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. Kim, I. Otto, G.A. Puglisi, J.D. 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 US Nat.Struct.Biol. NSBIEW 2024 1072-8368 10 1033 1038 10.1038/nsb1004 14578934 Structure of HCV IRES domain II determined by NMR. 2003 10.2210/pdb1p5m/pdb pdb_00001p5m 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 17625.432 55-MER HCV IRES domain IIa (residues 45-69,98-117) 1 syn polymer no no GGCUGUGAGGAACUACUGUCUUCACGCCUUCGGGAGUGUCGUGCAGCCUCCAGCC GGCUGUGAGGAACUACUGUCUUCACGCCUUCGGGAGUGUCGUGCAGCCUCCAGCC 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 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 43.754 1 A 1 A 55 -2.445 A_G1:C55_A 1 -42.911 -0.501 0.385 -0.148 18.600 A 2 A 54 -16.352 A_G2:C54_A 2 -34.850 0.502 0.326 -0.138 10.685 1 19 A 3 A 53 1.887 A_C3:G53_A 3 -30.524 -0.579 0.569 -0.108 15.715 1 20 A 4 A 52 -6.044 A_U4:A52_A 4 -11.740 -0.745 0.552 -0.122 -6.240 1 19 A 5 A 51 4.877 A_G5:C51_A 5 -25.631 0.380 0.301 -0.035 -17.598 1 19 A 7 A 50 5.249 A_G7:C50_A 6 -25.779 0.378 -0.133 -0.005 -20.611 1 20 A 8 A 49 11.316 A_A8:U49_A 7 -23.087 -0.215 0.189 -0.107 -12.579 1 19 A 9 A 48 4.560 A_G9:C48_A 8 -23.360 0.553 0.100 -0.038 10.763 1 19 A 10 A 47 -6.989 A_G10:C47_A 9 -9.433 0.464 0.597 -0.148 7.901 1 19 A 16 A 46 4.727 A_C16:G46_A 10 -27.520 -0.302 0.011 -0.083 10.318 1 20 A 17 A 45 5.084 A_U17:A45_A 11 -17.800 0.708 0.546 -0.354 5.878 1 19 A 18 A 44 -6.006 A_G18:C44_A 12 -29.082 0.214 -0.294 -0.273 -4.471 28 A 19 A 43 -9.289 A_U19:G43_A 13 -16.719 2.196 -0.338 -0.598 2.550 1 19 A 20 A 41 -5.579 A_C20:G41_A 14 2.174 -0.410 -0.306 -0.140 18.598 1 18 A 21 A 40 18.879 A_U21:C40_A 15 -12.085 -0.226 -0.208 -1.592 -1.887 A 22 A 39 4.149 A_U22:U39_A 16 -29.552 -1.066 -1.178 -1.564 5.020 1 19 A 23 A 38 2.765 A_C23:G38_A 17 -17.741 -0.577 -1.337 -0.457 0.063 1 20 A 24 A 37 -0.455 A_A24:U37_A 18 -10.244 -0.325 -0.621 -0.421 21.486 1 19 A 25 A 36 -0.960 A_C25:G36_A 19 -14.962 -0.202 -0.926 -0.167 7.012 A 26 A 35 76.815 A_G26:A35_A 20 -11.140 0.244 1.955 -3.956 2.628 1 19 A 27 A 34 -0.344 A_C27:G34_A 21 7.566 -0.371 0.152 -0.089 26.500 1 19 A 28 A 33 -7.180 A_C28:G33_A 22 -6.335 -0.361 -1.668 -0.347 -2.444 A 29 A 32 -79.769 A_U29:G32_A 23 -21.814 2.276 -0.084 -4.053 3.589 39.864 A A 1 2 23.778 A A 55 54 4.044 15.795 -0.721 -0.459 AA_G1G2:C54C55_AA 1 -1.887 2.841 36.671 -2.900 0.791 3.256 37.954 A A 2 3 -8.926 A A 54 53 2.960 -5.777 1.789 -1.244 AA_G2C3:G53C54_AA 2 3.449 -5.329 37.375 -1.206 -2.329 3.415 29.953 A A 3 4 -14.093 A A 53 52 3.231 -7.197 0.137 -1.348 AA_C3U4:A52G53_AA 3 -3.781 7.404 28.853 -1.068 -1.074 3.475 34.671 A A 4 5 4.520 A A 52 51 3.604 2.688 0.345 -1.787 AA_U4G5:C51A52_AA 4 2.726 -4.583 34.465 -3.446 -0.125 2.908 37.379 A A 5 7 14.490 A A 51 50 3.231 9.196 -0.807 -0.879 AA_G5G7:C50C51_AA 5 0.953 -1.502 36.257 -2.526 