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/pdb1p5n/pdb pdb_00001p5n 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 10970.565 34-MER HCV IRES domain IIa (residues 69-98) 1 syn polymer no no GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC 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 28.061 1 19 A 1 A 34 18.413 A_G1:C34_A 1 -25.618 0.107 -0.608 -0.351 2.527 1 19 A 2 A 33 9.576 A_G2:C33_A 2 -22.536 0.239 -0.528 -0.110 19.075 1 19 A 3 A 32 4.161 A_C3:G32_A 3 -28.690 -0.038 -1.034 -0.191 -37.722 1 20 A 4 A 31 -6.450 A_A4:U31_A 4 -0.430 0.392 -1.420 0.163 -0.429 9 11 A 5 A 30 -5.701 A_G5:A30_A 5 9.448 6.503 -0.911 -3.229 0.468 4 24 A 6 A 29 -109.859 A_A6:U29_A 6 -16.713 -4.043 -0.941 -1.469 -19.135 8 2 A 7 A 27 -177.190 A_A7:A27_A 7 -10.294 -5.569 0.681 4.838 18.339 5 A 8 A 26 11.387 A_A8:U26_A 8 -18.698 -7.110 -0.084 -4.101 10.412 28 A 9 A 25 9.447 A_G9:U25_A 9 -32.654 -2.281 -0.140 -0.389 13.838 1 19 A 10 A 24 6.623 A_C10:G24_A 10 -32.665 -0.117 -0.485 -0.119 -3.816 1 19 A 11 A 23 -2.802 A_G11:C23_A 11 -21.733 0.258 -0.130 -0.292 4.348 28 A 12 A 22 -8.860 A_U12:G22_A 12 -20.345 1.472 -0.471 -0.434 2.211 1 19 A 13 A 21 -2.538 A_C13:G21_A 13 0.466 -0.417 -0.102 -0.094 2.599 36.867 A A 1 2 41.913 A A 34 33 3.858 24.374 -0.382 -0.545 AA_G1G2:C33C34_AA 1 -1.980 3.405 27.802 -4.621 0.299 2.562 33.556 A A 2 3 3.075 A A 33 32 2.641 1.771 -0.218 -0.717 AA_G2C3:G32C33_AA 2 3.704 -6.431 33.311 -1.474 0.863 2.609 38.336 A A 3 4 41.150 A A 32 31 5.132 24.951 0.122 -2.111 AA_C3A4:U31G32_AA 3 -1.048 1.728 29.320 -7.452 -0.364 2.292 61.463 A A 4 5 -3.153 A A 31 30 2.274 -3.220 -0.369 -0.169 AA_A4G5:A30U31_AA 4 -2.662 2.606 61.334 -0.060 0.274 2.563 -14.395 A A 5 6 -67.232 A A 30 29 3.251 13.267 -4.654 -1.344 AA_G5A6:U29A30_AA 5 0.183 0.927 -5.595 -10.016 -18.361 2.704 87.261 A A 6 7 -6.525 A A 29 27 2.702 -8.991 1.659 -1.190 AA_A6A7:A27U29_AA 6 -5.479 3.977 86.751 -0.700 -1.301 2.736 -59.744 A A 7 8 -5.652 A A 27 26 2.820 5.623 -0.821 0.981 AA_A7A8:U26A27_AA 7 0.781 0.785 -59.499 -1.224 -0.791 3.466 58.407 A A 8 9 8.022 A A 26 25 3.485 7.795 0.041 0.249 AA_A8G9:U25U26_AA 8 -6.655 6.850 57.579 -0.182 -0.415 3.224 44.542 A A 9 10 -6.304 A A 25 24 3.181 -4.770 -0.219 -0.578 AA_G9C10:G24U25_AA 9 -0.109 0.143 44.299 -0.331 0.280 3.064 38.075 A A 10 11 30.368 A A 24 23 3.715 18.943 -0.864 -0.527 AA_C10G11:C23G24_AA 10 -4.212 6.752 32.917 -3.498 0.727 2.811 41.630 A A 11 12 -1.433 A A 23 22 2.801 -1.018 -0.245 -1.133 AA_G11U12:G22C23_AA 11 2.240 -3.154 41.561 -1.501 0.548 3.489 28.661 A A 12 13 -2.132 A A 22 21 3.450 -1.055 0.879 -1.614 AA_U12C13:G21G22_AA 12 -0.562 1.135 28.637 -3.009 -1.910 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 20 2D S-NOESY 2D NOESY DQF-COSY 2D HP-COSY 3D_13C-separated_NOESY 3D HCP 3D HMQC TOCSY 10mM posphate buffer 6.40 ambient 288 K 10mM posphate buffer 6.40 ambient 298 K 10mM posphate buffer 6.40 ambient 303 K see reference above see reference above 1 minimized average structure 1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer 96% D2O, 4% H2O 1-2mM HCV IRES domain IIb RNA 10mM phosphate buffer 100% D2O 1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer 96% D2O, 4% H2O 1-2mM HCV IRES domain IIb RNA U-15N,13C 10mM phosphate buffer 100% D2O Varian processing VNMR 6.1C Goddard, T.D. & Kneller D.G. data analysis Sparky 3 Brunger, A.T. refinement X-PLOR 3.1 Brunger, A.T. refinement CNS 1.1 Zweckstetter, M. & Bax, A. 