1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Reiter, N.J. Nikstad, L.J. Allman, A.M. Johnson, R.J. Butcher, S.E. 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 O8 P S 340.247 n URIDINE-5'-PHOSPHOROTHIOATE SP-SULFUR-SUBSTITUTED URIDINE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK RNA RNARFU 2122 1355-8382 9 533 542 10.1261/rna.2199103 12702812 Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification. 2003 10.2210/pdb1nz1/pdb pdb_00001nz1 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 A62G, SP phoshphorothioate modified U80 7684.681 SP U6 Intramolecular Stem-Loop RNA A62G 1 syn polymer SP ISL RNA no yes GGUUCCCCUGCAUAAGGA(SSU)GAACC GGUUCCCCUGCAUAAGGAUGAACC 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 0.674 1 19 A 1 A 24 -4.845 A_G1:C24_A 1 0.712 -0.656 0.032 -0.064 -0.711 1 19 A 2 A 23 2.087 A_G2:C23_A 2 -0.186 -0.908 0.052 -0.206 -0.255 1 20 A 3 A 22 -11.622 A_U3:A22_A 3 -0.906 0.582 0.086 -0.150 1.269 1 20 A 4 A 21 -4.926 A_U4:A21_A 4 0.570 -0.894 -0.078 -0.086 -0.245 1 19 A 5 A 20 -0.618 A_C5:G20_A 5 -0.961 -0.097 0.053 -0.183 4.896 1 A 6 A 18 7.897 A_C6:A18_A 6 -4.838 2.281 -0.220 -0.596 -3.237 1 19 A 7 A 17 -3.392 A_C7:G17_A 7 -3.134 0.516 0.086 -0.253 1.602 1 19 A 8 A 16 2.261 A_C8:G16_A 8 0.864 0.694 -0.072 -0.090 0.828 1 20 A 9 A 15 -8.116 A_U9:A15_A 9 -0.707 -0.849 0.051 -0.030 6.029 9 11 A 10 A 14 11.888 A_G10:A14_A 10 6.307 6.595 -0.043 -3.599 4.612 33.705 A A 1 2 -12.813 A A 24 23 4.480 -7.370 -0.056 -1.116 AA_G1G2:C23C24_AA 1 -1.644 2.858 32.872 -0.237 -0.280 2.152 44.537 A A 2 3 28.194 A A 23 22 3.251 20.626 -1.003 -1.677 AA_G2U3:A22C23_AA 2 0.663 -0.906 39.684 -3.885 1.378 4.251 27.292 A A 3 4 -10.028 A A 22 21 4.068 -4.709 0.513 -1.364 AA_U3U4:A21A22_AA 3 0.689 -1.467 26.882 -1.387 -0.866 2.138 41.877 A A 4 5 40.064 A A 21 20 3.570 26.594 0.122 -1.079 AA_U4C5:G20A21_AA 4 -0.906 1.364 32.634 -4.271 -0.265 3.898 60.690 A A 5 6 4.148 A A 20 18 5.110 4.148 4.405 0.165 AA_C5C6:A18G20_AA 5 -16.050 16.052 58.591 -0.119 -5.451 2.459 22.634 A A 6 7 24.009 A A 18 17 3.694 9.141 -0.949 -2.014 AA_C6C7:G17A18_AA 6 2.416 -6.346 20.588 -8.409 3.284 3.377 39.199 A A 7 8 3.006 A A 17 16 3.263 2.007 1.186 -0.669 AA_C7C8:G16G17_AA 7 6.706 -10.045 38.593 -1.242 -0.947 1.817 27.763 A A 8 9 32.984 A A 16 15 3.120 15.010 -1.926 -1.525 AA_C8U9:A15G16_AA 8 0.148 -0.325 23.423 -6.150 4.044 3.772 68.840 A A 9 10 -25.652 A A 15 14 4.549 -28.207 2.295 0.115 AA_U9G10:A14A15_AA 9 -11.895 10.818 62.424 1.515 -2.626 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-05-13 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag Solution structure of the U6 intramolecular stem-loop RNA Refined solution structure of the U6 intramolecular stem-loop RNA using residual dipolar couplings (RDCs) U80G U6 Intramolecular Stem-Loop RNA from Saccharomyces cerevisiae RCSB Y RCSB 2003-02-14 REL Synthetic RNA (Dharmacon, Inc.) was prepared containing an SP phosphorothioate modification at nucleotide U80. The Sp RNA was separated from the Rp RNA diastereomer using reverse-phase high pressure liquid chromatography. sample Solution structure based on 322 NOE derived distance restraints, 144 dihedral angle restraints, 25 hydrogen bond restraints, and 40 residual dipolar copupling restraints. structures with the lowest energy 100 17 2D NOESY HSQC HSQC 2D NOESY 2D TOCSY 50 mM NaCl 7.0 ambient 283 K 50 mM NaCl 7.2 ambient 303 K 50 mM NaCl 7.0 ambient 303 K Torsion angle and molecular dynamics, simulated annealing, residual dipolar coupling 15 lowest energy 0.8-1.2 mM RNA, 50 mM NaCL, pH 7.0 H2O 0.8-1.2 mM RNA, 50 mM NaCL, pH 7.0, 17 mg/mL PF1 Phage H2O 0.8-1.2 mM RNA, 50 mM NaCL, pH 7.0 D2O Bruker collection XwinNMR 2.6 Accelrys processing Felix 98 Goddard, T.D. and D.G. Kneller data