1.380 2.628 39.013 A A 7 8 12.869 A A 50 49 2.896 8.528 0.190 -0.923 AA_G7A8:U49C50_AA 6 -1.586 2.393 38.073 -2.262 -0.448 2.560 33.639 A A 8 9 16.396 A A 49 48 2.844 9.370 -0.693 -0.677 AA_A8G9:C48U49_AA 7 -0.322 0.563 32.342 -2.460 1.153 2.338 33.822 A A 9 10 5.084 A A 48 47 2.417 2.948 -0.064 -0.734 AA_G9G10:C47C48_AA 8 -3.943 6.801 33.473 -1.610 -0.356 2.816 40.399 A A 16 17 24.108 A A 46 45 3.169 16.183 -0.237 -0.289 AA_C16U17:A45G46_AA 9 -4.426 6.593 36.883 -2.167 -0.135 2.105 37.620 A A 17 18 28.043 A A 45 44 3.043 17.328 -0.693 -0.959 AA_U17G18:C44A45_AA 10 7.133 -11.543 32.768 -3.395 1.860 3.361 51.166 A A 18 19 -3.375 A A 44 43 3.289 -2.913 0.805 -0.795 AA_G18U19:G43C44_AA 11 2.630 -3.048 51.025 -0.716 -0.747 2.992 26.809 A A 19 20 4.078 A A 43 41 3.158 1.888 0.510 -1.679 AA_U19C20:G41G43_AA 12 -1.859 4.016 26.680 -4.080 -1.552 2.645 36.245 A A 20 21 35.126 A A 41 40 2.992 20.597 1.210 0.465 AA_C20U21:C40G41_AA 13 -2.785 4.750 29.859 -2.005 -2.317 3.957 38.763 A A 21 22 8.855 A A 40 39 4.374 5.801 -0.613 -0.712 AA_U21U22:U39C40_AA 14 9.462 -14.443 37.199 -1.997 2.430 2.761 36.178 A A 22 23 12.426 A A 39 38 2.898 7.659 -0.707 -0.497 AA_U22C23:G38U39_AA 15 -1.495 2.425 35.354 -1.745 0.955 3.022 34.164 A A 23 24 39.854 A A 38 37 3.657 21.579 -0.103 0.325 AA_C23A24:U37G38_AA 16 -5.757 10.632 26.020 -3.441 -0.891 2.705 37.096 A A 24 25 -0.418 A A 37 36 2.663 -0.266 0.692 -0.941 AA_A24C25:G36U37_AA 17 2.172 -3.416 37.034 -1.450 -0.849 -0.504 -179.947 A A 25 26 8.100 A A 36 35 -0.509 -16.200 -0.651 4.469 AA_C25G26:A35G36_AA 18 166.887 83.443 -179.505 -2.234 -0.327 0.979 -170.536 A A 26 27 47.224 A A 35 34 -3.168 -90.111 -3.455 -2.814 AA_G26C27:G34A35_AA 19 144.670 75.816 -16.316 0.909 -2.541 2.536 30.048 A A 27 28 2.351 A A 34 33 2.736 1.194 0.032 -1.105 AA_C27C28:G33G34_AA 20 10.509 -20.694 28.165 -2.335 1.735 3.463 101.804 A A 28 29 8.090 A A 33 32 3.623 12.540 1.860 -1.912 AA_C28U29:G32G33_AA 21 1.935 -1.248 101.229 -1.436 -1.167 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 2003-11-04 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 RCSB Y RCSB 2003-04-27 REL REL Synthesized by in vitro transcription from linearized plasmid DNA using T7 RNA polymerase sample The structure was solved using triple resonance, multidimensional NMR spectroscopy and TROSY-type experiments to measure residual dipolar couplings lowest restraint violation and total energy 100 22 2D S-NOESY 2D NOESY DQF-COSY 2D HP-COSY 3D_13C-separated_NOESY 3D HCP 3D HMQC TOCSY 100mM NaCl, 5mM MgCl2 6.40 ambient 288 K 100mM NaCl, 5mM MgCl2 6.40 ambient 298 K 100mM NaCl, 5mM MgCl2 6.40 ambient 303 K see reference above see reference above 1 closest to the average 1-2mM HCV IRES domain IIa RNA 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride 96% D2O, 4% H2O 1-2mM HCV IRES domain IIa RNA 