1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kaluarachchi, K. Rijnbrand, R. Lemon, S.M. Gorenstein, D.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 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 343 805 817 10.1016/j.jmb.2004.08.095 15476802 Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites 2004 10.2210/pdb1idv/pdb pdb_00001idv 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 3207.965 HEPATITIS C IRES RNA DOMAIN IIIC 1 syn polymer no no GGGCGUGCCC GGGCGUGCCC A polyribonucleotide n n n n n n n n n n -10.843 1 19 A 1 A 10 -12.217 A_G1:C10_A 1 5.838 -0.887 0.145 -0.499 -1.545 1 19 A 2 A 9 0.265 A_G2:C9_A 2 -7.912 0.638 0.096 0.105 0.484 1 19 A 3 A 8 -11.609 A_G3:C8_A 3 -13.270 1.421 1.541 -1.020 3.273 28.256 A A 1 2 2.631 A A 10 9 3.340 1.282 0.300 -1.736 AA_G1G2:C9C10_AA 1 2.657 -5.453 28.105 -3.857 0.011 3.939 39.132 A A 2 3 -5.853 A A 9 8 3.648 -3.882 -1.577 -0.528 AA_G2G3:C8C9_AA 2 -8.938 13.476 37.946 -0.239 1.090 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2001-10-05 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2001-04-05 REL Synthesized by in vitro transcription using T7 RNA polymerase sample This structure was determined using standard 2D homonuclear techniques. back calculated data agree with experimental NOESY spectrum 20 10 2D NOESY 2D NOESY DQF-COSY 2D TOCSY 31P Hetero-TOCSY 1H-13C HSQC 10 mM KCl 6.8 ambient 283 K 10 mM KCl 6.8 ambient 298 K The structures are based on 254 NOE restraints, 12 sugar pucker restraints and 9 hydrogen bonds simulated annealing molecular dynamics relaxation matrix analysis 10 fewest noe violations 10 mM Sodium Phosphate buffer, 10 mM KCl, 0.05 mM EDTA, pH 6.8 90% H2O/10% D2O 10 mM Sodium Phosphate buffer, 10 mM KCl, 0.05 mM EDTA, pH 6.8 99.996% D2O BRUNGER refinement X-PLOR 3.1 POST, MEADOWS, LUXON and GORENSTEIN refinement MORASS 2.51 750 Varian UNITYPLUS 600 Varian UNITYPLUS G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A C 4 n 4 C 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A C 9 n 9 C 9 A C 10 n 10 C 10 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 O2' H5' G U 5 6 1.32 1 A A O2' H5' G G 2 3 1.48 1 A A O6 H41 G C 1 10 1.57 2 A A O2' H5' G U 5 6 1.55 2 A A O2' H5' G G 2 3 1.57 3 A A O2' H5' G U 5 6 1.43 4 A A O2' H5' G U 5 6 1.13 5 A A O2' H8 C G 4 5 1.55 6 A A O2' H5' G U 5 6 1.30 6 A A O6 H41 G C 1 10 1.53 7 A A O2' H5' G G 2 3 1.47 7 A A O6 H41 G C 1 10 1.52 8 A A O2' H5' G U 5 6 1.17 8 A A O2' H5' G G 2 3 1.40 8 A A O6 H41 G C 2 9 1.57 9 A A O2' H8 C G 4 5 1.27 9 A A O2' C8 C G 4 5 1.65 9 A A O2' N7 C G 4 5 1.74 1 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 1 1 1 N 1 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 2 2 2 N 1 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 3 3 3 N 1 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 3 3 3 N 1 4.51 0.50 113.10 117.61 A A A N7 C8 N9 G G G 5 5 5 N 1 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 5 5 5 N 1 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 7 7 7 N 1 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 G G G 7 7 7 N 2 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 1 1 1 N 2 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 1 1 1 N 2 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 2 2 2 N 2 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 2 2 2 N 2 4.62 0.50 113.10 117.72 A A A N7 C8 N9 G G G 3 3 3 N 2 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 3 3 3 N 2 4.62 0.50 113.10 117.72 A A A N7 C8 N9 G G G 5 5 5 N 2 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 5 5 5 N 2 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 7 7 7 N 2 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 7 7 7 N 3 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 1 1 1 N 3 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 1 1 1 N 3 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 2 2 2 N 3 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 2 2 2 N 3 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 3 3 3 N 3 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 G G G 3 3 3 N 3 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 5 5 5 N 3 -2.75 0.40 106.40 103.65 A A A C8 N9 C4 G G G 5 5 5 N 3 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 7 7 7 N 3 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 7 7 7 N 4 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 1 1 1 N 4 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 1 1 1 N 4 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 2 2 2 N 4 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 2 2 2 N 4 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 3 3 3 N 4 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 G G G 3 3 3 N 4 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 5 5 5 N 4 