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 ADE 4 n 4 A 4 A GUA 5 n 5 G 5 A ADE 6 n 6 A 6 A ADE 7 n 7 A 7 A ADE 8 n 8 A 8 A GUA 9 n 9 G 9 A CYT 10 n 10 C 10 A GUA 11 n 11 G 11 A URI 12 n 12 U 12 A CYT 13 n 13 C 13 A URI 14 n 14 U 14 A ADE 15 n 15 A 15 A GUA 16 n 16 G 16 A CYT 17 n 17 C 17 A CYT 18 n 18 C 18 A ADE 19 n 19 A 19 A URI 20 n 20 U 20 A GUA 21 n 21 G 21 A GUA 22 n 22 G 22 A CYT 23 n 23 C 23 A GUA 24 n 24 G 24 A URI 25 n 25 U 25 A URI 26 n 26 U 26 A ADE 27 n 27 A 27 A GUA 28 n 28 G 28 A URI 29 n 29 U 29 A ADE 30 n 30 A 30 A URI 31 n 31 U 31 A GUA 32 n 32 G 32 A CYT 33 n 33 C 33 A CYT 34 n 34 C 34 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 O6 HO2' G G 5 28 1.59 3 A A O2' H8 U G 20 21 1.57 4 A A O6 HO2' G G 5 28 1.60 8 A A O6 HO2' G G 5 28 1.59 9 A A O6 HO2' G G 5 28 1.57 10 A A H61 O2' A U 8 26 1.60 11 A A O6 HO2' G G 5 28 1.58 13 A A O2' H8 U G 20 21 1.59 15 A A O6 HO2' G G 5 28 1.56 15 A A H61 O2' A U 8 26 1.58 minimized average Solution Structure of HCV IRES Domain IIb 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 34 A N3 C 34 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 34 A O2 C 34 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 34 A N4 C 34 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 33 A N3 C 33 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 33 A O2 C 33 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 33 A N4 C 33 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 32 A N1 G 32 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 32 A O6 G 32 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 32 A N2 G 32 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 31 A N3 U 31 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 31 A O4 U 31 1_555 hydrog TYPE_11_PAIR A G 5 A N2 G 5 1_555 A A 30 A N7 A 30 1_555 hydrog TYPE_11_PAIR A G 5 A N3 G 5 1_555 A A 30 A N6 A 30 1_555 hydrog G-U MISPAIR A G 5 A N2 G 5 1_555 A U 31 A O4 U 31 1_555 hydrog REVERSED HOOGSTEEN A A 6 A N6 A 6 1_555 A U 29 A O2 U 29 1_555 hydrog REVERSED HOOGSTEEN A A 6 A N7 A 6 1_555 A U 29 A N3 U 29 1_555 hydrog TYPE_2_PAIR A A 7 A N6 A 7 1_555 A A 27 A N7 A 27 1_555 hydrog TYPE_2_PAIR A A 7 A N7 A 7 1_555 A A 27 A N6 A 27 1_555 hydrog A-U PAIR A A 8 A N6 A 8 1_555 A U 26 A O2 U 26 1_555 hydrog TYPE_28_PAIR A G 9 A N1 G 9 1_555 A U 25 A O2 U 25 1_555 hydrog TYPE_28_PAIR A G 9 A O6 G 9 1_555 A U 25 A N3 U 25 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 A G 24 A N1 G 24 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 A G 24 A O6 G 24 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 A G 24 A N2 G 24 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 23 A N3 C 23 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 23 A N4 C 23 1_555 hydrog TYPE_28_PAIR A U 12 A N3 U 12 1_555 A G 22 A O6 G 22 1_555 hydrog TYPE_28_PAIR A U 12 A O2 U 12 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 13 A N3 C 13 1_555 A G 21 A N1 G 21 1_555 hydrog WATSON-CRICK A C 13 A N4 C 13 1_555 A G 21 A O6 G 21 1_555 hydrog WATSON-CRICK A C 13 A O2 C 13 1_555 A G 21 A N2 G 21 1_555 hydrog U-G MISPAIR A U 14 A O2 U 14 1_555 A G 21 A N1 G 21 1_555 hydrog A-G MISPAIR A A 27 A N1 A 27 1_555 A G 28 A N2 G 28 1_555 hydrog G-U MISPAIR A G 28 A N2 G 28 1_555 A U 29 A O4 U 29 1_555 RNA RIBONUCLEIC ACID, HEPATITIS C VIRUS, INTERNAL RIBOSOME ENTRY SITE, LOOP E MOTIF, HAIRPIN LOOP, RNA 1P5N PDB 1 1P5N 1 34 1P5N 1 34 1P5N A 1 1 34