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride 100% D2O 1mM HCV IRES domain IIa RNA U-15N,13C 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride 96% D2O, 4% H2O 1mM HCV IRES domain IIa RNA U-15N,13C 10mM phosphate buffer 100mM sodium chloride 5mM magnesium chloride 100% D2O Varian processing VNMR 6.1C Goddard, Kneller data analysis Sparky 3 Brunger refinement X-PLOR 3.1 Brunger refinement CNS 1.1 Zweckstetter, Bax refinement PALES 1 500 Varian INOVA 800 Varian INOVA GUA 1 n 1 G 1 A GUA 2 n 2 G 2 A CYT 3 n 3 C 3 A URI 4 n 4 U 4 A GUA 5 n 5 G 5 A URI 6 n 6 U 6 A GUA 7 n 7 G 7 A ADE 8 n 8 A 8 A GUA 9 n 9 G 9 A GUA 10 n 10 G 10 A ADE 11 n 11 A 11 A ADE 12 n 12 A 12 A CYT 13 n 13 C 13 A URI 14 n 14 U 14 A ADE 15 n 15 A 15 A CYT 16 n 16 C 16 A URI 17 n 17 U 17 A GUA 18 n 18 G 18 A URI 19 n 19 U 19 A CYT 20 n 20 C 20 A URI 21 n 21 U 21 A URI 22 n 22 U 22 A CYT 23 n 23 C 23 A ADE 24 n 24 A 24 A CYT 25 n 25 C 25 A GUA 26 n 26 G 26 A CYT 27 n 27 C 27 A CYT 28 n 28 C 28 A URI 29 n 29 U 29 A URI 30 n 30 U 30 A CYT 31 n 31 C 31 A GUA 32 n 32 G 32 A GUA 33 n 33 G 33 A GUA 34 n 34 G 34 A ADE 35 n 35 A 35 A GUA 36 n 36 G 36 A URI 37 n 37 U 37 A GUA 38 n 38 G 38 A URI 39 n 39 U 39 A CYT 40 n 40 C 40 A GUA 41 n 41 G 41 A URI 42 n 42 U 42 A GUA 43 n 43 G 43 A CYT 44 n 44 C 44 A ADE 45 n 45 A 45 A GUA 46 n 46 G 46 A CYT 47 n 47 C 47 A CYT 48 n 48 C 48 A URI 49 n 49 U 49 A CYT 50 n 50 C 50 A CYT 51 n 51 C 51 A ADE 52 n 52 A 52 A GUA 53 n 53 G 53 A CYT 54 n 54 C 54 A CYT 55 n 55 C 55 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 18 A A O6 H41 G C 18 44 1.60 19 A A HO2' O4' G C 26 27 1.57 21 A A O6 H41 G C 18 44 1.59 Solution Structure of HCV IRES Domain IIa 1 N N hydrog G-C PAIR A G 1 A N1 G 1 1_555 A C 55 A O2 C 55 1_555 hydrog G-G MISPAIR A G 2 A O6 G 2 1_555 A G 53 A N1 G 53 1_555 hydrog G-C PAIR A G 2 A N1 G 2 1_555 A C 54 A N3 C 54 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 53 A N1 G 53 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 53 A O6 G 53 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 53 A N2 G 53 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 A A 52 A N1 A 52 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 A A 52 A N6 A 52 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 51 A N3 C 51 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 51 A O2 C 51 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 51 A N4 C 51 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 A C 50 A N3 C 50 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 A C 50 A O2 C 50 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 A C 50 A N4 C 50 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 A U 49 A N3 U 49 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 A U 49 A O4 U 49 1_555 hydrog G-C PAIR A G 9 A O6 G 9 1_555 A C 47 A N4 C 47 