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 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/pdb1f85/pdb pdb_00001f85 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 4518.731 HCV-1B IRES RNA DOMAIN IIIE HCV IRES RNA DOMAIN IIIE (NUCLEOTIDES 290-303 OF GENOMIC HEPATITIS C VIRAL RNA) U290G, G303C 1 syn polymer no no GGCCUGAUAGGGUC GGCCUGAUAGGGUC A polyribonucleotide n n n n n n n n n n n n n n -15.101 1 19 A 1 A 14 1.712 A_G1:C14_A 1 -6.686 0.367 -1.036 -0.074 10.193 28 A 2 A 13 -11.080 A_G2:U13_A 2 2.183 -1.715 -0.706 -0.528 33.804 1 19 A 3 A 12 -1.786 A_C3:G12_A 3 -4.435 -0.380 -1.628 -0.194 20.116 1 19 A 4 A 11 0.655 A_C4:G11_A 4 -11.466 -0.261 -1.636 -0.372 -3.815 1 A 5 A 10 33.947 A_U5:G10_A 5 17.838 2.256 -1.210 1.130 -0.275 9 11 A 6 A 9 7.717 A_G6:A9_A 6 1.965 6.732 0.632 -3.314 1.813 17.335 A A 1 2 26.586 A A 14 13 2.581 7.553 -0.282 -0.985 AA_G1G2:U13C14_AA 1 -6.139 21.608 14.362 -6.723 -1.873 2.967 40.913 A A 2 3 -6.167 A A 13 12 2.806 -4.299 0.884 -1.130 AA_G2C3:G12U13_AA 2 3.389 -4.862 40.561 -1.199 -0.935 2.898 47.236 A A 3 4 26.667 A A 12 11 3.594 20.695 0.706 -0.981 AA_C3C4:G11G12_AA 3 3.800 -4.896 42.533 -3.001 -0.555 2.647 29.344 A A 4 5 27.032 A A 11 10 4.030 13.213 0.788 -2.068 AA_C4U5:G10G11_AA 4 -1.699 3.476 26.205 -7.159 -1.952 2.449 51.374 A A 5 6 28.233 A A 10 9 2.899 23.628 -0.378 -0.259 AA_U5G6:A9G10_AA 5 5.010 -5.986 45.686 -1.714 0.737 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 2000-11-17 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 2000-06-28 REL REL Synthesized enzymatically in-vitro using T7 RNA Polymerase sample THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. NATURAL ABUNDANCE 13C HMQC EXPERIMENTS WERE PERFORMED. structures with the least restraint violations,structures with the lowest energy 100 20 31P-decoupled DQF COSY, HP COSY, D2O NOESY, H2O NOESY 10mM 6.40 ambient 283 K SEE REFERENCE ABOVE Simulated annealing and restrained molecular dynamics 19 closest to the average 2.5mM RNA, non-isotopically labelled sodium phosphate buffer, 96% H2O/4% D2O or 100% D2O BRUNGER refinement X-PLOR 3.1 GODDARD data analysis Sparky 3.8 VARIAN processing VNMR 6.1B VARIAN collection VNMR 6.1B 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 CYT 4 n 4 C 4 A URA 5 n 5 U 5 A GUA 6 n 6 G 6 A ADE 7 n 7 A 7 A URA 8 n 8 U 8 A ADE 9 n 9 A 9 A GUA 10 n 10 G 10 A GUA 11 n 11 G 11 A GUA 12 n 12 G 12 A URA 13 n 13 U 13 A CYT 14 n 14 C 14 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 2 A A O2' H6 A U 7 8 1.53 3 A A O2' H6 A U 7 8 1.53 4 A A O2' H6 A U 7 8 1.57 5 A A O2' H6 A U 7 8 1.51 11 A A O2' H6 A U 7 8 1.50 12 A A O2' H6 A U 7 8 1.55 13 A A O2' H6 A U 7 8 1.53 14 A A O2' H6 A U 7 8 1.56 17 A A O2' H6 A U 7 8 1.53 18 A A O2' H6 A U 7 8 1.54 20 A A O2' H5' G A 6 7 1.59 SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIIE 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 14 A N4 C 14 1_555 hydrog TYPE_28_PAIR A G 2 A N1 G 2 1_555 A U 13 A O2 U 13 1_555 hydrog TYPE_28_PAIR A G 2 A O6 G 2 1_555 A U 13 A N3 U 13 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 14 A N4 C 14 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 12 A N1 G 12 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 12 A O6 G 12 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 12 A N2 G 12 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A G 11 A N1 G 11 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 11 A O6 G 11 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 11 A N2 G 11 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A G 12 A N1 G 12 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 12 A O6 G 12 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 12 A N2 G 12 1_555 hydrog U-G MISPAIR A U 5 A O2 U 5 1_555 A G 10 A N1 G 10 1_555 hydrog TYPE_11_PAIR A G 6 A N2 G 6 1_555 A A 9 A N7 A 9 1_555 hydrog TYPE_11_PAIR A G 6 A N3 G 6 1_555 A A 9 A N6 A 9 1_555 hydrog G-G MISPAIR A G 6 A N2 G 6 1_555 A G 10 A O6 G 10 1_555 RNA Ribonucleic Acid, Hepatitis C virus internal ribosome entry site, Hairpin loop, Tetraloop, RNA structure, RNA 1F85 PDB 1 1F85 1 14 1F85 1 14 1F85 A 1 1 14 1 P 1