analysis Sparky 3 Brunger structure solution CNS 1.1 Brunger refinement X-PLOR 3.1 750 Bruker DMX 600 Bruker DMX 500 Bruker DMX 400 Bruker DMX G 1 n 1 G 1 A G 2 n 2 G 2 A U 3 n 3 U 3 A U 4 n 4 U 4 A C 5 n 5 C 5 A C 6 n 6 C 6 A C 7 n 7 C 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A G 10 n 10 G 10 A C 11 n 11 C 11 A A 12 n 12 A 12 A U 13 n 13 U 13 A A 14 n 14 A 14 A A 15 n 15 A 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A SSU 19 n 19 SSU 19 A G 20 n 20 G 20 A A 21 n 21 A 21 A A 22 n 22 A 22 A C 23 n 23 C 23 A C 24 n 24 C 24 A author_defined_assembly 1 monomeric A SSU 19 URIDINE-5'-PHOSPHOROTHIOATE A SSU 19 U 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 HO2' O4' C A 11 12 1.53 3 A A HO2' O4' C A 11 12 1.47 5 A A O2' H2' A U 12 13 1.45 5 A A H2' OP2 G A 10 12 1.58 6 A A HO2' O4' C A 11 12 1.47 6 A A HO2' O5' G A 17 18 1.51 7 A A H2' OP2 G A 10 12 1.57 8 A A H2' OP2 G A 10 12 1.51 9 A A HO2' O5' C U 8 9 1.26 10 A A HO2' O5' G A 20 21 1.46 10 A A H2' OP2 G A 10 12 1.53 11 A A HO2' O5' C U 8 9 1.30 11 A A H2' OP2 G A 10 12 1.47 12 A A HO2' O4' C A 11 12 1.42 12 A A O2' H8 C A 11 12 1.43 12 A A O2' H2' G C 10 11 1.47 12 A A O2' H5'' C A 11 12 1.49 12 A A HO2' O4' C C 23 24 1.59 14 A A H2' OP2 G A 10 12 1.49 14 A A HO2' O4' C C 5 6 1.54 15 A A O2' H5' U C 4 5 1.58 16 A A HO2' O4' C A 11 12 1.37 16 A A O2' H8 C A 11 12 1.42 16 A A O2' H2' G C 10 11 1.48 17 A A HO2' O4' C A 11 12 1.33 17 A A O2' H8 C A 11 12 1.38 17 A A O2' H2' G C 10 11 1.38 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 1 1 1 N 1 4.69 0.50 113.10 117.79 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.77 0.40 106.40 103.63 A A A C8 N9 C4 G G G 2 2 2 N 1 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 10 10 10 N 1 -2.56 0.40 106.40 103.84 A A A C8 N9 C4 G G G 10 10 10 N 1 3.60 0.50 113.80 117.40 A A A N7 C8 N9 A A A 12 12 12 N 1 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 14 14 14 N 1 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 15 15 15 N 1 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 16 16 16 N 1 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 16 16 16 N 1 4.65 0.50 113.10 117.75 A A A N7 C8 N9 G G G 17 17 17 N 1 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 G G G 17 17 17 N 1 3.78 0.50 113.80 117.58 A A A N7 C8 N9 A A A 18 18 18 N 1 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 20 20 20 N 1 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 20 20 20 N 1 3.68 0.50 113.80 117.48 A A A N7 C8 N9 A A A 21 21 21 N 1 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 22 22 22 N 2 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 1 1 1 N 2 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 1 1 1 N 2 4.62 0.50 113.10 117.72 A A A N7 C8 N9 G G G 2 2 2 N 2 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 2 2 2 N 2 4.64 0.50 113.10 117.74 A A A N7 C8 N9 G G G 10 10 10 N 2 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 G G G 10 10 10 N 2 3.69 0.50 113.80 117.49 A A A N7 C8 N9 A A A 12 12 12 N 2 3.82 0.50 113.80 117.62 A A A N7 C8 N9 A A A 14 14 14 N 2 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 15 15 15 N 2 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 16 16 16 N 2 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 16 16 16 N 2 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 17 17 17 N 2 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 G G G 17 17 17 N 2 3.75 0.50 113.80 117.55 A A A N7 C8 N9 A A A 18 18 18 N 2 4.66 0.50 113.10 117.76 A A A N7 C8 N9 G G G 20 20 20 N 2 -2.78 0.40 106.40 103.63 A A A C8 N9 C4 G G G 20 20 20 N 2 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 21 21 21 N 2 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 22 22 22 N 3 4.45 0.50 113.10 117.55 A A A N7 C8 N9 G