1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Klinck, R. Westhof, E. Walker, S. Afshar, M. Collier, A. Aboul-ela, F. 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 UK RNA RNARFU 2122 1355-8382 6 1423 1431 10.1017/S1355838200000935 11073218 A potential RNA drug target in the hepatitis C virus internal ribosomal entry site. 2000 10.2210/pdb1fqz/pdb pdb_00001fqz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8800.279 HEPATITIS C VIRUS IRES DOMAIN IIID 1 syn polymer no no GCCGAGUAGUGUUGGGUCGCGAAAGGC GCCGAGUAGUGUUGGGUCGCGAAAGGC 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 9.480 1 19 A 1 A 27 -7.037 A_G1:C27_A 1 -2.036 -1.132 0.013 -0.210 9.805 1 19 A 2 A 26 0.268 A_C2:G26_A 2 -12.096 1.244 -0.332 -0.167 -3.774 1 19 A 3 A 25 -1.699 A_C3:G25_A 3 -12.708 1.083 -0.282 -0.236 -2.074 10 11 A 4 A 24 -7.827 A_G4:A24_A 4 -8.198 7.022 0.002 -4.575 -15.371 8 2 A 5 A 23 -174.790 A_A5:A23_A 5 2.911 -6.412 0.007 5.484 15.454 4 24 A 7 A 22 -105.743 A_U7:A22_A 6 -30.792 4.142 -1.508 -1.338 -3.784 10 11 A 8 A 21 -6.783 A_A8:G21_A 7 3.136 -7.026 -0.355 -4.316 -3.117 1 19 A 9 A 20 -5.884 A_G9:C20_A 8 -5.484 -0.763 -0.467 -0.109 -6.290 28 A 10 A 19 -12.489 A_U10:G19_A 9 -4.434 1.828 -0.089 -0.398 -4.069 1 19 A 11 A 18 -11.009 A_G11:C18_A 10 -11.327 -0.368 0.403 -0.106 -13.522 27 A 12 A 16 -159.547 A_U12:G16_A 11 -1.044 -0.270 -0.150 1.318 3.142 44.301 A A 1 2 4.172 A A 27 26 3.233 3.143 0.199 -1.311 AA_G1C2:G26C27_AA 1 1.594 -2.116 44.167 -2.024 -0.119 2.845 32.555 A A 2 3 16.539 A A 26 25 3.503 9.141 0.155 -1.911 AA_C2C3:G25G26_AA 2 2.973 -5.379 31.141 -4.992 0.238 3.213 59.763 A A 3 4 6.860 A A 25 24 3.404 6.814 -0.195 -1.348 AA_C3G4:A24G25_AA 3 6.120 -6.162 59.121 -1.699 0.507 0.070 178.611 A A 4 5 75.356 A A 24 23 0.704 150.507 -3.624 0.114 AA_G4A5:A23A24_AA 4 90.924 -45.524 140.985 0.000 1.847 0.510 -175.965 A A 5 7 -64.238 A A 23 22 0.851 127.759 2.589 -1.560 AA_A5U7:A22A23_AA 5 113.725 57.181 -126.399 0.660 1.403 4.136 -6.562 A A 7 8 -22.556 A A 22 21 3.758 2.515 5.559 -0.998 AA_U7A8:G21A22_AA 6 -0.340 -3.054 -6.052 -5.016 46.706 3.315 62.325 A A 8 9 4.724 A A 21 20 3.427 4.884 0.257 -1.310 AA_A8G9:C20G21_AA 7 -2.454 2.373 62.109 -1.496 -0.364 3.218 41.482 A A 9 10 5.469 A A 20 19 3.372 3.868 -0.442 -1.696 AA_G9U10:G19C20_AA 8 -1.144 1.618 41.294 -2.811 0.501 2.930 26.791 A A 10 11 7.282 A A 19 18 3.173 3.365 0.120 -1.790 AA_U10G11:C18G19_AA 9 0.807 -1.747 26.571 -4.678 -0.063 3.171 92.942 A A 11 12 -2.642 A A 18 16 3.206 -3.830 -1.175 -0.483 AA_G11U12:G16C18_AA 10 4.742 -3.272 92.788 -0.263 0.897 