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 48 A N3 C 48 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 48 A O2 C 48 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 48 A N4 C 48 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 A C 47 A N3 C 47 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 A C 47 A O2 C 47 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 A C 47 A N4 C 47 1_555 hydrog WATSON-CRICK A C 16 A N3 C 16 1_555 A G 46 A N1 G 46 1_555 hydrog WATSON-CRICK A C 16 A N4 C 16 1_555 A G 46 A O6 G 46 1_555 hydrog WATSON-CRICK A C 16 A O2 C 16 1_555 A G 46 A N2 G 46 1_555 hydrog WATSON-CRICK A U 17 A N3 U 17 1_555 A A 45 A N1 A 45 1_555 hydrog WATSON-CRICK A U 17 A O4 U 17 1_555 A A 45 A N6 A 45 1_555 hydrog WATSON-CRICK A G 18 A N1 G 18 1_555 A C 44 A N3 C 44 1_555 hydrog WATSON-CRICK A G 18 A N2 G 18 1_555 A C 44 A O2 C 44 1_555 hydrog WATSON-CRICK A G 18 A O6 G 18 1_555 A C 44 A N4 C 44 1_555 hydrog TYPE_28_PAIR A U 19 A N3 U 19 1_555 A G 43 A O6 G 43 1_555 hydrog TYPE_28_PAIR A U 19 A O2 U 19 1_555 A G 43 A N1 G 43 1_555 hydrog WATSON-CRICK A C 20 A N3 C 20 1_555 A G 41 A N1 G 41 1_555 hydrog WATSON-CRICK A C 20 A N4 C 20 1_555 A G 41 A O6 G 41 1_555 hydrog WATSON-CRICK A C 20 A O2 C 20 1_555 A G 41 A N2 G 41 1_555 hydrog TYPE_18_PAIR A U 21 A N3 U 21 1_555 A C 40 A N3 C 40 1_555 hydrog TYPE_18_PAIR A U 21 A O4 U 21 1_555 A C 40 A N4 C 40 1_555 hydrog U-U MISPAIR A U 22 A O4 U 22 1_555 A U 39 A N3 U 39 1_555 hydrog WATSON-CRICK A C 23 A N3 C 23 1_555 A G 38 A N1 G 38 1_555 hydrog WATSON-CRICK A C 23 A N4 C 23 1_555 A G 38 A O6 G 38 1_555 hydrog WATSON-CRICK A C 23 A O2 C 23 1_555 A G 38 A N2 G 38 1_555 hydrog WATSON-CRICK A A 24 A N1 A 24 1_555 A U 37 A N3 U 37 1_555 hydrog WATSON-CRICK A A 24 A N6 A 24 1_555 A U 37 A O4 U 37 1_555 hydrog WATSON-CRICK A C 25 A N3 C 25 1_555 A G 36 A N1 G 36 1_555 hydrog WATSON-CRICK A C 25 A N4 C 25 1_555 A G 36 A O6 G 36 1_555 hydrog WATSON-CRICK A C 25 A O2 C 25 1_555 A G 36 A N2 G 36 1_555 hydrog G-A MISPAIR A G 26 A O6 G 26 1_555 A A 35 A N6 A 35 1_555 hydrog WATSON-CRICK A C 27 A N3 C 27 1_555 A G 34 A N1 G 34 1_555 hydrog WATSON-CRICK A C 27 A N4 C 27 1_555 A G 34 A O6 G 34 1_555 hydrog WATSON-CRICK A C 27 A O2 C 27 1_555 A G 34 A N2 G 34 1_555 hydrog WATSON-CRICK A C 28 A N3 C 28 1_555 A G 33 A N1 G 33 1_555 hydrog WATSON-CRICK A C 28 A N4 C 28 1_555 A G 33 A O6 G 33 1_555 hydrog WATSON-CRICK A C 28 A O2 C 28 1_555 A G 33 A N2 G 33 1_555 hydrog WATSON-CRICK A C 28 A N3 C 28 1_555 A G 34 A N1 G 34 1_555 hydrog WATSON-CRICK A C 28 A N4 C 28 1_555 A G 34 A O6 G 34 1_555 hydrog WATSON-CRICK A C 28 A O2 C 28 1_555 A G 34 A N2 G 34 1_555 hydrog U-G MISPAIR A U 29 A O2 U 29 1_555 A G 32 A N1 G 32 1_555 RNA RIBONUCLEIC ACID, HEPATITIS C VIRUS, INTERNAL RIBOSOME ENTRY SITE, tRNA, RNA 1P5M PDB 1 1P5M 1 55 1P5M 1 55 1P5M A 1 1 55