G G 1 1 1 N 3 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 1 1 1 N 3 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 2 2 2 N 3 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 G G G 2 2 2 N 3 4.66 0.50 113.10 117.76 A A A N7 C8 N9 G G G 10 10 10 N 3 -2.59 0.40 106.40 103.81 A A A C8 N9 C4 G G G 10 10 10 N 3 3.68 0.50 113.80 117.48 A A A N7 C8 N9 A A A 12 12 12 N 3 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 14 14 14 N 3 3.65 0.50 113.80 117.45 A A A N7 C8 N9 A A A 15 15 15 N 3 4.65 0.50 113.10 117.75 A A A N7 C8 N9 G G G 16 16 16 N 3 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 16 16 16 N 3 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 17 17 17 N 3 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 G G G 17 17 17 N 3 3.75 0.50 113.80 117.55 A A A N7 C8 N9 A A A 18 18 18 N 3 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 20 20 20 N 3 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 20 20 20 N 3 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 21 21 21 N 3 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 22 22 22 N 4 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 1 1 1 N 4 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 1 1 1 N 4 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 2 2 2 N 4 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 2 2 2 N 4 4.67 0.50 113.10 117.77 A A A N7 C8 N9 G G G 10 10 10 N 4 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 10 10 10 N 4 3.60 0.50 113.80 117.40 A A A N7 C8 N9 A A A 12 12 12 N 4 3.69 0.50 113.80 117.49 A A A N7 C8 N9 A A A 14 14 14 N 4 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 15 15 15 N 4 4.46 0.50 113.10 117.56 A A A N7 C8 N9 G G G 16 16 16 N 4 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 G G G 16 16 16 N 4 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 17 17 17 N 4 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 17 17 17 N 4 3.84 0.50 113.80 117.64 A A A N7 C8 N9 A A A 18 18 18 N 4 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 20 20 20 N 4 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 20 20 20 N 4 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 21 21 21 N 4 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 22 22 22 N 5 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 1 1 1 N 5 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 1 1 1 N 5 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 2 2 2 N 5 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 2 2 2 N 5 4.69 0.50 113.10 117.79 A A A N7 C8 N9 G G G 10 10 10 N 5 -2.55 0.40 106.40 103.85 A A A C8 N9 C4 G G G 10 10 10 N 5 3.51 0.50 113.80 117.31 A A A N7 C8 N9 A A A 12 12 12 N 5 3.83 0.50 113.80 117.63 A A A N7 C8 N9 A A A 14 14 14 N 5 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 15 15 15 N 5 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 16 16 16 N 5 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 16 16 16 N 5 4.65 0.50 113.10 117.75 A A A N7 C8 N9 G G G 17 17 17 N 5 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 G G G 17 17 17 N 5 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 18 18 18 N 5 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 20 20 20 N 5 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 G G G 20 20 20 N 5 3.83 0.50 113.80 117.63 A A A N7 C8 N9 A A A 21 21 21 N 5 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 22 22 22 N 6 4.46 0.50 113.10 117.56 A A A N7 C8 N9 G G G 1 1 1 N 6 -2.59 0.40 106.40 103.81 A A A C8 N9 C4 G G G 1 1 1 N 6 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 2 2 2 N 6 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 2 2 2 N 6 4.69 0.50 113.10 117.79 A A A N7 C8 N9 G G G 10 10 10 N 6 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 G