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 2001-01-17 1 1 2008-04-27 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 2000-09-07 REL Transcribed using T7 RNA polymerase sample structures with acceptable covalent geometry, structures with favorable non-bond energy 1 1 2D NOESY 2D NOESY 2D NOESY 2D NOESY 8mM Na phosphate 6.6 ambient 278 K 8mM Na phosphate 6.6 ambient 298 K 8mM Na phosphate 6.6 ambient 303 K Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually. Using a motif-based approach, a model was constructed from X-ray and NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data. 1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6 90% H2O/10% D2O 1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6 100% D2O Bruker collection XwinNMR 2.5 Delaglio processing NMRPipe 1.7 Goddard & Kneller data analysis Sparky 3.66 Brooks et al. refinement CHARMM 25.2 MSI refinement Insight II 97.0 500 Bruker DRX 600 Bruker DMX G 1 n 1 G 1 A C 2 n 2 C 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A G 6 n 6 G 6 A U 7 n 7 U 7 A A 8 n 8 A 8 A G 9 n 9 G 9 A U 10 n 10 U 10 A G 11 n 11 G 11 A U 12 n 12 U 12 A U 13 n 13 U 13 A G 14 n 14 G 14 A G 15 n 15 G 15 A G 16 n 16 G 16 A U 17 n 17 U 17 A C 18 n 18 C 18 A G 19 n 19 G 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A A 22 n 22 A 22 A A 23 n 23 A 23 A A 24 n 24 A 24 A G 25 n 25 G 25 A G 26 n 26 G 26 A C 27 n 27 C 27 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 U 12 0.075 SIDE CHAIN 1 6.43 0.70 119.90 126.33 A A A N3 C2 N2 G G G 1 1 1 N 1 3.73 0.60 119.90 123.63 A A A N1 C6 O6 G G G 1 1 1 N 1 4.45 0.70 108.50 112.95 A A A O4' C1' N1 C C C 3 3 3 N 1 6.72 0.70 119.90 126.62 A A A N3 C2 N2 G G G 4 4 4 N 1 6.67 0.60 118.60 125.27 A A A N1 C6 N6 A A A 5 5 5 N 1 5.54 0.70 119.90 125.44 A A A N3 C2 N2 G G G 6 6 6 N 1 6.64 0.60 118.60 125.24 A A A N1 C6 N6 A A A 8 8 8 N 1 6.39 0.70 119.90 126.29 A A A N3 C2 N2 G G G 9 9 9 N 1 6.76 0.70 119.90 126.66 A A A N3 C2 N2 G G G 11 11 11 N 1 3.79 0.60 119.90 123.69 A A A N1 C6 O6 G G G 11 11 11 N 1 -3.61 0.60 128.60 124.99 A A A C5 C6 O6 G G G 11 11 11 N 1 4.31 0.70 108.50 112.81 A A A O4' C1' N1 U U U 12 12 12 N 1 6.22 0.70 119.90 126.12 A A A N3 C2 N2 G G G 14 14 14 N 1 6.18 0.70 119.90 126.08 A A A N3 C2 N2 G G G 15 15 15 N 1 3.63 0.60 119.90 123.53 A A A N1 C6 O6 G G G 15 15 15 N 1 6.53 0.70 119.90 126.43 A A A N3 C2 N2 G G G 16 16 16 N 1 3.92 0.60 119.90 123.82 A A A N1 C6 O6 G G G 16 16 16 N 1 -3.67 0.60 128.60 124.93 A A A C5 C6 O6 G G G 16 16 16 N 1 6.49 0.70 119.90 126.39 A A A N3 C2 N2 G G G 19 19 19 N 1 3.83 