1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yuan, Y. Kerwood, D.J. Paoletti, A.C. Shubsda, M.F. Borer, P.N. 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 Biochemistry BICHAW 0033 0006-2960 42 5259 5269 10.1021/bi034084a 12731867 Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop 2003 10.2210/pdb1osw/pdb pdb_00001osw CHIRALITY ERRORS EXIST IN SOME MODELS. 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 stem of SL1 RNA 7472.528 5'-R(*GP*GP*AP*GP*GP*CP*GP*CP*UP*AP*CP*GP*GP*CP*GP*AP*GP*GP*CP*UP*CP*CP*A)-3' 1 syn polymer no no GGAGGCGCUACGGCGAGGCUCCA GGAGGCGCUACGGCGAGGCUCCA 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 -25.698 1 19 A 1 A 22 -1.669 A_G1:C22_A 1 -11.764 -0.347 -0.344 0.051 -19.201 1 19 A 2 A 21 -3.455 A_G2:C21_A 2 -13.755 -0.246 -0.270 0.090 -14.790 1 20 A 3 A 20 -3.702 A_A3:U20_A 3 -15.385 -0.049 -0.176 0.111 -36.587 1 19 A 4 A 19 2.737 A_G4:C19_A 4 -37.646 -0.627 -0.619 0.057 13.144 1 8 A 5 A 16 -20.772 A_G5:A16_A 5 8.071 0.573 -0.307 1.704 12.731 1 19 A 6 A 15 1.248 A_C6:G15_A 6 -15.863 0.281 -0.587 0.038 13.792 1 19 A 7 A 14 2.916 A_G7:C14_A 7 -10.972 -1.000 -0.101 -0.161 23.123 1 19 A 8 A 13 -3.433 A_C8:G13_A 8 -1.379 0.102 -0.265 0.108 -8.775 2 A 9 A 12 -151.640 A_U9:G12_A 9 -47.768 0.148 0.370 -5.336 3.009 29.433 A A 1 2 8.814 A A 22 21 3.316 4.422 0.532 -2.066 AA_G1G2:C21C22_AA 1 6.882 -13.719 28.298 -5.000 0.405 3.062 30.342 A A 2 3 6.857 A A 21 20 3.278 3.577 0.191 -1.727 AA_G2A3:U20C21_AA 2 2.483 -4.760 30.035 -4.001 0.122 3.504 32.466 A A 3 4 17.367 A A 20 19 4.104 9.533 0.158 -1.397 AA_A3G4:C19U20_AA 3 5.138 -9.360 30.652 -4.504 0.797 3.666 78.274 A A 4 5 -14.189 A A 19 16 5.084 -16.980 1.958 -2.102 AA_G4G5:A16C19_AA 4 -44.804 37.441 63.847 -0.935 -3.477 2.395 24.768 A A 5 6 18.214 A A 16 15 3.255 7.681 0.510 -2.166 AA_G5C6:G15A16_AA 5 -1.697 4.024 23.504 -7.115 -1.644 2.665 40.342 A A 6 7 31.903 A A 15 14 3.397 20.958 -0.169 -0.529 AA_C6G7:C14G15_AA 6 -4.298 6.543 34.405 -3.150 -0.244 2.846 30.850 A A 7 8 17.349 A A 14 13 3.249 9.097 -0.354 -0.948 AA_G7C8:G13C14_AA 7 -0.907 1.730 29.496 -3.471 0.497 2.484 95.128 A A 8 9 13.636 A A 13 12 2.785 20.004 -4.226 1.165 AA_C8U9:G12G13_AA 8 12.786 -8.716 92.817 0.498 3.050 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 2003-05-20 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 2003-03-20 REL REL RNA sequence obtained from Dharmacon sample Structures were determined using 2D NOESY at different temperatures and mixing times. The last residue, A23, was eliminated from the pdb file due to ambiguity in orientation. structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function 50 23 2D NOESY 2D TOCSY HP-COSY 2D NOESY H-C HSQC 25 mM NaCl 6.3 ambient 300 K 25 mM NaCl 5.5 ambient 278 K DYANA followed by molecular dynamics using AMBER 17 closest to the average 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 99.996% D2O or 90% D2O, 10% H2O Bruker collection XwinNMR 2.6 Tripos