G G 10 10 10 N 6 3.66 0.50 113.80 117.46 A A A N7 C8 N9 A A A 12 12 12 N 6 3.67 0.50 113.80 117.47 A A A N7 C8 N9 A A A 14 14 14 N 6 3.67 0.50 113.80 117.47 A A A N7 C8 N9 A A A 15 15 15 N 6 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 16 16 16 N 6 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 16 16 16 N 6 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 17 17 17 N 6 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 17 17 17 N 6 3.88 0.50 113.80 117.68 A A A N7 C8 N9 A A A 18 18 18 N 6 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 20 20 20 N 6 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 20 20 20 N 6 3.68 0.50 113.80 117.48 A A A N7 C8 N9 A A A 21 21 21 N 6 3.66 0.50 113.80 117.46 A A A N7 C8 N9 A A A 22 22 22 N 7 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 1 1 1 N 7 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 1 1 1 N 7 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 2 2 2 N 7 -2.61 0.40 106.40 103.79 A A A C8 N9 C4 G G G 2 2 2 N 7 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 10 10 10 N 7 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 G G G 10 10 10 N 7 3.67 0.50 113.80 117.47 A A A N7 C8 N9 A A A 12 12 12 N 7 3.92 0.50 113.80 117.72 A A A N7 C8 N9 A A A 14 14 14 N 7 3.84 0.50 113.80 117.64 A A A N7 C8 N9 A A A 15 15 15 N 7 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 16 16 16 N 7 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 16 16 16 N 7 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 17 17 17 N 7 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 17 17 17 N 7 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 18 18 18 N 7 4.68 0.50 113.10 117.78 A A A N7 C8 N9 G G G 20 20 20 N 7 -2.79 0.40 106.40 103.61 A A A C8 N9 C4 G G G 20 20 20 N 7 3.77 0.50 113.80 117.57 A A A N7 C8 N9 A A A 21 21 21 N 7 3.69 0.50 113.80 117.49 A A A N7 C8 N9 A A A 22 22 22 N 8 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 1 1 1 N 8 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 1 1 1 N 8 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 2 2 2 N 8 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 2 2 2 N 8 4.69 0.50 113.10 117.79 A A A N7 C8 N9 G G G 10 10 10 N 8 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 G G G 10 10 10 N 8 3.65 0.50 113.80 117.45 A A A N7 C8 N9 A A A 12 12 12 N 8 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 14 14 14 N 8 3.64 0.50 113.80 117.44 A A A N7 C8 N9 A A A 15 15 15 N 8 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 16 16 16 N 8 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 16 16 16 N 8 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 17 17 17 N 8 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 17 17 17 N 8 3.84 0.50 113.80 117.64 A A A N7 C8 N9 A A A 18 18 18 N 8 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 20 20 20 N 8 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 20 20 20 N 8 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 21 21 21 N 8 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 22 22 22 N 9 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 1 1 1 N 9 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 G G G 1 1 1 N 9 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 2 2 2 N 9 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 2 2 2 N 9 4.66 0.50 113.10 117.76 A A A N7 C8 N9 G G G 10 10 10 N 9 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 10 10 10 N 9 3.49 0.50 113.80 117.29 A A A N7 C8 N9 A A A 12 12 12 N 9 3.80 0.50 113.80 117.60 A A A N7 C8 N9 A A A 14 14 14 N 9 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 15 15 15 N 9 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 16 16 16 N 9 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 16 16 16 N 