17 16 2.217 10.707 -0.509 0.046 AA_U6C7:G16U17_AA 6 7.852 -9.963 45.208 -0.532 1.070 2.008 33.105 A A 7 8 34.719 A A 16 15 3.083 18.661 -1.569 -1.184 AA_C7U8:A15G16_AA 7 -2.198 4.089 27.379 -4.776 2.436 2.870 35.725 A A 8 9 16.521 A A 15 14 2.775 9.748 1.604 -0.745 AA_U8C9:G14A15_AA 8 13.959 -23.658 31.524 -2.511 -0.756 3.849 54.540 A A 9 10 22.796 A A 14 13 4.069 20.436 -2.060 -0.258 AA_C9G10:A13G14_AA 9 -3.870 4.317 50.702 -1.844 1.952 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-08-19 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name CRYSTAL STRUCTURE OF AN RNA DOUBLE HELIX INCORPORATING A TRACK OF NON-WATSON-CRICK BASE PAIRS NMR structure with GAAA tetraloop RCSB Y RCSB 2002-11-08 REL REL structures with the lowest energy 100 20 5.8 ambient 288 K 5.5 ambient 288 K 5.5 ambient 273 K 5.5 ambient 288 K torsion angle dynamics followed by conjugate gradient minimization 1 lowest energy 3mM RNA D2O 3mM RNA D2O 3mM RNA 90% H2O/10% D2O 1-2mM RNA, U-13C,15N, C-13C,15N D2O Varian collection VNMR 6.1 Delaglio processing NMRPipe 2.1 ETH-Zurich data analysis XEASY 1.2.0 Brunger refinement X-PLOR 3.851 750 Varian INOVA 600 Varian INOVA 500 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A C 4 n 4 C 4 A C 5 n 5 C 5 A U 6 n 6 U 6 A C 7 n 7 C 7 A U 8 n 8 U 8 A C 9 n 9 C 9 A G 10 n 10 G 10 A A 11 n 11 A 11 A A 12 n 12 A 12 A A 13 n 13 A 13 A G 14 n 14 G 14 A A 15 n 15 A 15 A G 16 n 16 G 16 A U 17 n 17 U 17 A U 18 n 18 U 18 A G 19 n 19 G 19 A U 20 n 20 U 20 A C 21 n 21 C 21 A C 22 n 22 C 22 A author_defined_assembly 1 monomeric 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 H3 O2 U U 6 17 1.36 1 A A H21 O2 G C 1 22 1.51 1 A A O2 H3 C U 5 18 1.52 1 A A H21 OP2 G A 10 13 1.55 1 A A H22 N7 G A 10 13 1.57 2 A A H21 OP2 G A 10 13 1.39 2 A A H22 N7 G A 10 13 1.43 2 A A H3 O2 U U 6 17 1.48 2 A A O4 H3 U U 6 17 1.50 2 A A H21 O2 G C 1 22 1.51 2 A A O2 H21 C G 4 19 1.55 3 A A H3 O2 U U 6 17 1.41 3 A A O2 H3 C U 5 18 1.48 3 A A H21 OP2 G A 10 13 1.48 3 A A HO2' O4' U G 18 19 1.51 3 A A H21 O2 G C 1 22 1.51 3 A A H1 N3 G C 2 21 1.57 3 A A H22 N7 G A 10 13 1.57 3 A A O2 H21 C G 4 19 1.58 4 A A O4 H3 U U 6 17 1.48 4 A A H21 OP2 G A 10 13 1.50 4 A A H22 N7 G A 10 13 1.54 4 A A H21 O2 G C 1 22 1.56 4 A A O6 H41 G C 1 22 1.57 4 A A O2 H21 C G 7 16 1.59 5 A A H21 O2 G C 1 22 1.48 5 A A O2 H3 C U 5 18 1.48 5 A A H3 O2 U U 6 17 1.49 5 A A H21 OP2 G A 10 13 1.50 5 A A O2 H21 C G 4 19 1.56 5 A A O6 H41 G C 2 21 1.58 5 A A H1 N3 G C 2 21 1.58 5 A A H22 N7 G A 10 13 1.58 6 A A H3 O2 U U 6 17 1.48 6 A A H21 O2 G C 1 22 1.49 6 A A O2 H3 C U 5 18 1.51 6 A A H1 N3 G C 2 21 1.53 6 A A O6 H41 G C 2 21 1.54 6 A A O4 H3 U U 6 17 1.56 6 A A H21 O2 G C 2 21 1.59 6 A A O2 H21 C G 4 19 1.60 6 A A H21 OP2 G A 10 13 1.60 7 A A H22 N7 G A 10 13 1.44 7 A A H21 O2 G C 1 22 1.47 7 A A H21 OP2 G A 10 13 1.48 7 A A O4 H3 U U 6 17 1.48 7 A A O2 H3 C U 5 18 1.56 7 A A O6 H41 G C 2 21 1.57 7 A A H1 N3 G C 2 21 1.59 8 A A O2 H3 C U 5 18 1.41 8 A A H3 O2 U U 6 17 1.42 8 A A H21 O2 G C 1 22 1.49 8 A A O2 H21 C G 4 19 1.56 8 A A H1 N3 G C 2 21 1.57 9 A A H3 O2 U U 6 17 1.43 9 A A O2 H3 C U 5 18 1.47 9 A A H21 O2 G C 1 