0.60 119.90 123.73 A A A N1 C6 O6 G G G 19 19 19 N 1 -3.76 0.60 128.60 124.84 A A A C5 C6 O6 G G G 19 19 19 N 1 4.42 0.70 108.50 112.92 A A A O4' C1' N1 C C C 20 20 20 N 1 6.98 0.70 119.90 126.88 A A A N3 C2 N2 G G G 21 21 21 N 1 3.62 0.60 119.90 123.52 A A A N1 C6 O6 G G G 21 21 21 N 1 6.63 0.60 118.60 125.23 A A A N1 C6 N6 A A A 22 22 22 N 1 6.92 0.60 118.60 125.52 A A A N1 C6 N6 A A A 23 23 23 N 1 6.87 0.60 118.60 125.47 A A A N1 C6 N6 A A A 24 24 24 N 1 6.17 0.70 119.90 126.07 A A A N3 C2 N2 G G G 25 25 25 N 1 3.70 0.60 119.90 123.60 A A A N1 C6 O6 G G G 25 25 25 N 1 6.09 0.70 119.90 125.99 A A A N3 C2 N2 G G G 26 26 26 N 1 3.63 0.60 119.90 123.53 A A A N1 C6 O6 G G G 26 26 26 N 1 A A C2 N3 U U 7 7 0.042 0.007 1.373 1.415 N 1 A A C2 N3 U U 10 10 0.045 0.007 1.373 1.418 N 1 A A C2 N3 U U 13 13 0.046 0.007 1.373 1.419 N 1 A A C2 N3 U U 17 17 0.046 0.007 1.373 1.419 N NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 A G 26 A N1 G 26 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 A G 26 A O6 G 26 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 A G 26 A N2 G 26 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 25 A N1 G 25 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 25 A O6 G 25 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 25 A N2 G 25 1_555 hydrog TYPE_11_PAIR A G 4 A N2 G 4 1_555 A A 24 A N7 A 24 1_555 hydrog TYPE_11_PAIR A G 4 A N3 G 4 1_555 A A 24 A N6 A 24 1_555 hydrog TYPE_2_PAIR A A 5 A N6 A 5 1_555 A A 23 A N7 A 23 1_555 hydrog TYPE_2_PAIR A A 5 A N7 A 5 1_555 A A 23 A N6 A 23 1_555 hydrog G-U MISPAIR A G 6 A N2 G 6 1_555 A U 7 A O4 U 7 1_555 hydrog REVERSED HOOGSTEEN A U 7 A N3 U 7 1_555 A A 22 A N7 A 22 1_555 hydrog REVERSED HOOGSTEEN A U 7 A O2 U 7 1_555 A A 22 A N6 A 22 1_555 hydrog TYPE_11_PAIR A A 8 A N6 A 8 1_555 A G 21 A N3 G 21 1_555 hydrog TYPE_11_PAIR A A 8 A N7 A 8 1_555 A G 21 A N2 G 21 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 20 A N4 C 20 1_555 hydrog TYPE_28_PAIR A U 10 A N3 U 10 1_555 A G 19 A O6 G 19 1_555 hydrog TYPE_28_PAIR A U 10 A O2 U 10 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 18 A N3 C 18 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 18 A O2 C 18 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 18 A N4 C 18 1_555 hydrog TYPE_27_PAIR A U 12 A N3 U 12 1_555 A G 16 A O6 G 16 1_555 hydrog TYPE_27_PAIR A U 12 A O4 U 12 1_555 A G 16 A N1 G 16 1_555 RNA trans wobble G.U pair, S-turn, sarcin-ricin loop, loop E motif, sheared G.A pair, reverse Hoogsteen A.U pair, RNA 1FQZ PDB 1 1FQZ 1 27 1FQZ 1 27 1FQZ A 1 1 27 1 P 1