9 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 17 17 17 N 9 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 17 17 17 N 9 3.89 0.50 113.80 117.69 A A A N7 C8 N9 A A A 18 18 18 N 9 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 20 20 20 N 9 -2.62 0.40 106.40 103.78 A A A C8 N9 C4 G G G 20 20 20 N 9 3.75 0.50 113.80 117.55 A A A N7 C8 N9 A A A 21 21 21 N 9 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 22 22 22 N 10 4.60 0.50 113.10 117.70 A A A N7 C8 N9 G G G 1 1 1 N 10 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 1 1 1 N 10 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 2 2 2 N 10 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 2 2 2 N 10 4.63 0.50 113.10 117.73 A A A N7 C8 N9 G G G 10 10 10 N 10 -2.50 0.40 106.40 103.90 A A A C8 N9 C4 G G G 10 10 10 N 10 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 12 12 12 N 10 3.95 0.50 113.80 117.75 A A A N7 C8 N9 A A A 14 14 14 N 10 -2.43 0.40 105.80 103.37 A A A C8 N9 C4 A A A 14 14 14 N 10 3.75 0.50 113.80 117.55 A A A N7 C8 N9 A A A 15 15 15 N 10 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 16 16 16 N 10 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 16 16 16 N 10 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 17 17 17 N 10 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 17 17 17 N 10 3.75 0.50 113.80 117.55 A A A N7 C8 N9 A A A 18 18 18 N 10 4.45 0.50 113.10 117.55 A A A N7 C8 N9 G G G 20 20 20 N 10 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 G G G 20 20 20 N 10 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 21 21 21 N 10 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 22 22 22 N 11 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 1 1 1 N 11 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 1 1 1 N 11 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 2 2 2 N 11 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 2 2 2 N 11 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 10 10 10 N 11 -2.53 0.40 106.40 103.87 A A A C8 N9 C4 G G G 10 10 10 N 11 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 12 12 12 N 11 3.86 0.50 113.80 117.66 A A A N7 C8 N9 A A A 14 14 14 N 11 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 15 15 15 N 11 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 16 16 16 N 11 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 16 16 16 N 11 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 17 17 17 N 11 -2.57 0.40 106.40 103.83 A A A C8 N9 C4 G G G 17 17 17 N 11 3.80 0.50 113.80 117.60 A A A N7 C8 N9 A A A 18 18 18 N 11 4.48 0.50 113.10 117.58 A A A N7 C8 N9 G G G 20 20 20 N 11 -2.50 0.40 106.40 103.90 A A A C8 N9 C4 G G G 20 20 20 N 11 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 21 21 21 N 11 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 22 22 22 N 12 4.48 0.50 113.10 117.58 A A A N7 C8 N9 G G G 1 1 1 N 12 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 1 1 1 N 12 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 2 2 2 N 12 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 G G G 2 2 2 N 12 4.60 0.50 113.10 117.70 A A A N7 C8 N9 G G G 10 10 10 N 12 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 G G G 10 10 10 N 12 3.99 0.50 113.80 117.79 A A A N7 C8 N9 A A A 12 12 12 N 12 -2.67 0.40 105.80 103.13 A A A C8 N9 C4 A A A 12 12 12 N 12 3.85 0.50 113.80 117.65 A A A N7 C8 N9 A A A 14 14 14 N 12 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 15 15 15 N 12 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 16 16 16 N 12 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 16 16 16 N 12 4.64 0.50 113.10 117.74 A A A N7 C8 N9 G G G 17 17 17 N 12 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 17 17 17 N 12 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 