22 1.55 9 A A H22 N7 G A 10 13 1.56 9 A A H21 OP2 G A 10 13 1.57 9 A A O2 H21 C G 4 19 1.57 10 A A HO2' OP1 G A 10 11 1.48 10 A A H22 N7 G A 10 13 1.49 10 A A H3 O2 U U 6 17 1.53 10 A A H21 O2 G C 1 22 1.53 10 A A O2 H21 C G 4 19 1.55 10 A A O2 H3 C U 5 18 1.57 10 A A H1 N3 G C 2 21 1.59 11 A A H3 O2 U U 6 17 1.41 11 A A O2 H3 C U 5 18 1.47 11 A A H21 O2 G C 1 22 1.52 12 A A H21 OP2 G A 10 13 1.38 12 A A H22 N7 G A 10 13 1.43 12 A A H21 O2 G C 1 22 1.47 12 A A H1 N3 G C 2 21 1.53 12 A A O2 H21 C G 4 19 1.54 12 A A O4 H3 U U 6 17 1.55 12 A A O6 H41 G C 2 21 1.56 12 A A O2 H3 C U 5 18 1.56 12 A A H1 N3 G C 1 22 1.60 13 A A O4 H3 U U 6 17 1.42 13 A A H21 O2 G C 1 22 1.51 13 A A H41 O6 C G 9 14 1.59 13 A A O2 H21 C G 4 19 1.60 14 A A H3 O2 U U 6 17 1.42 14 A A H1 N3 G C 2 21 1.53 14 A A O2 H3 C U 5 18 1.53 14 A A H21 O2 G C 1 22 1.53 14 A A O6 H41 G C 2 21 1.54 14 A A H21 OP2 G A 10 13 1.57 14 A A H22 N7 G A 10 13 1.59 14 A A O6 H41 G C 1 22 1.59 14 A A O2 H21 C G 4 19 1.60 15 A A O4 H3 U U 6 17 1.46 15 A A H21 O2 G C 1 22 1.50 15 A A H21 OP2 G A 10 13 1.51 15 A A H3 O2 U U 6 17 1.51 15 A A O2 H3 C U 5 18 1.55 15 A A H22 N7 G A 10 13 1.59 15 A A O2 H21 C G 7 16 1.59 16 A A O2 H3 C U 5 18 1.36 16 A A H3 O2 U U 6 17 1.40 16 A A O2 H21 C G 4 19 1.52 16 A A H21 O2 G C 1 22 1.58 17 A A O4 H3 U U 6 17 1.48 17 A A H3 O2 U U 6 17 1.48 17 A A H21 OP2 G A 10 13 1.49 17 A A H22 N7 G A 10 13 1.56 18 A A HO2' OP1 G G 1 2 1.39 18 A A H21 OP2 G A 10 13 1.45 18 A A H3 O2 U U 6 17 1.49 18 A A O6 H41 G C 2 21 1.49 18 A A O2 H3 C U 5 18 1.51 18 A A H21 O2 G C 2 21 1.56 18 A A H22 N7 G A 10 13 1.58 18 A A O2 H21 C G 4 19 1.58 19 A A H21 O2 G C 1 22 1.46 19 A A H3 O2 U U 6 17 1.56 19 A A H21 OP2 G A 10 13 1.56 19 A A O2 H21 C G 4 19 1.59 20 A A O2 H21 C G 4 19 1.49 20 A A H3 O2 U U 6 17 1.52 20 A A H22 N7 G A 10 13 1.53 20 A A H21 O2 G C 1 22 1.54 Structure of the pyrimidine-rich internal loop in the Y-domain of poliovirus 3'UTR 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 22 A N4 C 22 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 21 A N4 C 21 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 20 A N3 U 20 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 20 A O4 U 20 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 19 A O6 G 19 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 19 A N2 G 19 1_555 hydrog C-U MISPAIR A C 5 A O2 C 5 1_555 A U 18 A N3 U 18 1_555 hydrog TYPE_16_PAIR A U 6 A N3 U 6 1_555 A U 17 A O2 U 17 1_555 hydrog TYPE_16_PAIR A U 6 A O4 U 6 1_555 A U 17 A N3 U 17 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 A G 16 A N2 G 16 1_555 hydrog WATSON-CRICK A U 8 A N3 U 8 1_555 A A 15 A N1 A 15 1_555 hydrog WATSON-CRICK A U 8 A O4 U 8 1_555 A A 15 A N6 A 15 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 14 A N1 G 14 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 14 A O6 G 14 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 14 A N2 G 14 1_555 hydrog C-A MISPAIR A C 9 A N3 C 9 1_555 A A 15 A N6 A 15 1_555 hydrog G-A MISPAIR A G 10 A N2 G 10 1_555 A A 13 A N7 A 13 1_555 RNA RNA internal loop, RNA 1N66 PDB 1 1N66 1 22 1N66 1 22 1N66 A 1 1 22 1 P 1