1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lukavsky, P.J. Otto, G.A. Lancaster, A.M. Sarnow, P. Puglisi, J.D. 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 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 Nat.Struct.Biol. NSBIEW 2024 1072-8368 7 1105 1110 10.1038/81951 11101890 Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function. 2000 10.2210/pdb1f84/pdb pdb_00001f84 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 9450.667 HCV-1B IRES RNA DOMAIN IIID HCV IRES RNA DOMAIN IIID (NUCLEOTIDES 252-290 OF GENOMIC HEPATITIS C VIRAL RNA) A252G 1 syn polymer no no GGCCGAGUAGUGUUGGGUCGCGAAAGGCC GGCCGAGUAGUGUUGGGUCGCGAAAGGCC 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 -0.191 1 19 A 2 A 28 -4.230 A_G2:C28_A 1 -25.787 0.295 0.411 -0.312 2.628 1 19 A 3 A 27 -3.312 A_C3:G27_A 2 -24.032 -0.451 0.481 -0.177 -0.735 1 19 A 4 A 26 -0.306 A_C4:G26_A 3 -30.035 -0.103 -0.307 -0.303 0.201 10 A 5 A 25 -15.806 A_G5:A25_A 4 -16.574 6.777 0.320 -5.786 11.989 8 2 A 6 A 24 179.451 A_A6:A24_A 5 -2.356 5.506 -0.414 -5.263 20.493 4 24 A 8 A 23 -104.471 A_U8:A23_A 6 -15.529 3.558 -0.759 -1.258 -0.341 9 11 A 9 A 22 -5.326 A_A9:G22_A 7 -3.235 -6.405 -0.563 -4.160 -15.161 1 19 A 10 A 21 2.045 A_G10:C21_A 8 -21.178 -0.001 -0.690 -0.357 -20.178 1 28 A 11 A 20 -4.911 A_U11:G20_A 9 -22.682 1.617 0.691 -0.460 -26.056 1 19 A 12 A 19 -14.342 A_G12:C19_A 10 5.941 0.738 -2.032 -0.578 49.885 A 14 A 17 -89.389 A_U14:G17_A 11 26.509 -0.946 0.694 -7.229 3.264 30.487 A A 2 3 -13.288 A A 28 27 2.914 -6.929 0.167 -1.912 AA_G2C3:G27C28_AA 1 -0.281 0.539 29.706 -2.315 -0.371 2.822 35.541 A A 3 4 14.775 A A 27 26 3.167 8.904 -0.284 -0.769 AA_C3C4:G26G27_AA 2 4.675 -7.758 34.133 -2.475 1.104 3.403 72.367 A A 4 5 7.570 A A 26 25 3.453 8.921 -0.741 -0.299 AA_C4G5:A25G26_AA 3 -0.175 0.148 71.890 -0.563 0.621 2.395 -175.787 A A 5 6 -47.223 A A 25 24 1.687 92.607 0.152 -3.774 AA_G5A6:A24A25_AA 4 -149.328 -76.148 -21.387 0.996 -1.362 1.020 174.166 A A 6 8 54.643 A A 24 23 1.106 107.867 1.444 2.258 AA_A6U8:A23A24_AA 5 -133.118 67.435 95.303 0.871 -1.043 -3.957 9.137 A A 8 9 45.257 A A 23 22 3.476 5.280 4.982 -1.592 AA_U8A9:G22A23_AA 6 -7.120 61.027 2.218 -8.592 -29.378 3.827 64.278 A A 9 10 5.008 A A 22 21 3.884 5.322 0.621 -0.918 AA_A9G10:C21G22_AA 7 2.853 -2.685 64.024 -1.132 -0.440 3.777 44.316 A A 10 11 -16.666 A A 21 20 3.644 -12.379 -0.509 -0.865 AA_G10U11:G20C21_AA 8 -6.345 8.542 42.181 0.195 -0.013 2.879 34.685 A A 11 12 9.454 A A 20 19 3.698 5.442 -0.305 -2.029 AA_U11G12:C19G20_AA 9 14.768 -25.657 31.006 -4.294 2.927 4.723 134.941 A A 12 14 14.543 A A 19 17 4.476 26.802 3.487 0.370 AA_G12U14:G17C19_AA 10 18.766 -10.183 132.927 -0.049 -1.713 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2000-11-17 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2000-06-28 REL REL Synthesized enzymatically in-vitro using T7 RNA