18 18 18 N 12 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 20 20 20 N 12 -2.62 0.40 106.40 103.78 A A A C8 N9 C4 G G G 20 20 20 N 12 3.82 0.50 113.80 117.62 A A A N7 C8 N9 A A A 21 21 21 N 12 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 22 22 22 N 13 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 1 1 1 N 13 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 1 1 1 N 13 4.46 0.50 113.10 117.56 A A A N7 C8 N9 G G G 2 2 2 N 13 -2.56 0.40 106.40 103.84 A A A C8 N9 C4 G G G 2 2 2 N 13 4.67 0.50 113.10 117.77 A A A N7 C8 N9 G G G 10 10 10 N 13 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 G G G 10 10 10 N 13 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 12 12 12 N 13 3.82 0.50 113.80 117.62 A A A N7 C8 N9 A A A 14 14 14 N 13 3.84 0.50 113.80 117.64 A A A N7 C8 N9 A A A 15 15 15 N 13 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 16 16 16 N 13 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 16 16 16 N 13 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 17 17 17 N 13 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 17 17 17 N 13 3.83 0.50 113.80 117.63 A A A N7 C8 N9 A A A 18 18 18 N 13 4.63 0.50 113.10 117.73 A A A N7 C8 N9 G G G 20 20 20 N 13 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 20 20 20 N 13 3.76 0.50 113.80 117.56 A A A N7 C8 N9 A A A 21 21 21 N 13 3.78 0.50 113.80 117.58 A A A N7 C8 N9 A A A 22 22 22 N 14 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 1 1 1 N 14 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 G G G 1 1 1 N 14 4.48 0.50 113.10 117.58 A A A N7 C8 N9 G G G 2 2 2 N 14 -2.61 0.40 106.40 103.79 A A A C8 N9 C4 G G G 2 2 2 N 14 4.68 0.50 113.10 117.78 A A A N7 C8 N9 G G G 10 10 10 N 14 -2.51 0.40 106.40 103.89 A A A C8 N9 C4 G G G 10 10 10 N 14 3.63 0.50 113.80 117.43 A A A N7 C8 N9 A A A 12 12 12 N 14 3.63 0.50 113.80 117.43 A A A N7 C8 N9 A A A 14 14 14 N 14 3.73 0.50 113.80 117.53 A A A N7 C8 N9 A A A 15 15 15 N 14 4.73 0.50 113.10 117.83 A A A N7 C8 N9 G G G 16 16 16 N 14 -2.83 0.40 106.40 103.57 A A A C8 N9 C4 G G G 16 16 16 N 14 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 17 17 17 N 14 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 G G G 17 17 17 N 14 3.85 0.50 113.80 117.65 A A A N7 C8 N9 A A A 18 18 18 N 14 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 20 20 20 N 14 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 20 20 20 N 14 3.82 0.50 113.80 117.62 A A A N7 C8 N9 A A A 21 21 21 N 14 3.83 0.50 113.80 117.63 A A A N7 C8 N9 A A A 22 22 22 N 15 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 1 1 1 N 15 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 1 1 1 N 15 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 15 -2.61 0.40 106.40 103.79 A A A C8 N9 C4 G G G 2 2 2 N 15 4.48 0.50 113.10 117.58 A A A N7 C8 N9 G G G 10 10 10 N 15 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 10 10 10 N 15 3.88 0.50 113.80 117.68 A A A N7 C8 N9 A A A 12 12 12 N 15 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 14 14 14 N 15 3.66 0.50 113.80 117.46 A A A N7 C8 N9 A A A 15 15 15 N 15 4.60 0.50 113.10 117.70 A A A N7 C8 N9 G G G 16 16 16 N 15 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 16 16 16 N 15 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 17 17 17 N 15 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 17 17 17 N 15 3.80 0.50 113.80 117.60 A A A N7 C8 N9 A A A 18 18 18 N 15 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 20 20 20 N 15 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 20 20 20 N 15 3.70 0.50 113.80 117.50 A A A N7 C8 N9 A A A 21 21 21 N 15 3.81 0.50 113.80 117.61 A A A N7 C8 N9 A A A 22 22 22 N 16 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 1 1 1 N 16 