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 5 5 5 N 4 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 7 7 7 N 4 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 7 7 7 N 5 4.49 0.50 113.10 117.59 A A A N7 C8 N9 G G G 1 1 1 N 5 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 1 1 1 N 5 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 2 2 2 N 5 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 G G G 2 2 2 N 5 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 3 3 3 N 5 -2.73 0.40 106.40 103.67 A A A C8 N9 C4 G G G 3 3 3 N 5 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 5 5 5 N 5 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 5 5 5 N 5 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 7 7 7 N 5 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 7 7 7 N 6 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 1 1 1 N 6 -2.74 0.40 106.40 103.66 A A A C8 N9 C4 G G G 1 1 1 N 6 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 2 2 2 N 6 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 2 2 2 N 6 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 3 3 3 N 6 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 3 3 3 N 6 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 5 5 5 N 6 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 5 5 5 N 6 4.61 0.50 113.10 117.71 A A A N7 C8 N9 G G G 7 7 7 N 6 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 7 7 7 N 7 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 1 1 1 N 7 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 1 1 1 N 7 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 2 2 2 N 7 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 2 2 2 N 7 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 3 3 3 N 7 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 3 3 3 N 7 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 5 5 5 N 7 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 5 5 5 N 7 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 7 7 7 N 7 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 7 7 7 N 8 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 1 1 1 N 8 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 1 1 1 N 8 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 2 2 2 N 8 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 2 2 2 N 8 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 3 3 3 N 8 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 G G G 3 3 3 N 8 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 5 5 5 N 8 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 5 5 5 N 8 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 7 7 7 N 8 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 G G G 7 7 7 N 9 4.53 0.50 113.10 117.63 A A A N7 C8 N9 G G G 1 1 1 N 9 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 1 1 1 N 9 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 9 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 2 2 2 N 9 4.65 0.50 113.10 117.75 A A A N7 C8 N9 G G G 3 3 3 N 9 -2.78 0.40 106.40 103.62 A A A C8 N9 C4 G G G 3 3 3 N 9 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 5 5 5 N 9 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 5 5 5 N 9 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 7 7 7 N 9 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 7 7 7 N 10 4.57 0.50 113.10 117.67 A A A N7 C8 N9 G G G 1 1 1 N 10 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 G G G 1 1 1 N 10 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 10 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 2 2 2 N 10 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 3 3 3 N 10 -2.66 0.40 106.40 103.74 A A A C8 N9 C4 G G G 3 3 3 N 10 4.55 0.50 113.10 117.65 A A A N7 C8 N9 G G G 5 5 5 N 10 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 G G G 5 5 5 N 10 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 7 7 7 N 10 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 7 7 7 N NMR structure of HCV ires RNA domain IIIC 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 10 A N3 C 10 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 10 A O2 C 10 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 10 A N4 C 10 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 9 A N3 C 9 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 9 A O2 C 9 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 9 A N4 C 9 1_555 hydrog TYPE_7_PAIR A G 3 A N1 G 3 1_555 A G 7 A N7 G 7 1_555 hydrog TYPE_7_PAIR A G 3 A N2 G 3 1_555 A G 7 A O6 G 7 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 8 A N3 C 8 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 8 A O2 C 8 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 8 A N4 C 8 1_555 RNA Hepatitis C RNA, IRES, Stem-loop, Domain IIIC, RNA 1IDV PDB 1 1IDV 1 10 1IDV 1 10 1IDV A 1 1 10