processing NMRZ/TRIAD 6.1 University of California, San Francisco iterative matrix relaxation MARDIGRAS 3.2 Guntert, P., Mumenthaler, C. and Wuthrich, K. structure solution DYANA 1.5 University of California, San Francisco refinement Amber 5.0 500 Bruker DRX 600 Bruker DRX G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A A 10 n 10 A 10 A C 11 n 11 C 11 A G 12 n 12 G 12 A G 13 n 13 G 13 A C 14 n 14 C 14 A G 15 n 15 G 15 A A 16 n 16 A 16 A G 17 n 17 G 17 A G 18 n 18 G 18 A C 19 n 19 C 19 A U 20 n 20 U 20 A C 21 n 21 C 21 A C 22 n 22 C 22 A n 23 23 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 23 A A 23 1 Y 2 A A 23 A A 23 1 Y 3 A A 23 A A 23 1 Y 4 A A 23 A A 23 1 Y 5 A A 23 A A 23 1 Y 6 A A 23 A A 23 1 Y 7 A A 23 A A 23 1 Y 8 A A 23 A A 23 1 Y 9 A A 23 A A 23 1 Y 10 A A 23 A A 23 1 Y 11 A A 23 A A 23 1 Y 12 A A 23 A A 23 1 Y 13 A A 23 A A 23 1 Y 14 A A 23 A A 23 1 Y 15 A A 23 A A 23 1 Y 16 A A 23 A A 23 1 Y 17 A A 23 A A 23 1 Y 18 A A 23 A A 23 1 Y 19 A A 23 A A 23 1 Y 20 A A 23 A A 23 1 Y 21 A A 23 A A 23 1 Y 22 A A 23 A A 23 1 Y 23 A A 23 A A 23 1 Y 1 A G 12 0.068 SIDE CHAIN 2 A G 7 0.056 SIDE CHAIN 2 A C 14 0.069 SIDE CHAIN 3 A G 4 0.067 SIDE CHAIN 3 A G 18 0.073 SIDE CHAIN 4 A U 9 0.072 SIDE CHAIN 4 A G 18 0.078 SIDE CHAIN 4 A U 20 0.060 SIDE CHAIN 4 A C 21 0.065 SIDE CHAIN 5 A C 6 0.078 SIDE CHAIN 5 A G 18 0.061 SIDE CHAIN 6 A G 12 0.055 SIDE CHAIN 6 A G 13 0.076 SIDE CHAIN 7 A G 7 0.061 SIDE CHAIN 7 A U 9 0.065 SIDE CHAIN 7 A G 12 0.057 SIDE CHAIN 7 A C 19 0.098 SIDE CHAIN 7 A U 20 0.072 SIDE CHAIN 8 A U 9 0.098 SIDE CHAIN 8 A C 21 0.058 SIDE CHAIN 9 A U 9 0.076 SIDE CHAIN 9 A G 18 0.088 SIDE CHAIN 10 A U 9 0.074 SIDE CHAIN 11 A G 1 0.061 SIDE CHAIN 11 A G 18 0.076 SIDE CHAIN 13 A U 9 0.087 SIDE CHAIN 13 A G 13 0.080 SIDE CHAIN 13 A G 18 0.049 SIDE CHAIN 13 A U 20 0.063 SIDE CHAIN 14 A G 4 0.055 SIDE CHAIN 14 A U 9 0.076 SIDE CHAIN 14 A G 12 0.059 SIDE CHAIN 14 A G 18 0.052 SIDE CHAIN 15 A G 7 0.050 SIDE CHAIN 15 A G 12 0.053 SIDE CHAIN 16 A C 11 0.085 SIDE CHAIN 17 A G 7 0.056 SIDE CHAIN 17 A C 19 0.081 SIDE CHAIN 17 A C 21 0.078 SIDE CHAIN 18 A C 11 0.066 SIDE CHAIN 18 A C 14 0.073 SIDE CHAIN 19 A G 17 0.060 SIDE CHAIN 19 A G 18 0.056 SIDE CHAIN 20 A G 7 0.058 SIDE CHAIN 20 A C 19 0.087 SIDE CHAIN 21 A G 7 0.056 SIDE CHAIN 21 A G 12 0.064 SIDE CHAIN 21 A A 16 0.063 SIDE CHAIN 22 A G 5 0.054 SIDE CHAIN 22 A G 7 0.058 SIDE CHAIN 22 A U 9 0.087 SIDE CHAIN 22 A G 12 0.080 SIDE CHAIN 22 A G 13 0.051 SIDE CHAIN 22 A G 18 0.067 SIDE CHAIN 22 A C 22 0.090 SIDE CHAIN 23 A C 14 0.096 SIDE CHAIN 23 A G 18 0.055 SIDE CHAIN 1 5.40 0.70 108.50 113.90 A A A O4' C1' N1 C C C 6 6 6 N 1 6.09 0.70 108.50 114.59 A A A O4' C1' N1 C C C 14 14 14 N 1 8.21 1.20 119.70 127.91 A A A C3' O3' P G G C 18 18 19 Y 1 4.32 0.70 108.50 112.82 A A A O4' C1' N1 C C C 22 22 22 N 2 4.81 0.70 108.50 113.31 A A A O4' C1' N1 C C C 6 6 6 N 2 4.25 0.70 108.50 112.75 A A A O4' C1' N1 C C C 14 14 14 N 3 5.73 0.70 108.50 