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 1 1 1 N 16 4.60 0.50 113.10 117.70 A A A N7 C8 N9 G G G 2 2 2 N 16 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 2 2 2 N 16 4.64 0.50 113.10 117.74 A A A N7 C8 N9 G G G 10 10 10 N 16 -2.45 0.40 106.40 103.95 A A A C8 N9 C4 G G G 10 10 10 N 16 4.11 0.50 113.80 117.91 A A A N7 C8 N9 A A A 12 12 12 N 16 -2.78 0.40 105.80 103.02 A A A C8 N9 C4 A A A 12 12 12 N 16 3.98 0.50 113.80 117.78 A A A N7 C8 N9 A A A 14 14 14 N 16 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 15 15 15 N 16 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 16 16 16 N 16 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 16 16 16 N 16 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 17 17 17 N 16 -2.55 0.40 106.40 103.85 A A A C8 N9 C4 G G G 17 17 17 N 16 3.78 0.50 113.80 117.58 A A A N7 C8 N9 A A A 18 18 18 N 16 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 20 20 20 N 16 -2.76 0.40 106.40 103.64 A A A C8 N9 C4 G G G 20 20 20 N 16 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 21 21 21 N 16 3.60 0.50 113.80 117.40 A A A N7 C8 N9 A A A 22 22 22 N 17 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 1 1 1 N 17 -2.59 0.40 106.40 103.81 A A A C8 N9 C4 G G G 1 1 1 N 17 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 17 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 2 2 2 N 17 4.69 0.50 113.10 117.79 A A A N7 C8 N9 G G G 10 10 10 N 17 -2.41 0.40 106.40 103.99 A A A C8 N9 C4 G G G 10 10 10 N 17 4.33 0.50 113.80 118.13 A A A N7 C8 N9 A A A 12 12 12 N 17 -2.96 0.40 105.80 102.84 A A A C8 N9 C4 A A A 12 12 12 N 17 3.85 0.50 113.80 117.65 A A A N7 C8 N9 A A A 14 14 14 N 17 3.68 0.50 113.80 117.48 A A A N7 C8 N9 A A A 15 15 15 N 17 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 16 16 16 N 17 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 G G G 16 16 16 N 17 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 17 17 17 N 17 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 17 17 17 N 17 3.92 0.50 113.80 117.72 A A A N7 C8 N9 A A A 18 18 18 N 17 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 20 20 20 N 17 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 20 20 20 N 17 3.59 0.50 113.80 117.39 A A A N7 C8 N9 A A A 21 21 21 N 17 3.74 0.50 113.80 117.54 A A A N7 C8 N9 A A A 22 22 22 N Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80 1 N N covale 1.610 both A A 18 A O3' A 18 1_555 A SSU 19 A P SSU 19 1_555 covale 1.611 both A SSU 19 A O3' SSU 19 1_555 A G 20 A P G 20 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 24 A N3 C 24 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 24 A O2 C 24 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 24 A N4 C 24 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 23 A N3 C 23 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 23 A N4 C 23 1_555 hydrog WATSON-CRICK A U 3 A N3 U 3 1_555 A A 22 A N1 A 22 1_555 hydrog WATSON-CRICK A U 3 A O4 U 3 1_555 A A 22 A N6 A 22 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 A A 21 A N1 A 21 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 A A 21 A N6 A 21 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 20 A N2 G 20 1_555 hydrog C-A MISPAIR A C 6 A N3 C 6 1_555 A A 18 A N6 A 18 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 A G 17 A N2 G 17 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 16 A N2 G 16 1_555 hydrog WATSON-CRICK A U 9 A N3 U 9 1_555 A A 15 A N1 A 15 1_555 hydrog WATSON-CRICK A U 9 A O4 U 9 1_555 A A 15 A N6 A 15 1_555 hydrog TYPE_11_PAIR A G 10 A N2 G 10 1_555 A A 14 A N7 A 14 1_555 hydrog TYPE_11_PAIR A G 10 A N3 G 10 1_555 A A 14 A N6 A 14 1_555 RNA U6 RNA, stem-loop, phosphorothioate, Sp phosphorothioate, residual dipolar coupling, RDC, RNA 1NZ1 PDB 1 1NZ1 1 24 1NZ1 1 24 1NZ1 A 1 1 24