Polymerase sample THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE HCN AND HCP EXPERIMENTS ON N15,C13-LABELLED RNA structures with the least restraint violations,structures with the lowest energy 100 25 P31-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY P31-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY 3D HCP, 3D HMQC-TOCSY, 3D C13-edited NOESY 10mM 6.40 ambient 283 K 10mM 6.40 ambient 298 K SEE REFERENCE ABOVE Simulated annealing and restrained molecular dynamics 21 closest to the average 1.5mM RNA, non-isotopically labelled 10mM sodium phosphate buffer, pH 6.40 96% H2O, 4% D2O or 100% D2O 1mM RNA, U-15N,13C 10mM sodium phosphate buffer, pH 6.40 96% H2O, 4% D2O or 100% D2O Brunger refinement X-PLOR 3.1 Goddard data analysis Sparky 3.8 500 Varian INOVA 800 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A C 4 n 4 C 4 A G 5 n 5 G 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A U 8 n 8 U 8 A A 9 n 9 A 9 A G 10 n 10 G 10 A U 11 n 11 U 11 A G 12 n 12 G 12 A U 13 n 13 U 13 A U 14 n 14 U 14 A G 15 n 15 G 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A U 18 n 18 U 18 A C 19 n 19 C 19 A G 20 n 20 G 20 A C 21 n 21 C 21 A G 22 n 22 G 22 A A 23 n 23 A 23 A A 24 n 24 A 24 A A 25 n 25 A 25 A G 26 n 26 G 26 A G 27 n 27 G 27 A C 28 n 28 C 28 A C 29 n 29 C 29 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 5 A A HO2' O6 G G 7 22 1.52 18 A A H41 O6 C G 4 26 1.56 15 24.23 1.90 111.70 135.93 A A A O5' C5' C4' G G G 1 1 1 N 15 A A O5' C5' G G 1 1 -0.699 0.009 1.420 0.721 N SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIID 1 N N 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 C 4 A N3 C 4 1_555 A G 26 A N1 G 26 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 26 A O6 G 26 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 26 A N2 G 26 1_555 hydrog G-A MISPAIR A G 5 A N2 G 5 1_555 A A 25 A N7 A 25 1_555 hydrog A-G MISPAIR A A 6 A N1 A 6 1_555 A G 7 A N2 G 7 1_555 hydrog TYPE_2_PAIR A A 6 A N6 A 6 1_555 A A 24 A N7 A 24 1_555 hydrog TYPE_2_PAIR A A 6 A N7 A 6 1_555 A A 24 A N6 A 24 1_555 hydrog G-U MISPAIR A G 7 A N2 G 7 1_555 A U 8 A O4 U 8 1_555 hydrog REVERSED HOOGSTEEN A U 8 A N3 U 8 1_555 A A 23 A N7 A 23 1_555 hydrog REVERSED HOOGSTEEN A U 8 A O2 U 8 1_555 A A 23 A N6 A 23 1_555 hydrog TYPE_11_PAIR A A 9 A N6 A 9 1_555 A G 22 A N3 G 22 1_555 hydrog TYPE_11_PAIR A A 9 A N7 A 9 1_555 A G 22 A N2 G 22 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 A C 21 A N4 C 21 1_555 hydrog TYPE_28_PAIR A U 11 A N3 U 11 1_555 A G 20 A O6 G 20 1_555 hydrog TYPE_28_PAIR A U 11 A O2 U 11 1_555 A G 20 A N1 G 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 14 A O2 U 14 1_555 A G 17 A N2 G 17 1_555 RNA Ribonucleic Acid, Hepatitis C virus internal ribosome entry site, Sarcin/Ricin loop, Loop E motif, Hairpin loop, RNA structure, RNA 1F84 PDB 1 1F84 1 29 1F84 1 29 1F84 A 1 1 29 1 P 1