114.23 A A A O4' C1' N1 C C C 6 6 6 N 4 4.48 0.70 108.50 112.98 A A A O4' C1' N9 A A A 3 3 3 N 4 5.40 0.70 108.50 113.90 A A A O4' C1' N1 C C C 6 6 6 N 4 4.45 0.70 108.50 112.95 A A A O4' C1' N1 C C C 14 14 14 N 4 4.61 0.70 108.50 113.11 A A A O4' C1' N1 C C C 22 22 22 N 5 5.06 0.70 108.50 113.56 A A A O4' C1' N1 C C C 6 6 6 N 6 4.72 0.70 108.50 113.22 A A A O4' C1' N1 C C C 6 6 6 N 6 4.30 0.70 108.50 112.80 A A A O4' C1' N1 U U U 20 20 20 N 7 5.00 0.70 108.50 113.50 A A A O4' C1' N1 C C C 6 6 6 N 7 -4.31 0.70 109.70 105.39 A A A C1' O4' C4' G G G 12 12 12 N 7 5.97 0.70 108.50 114.47 A A A O4' C1' N1 C C C 14 14 14 N 7 5.42 0.70 108.50 113.92 A A A O4' C1' N1 C C C 21 21 21 N 8 5.14 0.70 108.50 113.64 A A A O4' C1' N1 C C C 6 6 6 N 8 4.72 0.70 108.50 113.22 A A A O4' C1' N1 C C C 21 21 21 N 8 4.37 0.70 108.50 112.87 A A A O4' C1' N1 C C C 22 22 22 N 9 5.44 0.70 108.50 113.94 A A A O4' C1' N1 C C C 6 6 6 N 9 4.21 0.70 108.50 112.71 A A A O4' C1' N1 C C C 19 19 19 N 10 4.82 0.70 108.50 113.32 A A A O4' C1' N1 C C C 6 6 6 N 10 4.90 0.70 108.50 113.40 A A A O4' C1' N1 C C C 14 14 14 N 10 5.15 0.70 108.50 113.65 A A A O4' C1' N9 G G G 17 17 17 N 11 4.51 0.70 108.50 113.01 A A A O4' C1' N1 C C C 14 14 14 N 11 4.45 0.70 108.50 112.95 A A A O4' C1' N1 U U U 20 20 20 N 12 5.09 0.70 108.50 113.59 A A A O4' C1' N1 C C C 6 6 6 N 13 5.34 0.70 108.50 113.84 A A A O4' C1' N1 C C C 6 6 6 N 13 4.43 0.70 108.50 112.93 A A A O4' C1' N1 U U U 20 20 20 N 14 5.14 0.70 108.50 113.64 A A A O4' C1' N1 C C C 14 14 14 N 15 4.58 0.70 108.50 113.08 A A A O4' C1' N9 G G G 18 18 18 N 15 8.35 1.20 119.70 128.05 A A A C3' O3' P G G C 18 18 19 Y 16 5.16 0.70 108.50 113.66 A A A O4' C1' N1 C C C 6 6 6 N 16 4.37 0.70 108.50 112.87 A A A O4' C1' N1 C C C 14 14 14 N 16 5.24 0.70 108.50 113.74 A A A O4' C1' N1 C C C 19 19 19 N 16 4.43 0.70 108.50 112.93 A A A O4' C1' N1 U U U 20 20 20 N 17 4.92 0.70 108.50 113.42 A A A O4' C1' N1 C C C 6 6 6 N 17 -3.10 0.50 128.60 125.50 A A A N3 C4 C5 G G G 12 12 12 N 18 4.60 0.70 108.50 113.10 A A A O4' C1' N1 C C C 6 6 6 N 18 5.68 0.70 108.50 114.18 A A A O4' C1' N1 C C C 14 14 14 N 18 4.54 0.70 108.50 113.04 A A A O4' C1' N1 U U U 20 20 20 N 19 5.05 0.70 108.50 113.55 A A A O4' C1' N1 C C C 6 6 6 N 19 4.68 0.70 108.50 113.18 A A A O4' C1' N1 C C C 14 14 14 N 19 4.40 0.70 108.50 112.90 A A A O4' C1' N1 C C C 22 22 22 N 20 4.67 0.70 108.50 113.17 A A A O4' C1' N9 G G G 1 1 1 N 20 4.77 0.70 108.50 113.27 A A A O4' C1' N1 C C C 6 6 6 N 20 4.62 0.70 108.50 113.12 A A A O4' C1' N1 C C C 14 14 14 N 20 4.51 0.70 108.50 113.01 A A A O4' C1' N1 U U U 20 20 20 N 20 4.44 0.70 108.50 112.94 A A A O4' C1' N1 C C C 22 22 22 N 21 5.27 0.70 108.50 113.77 A A A O4' C1' N1 C C C 6 6 6 N 21 4.68 0.70 108.50 113.18 A A A O4' C1' N1 C C C 14 14 14 N 22 4.32 0.70 108.50 112.82 A A A O4' C1' N9 G G G 1 1 1 N 22 4.25 0.70 108.50 112.75 A A A O4' C1' N1 C C C 6 6 6 N 22 4.73 0.70 108.50 113.23 A A A O4' C1' N1 U U U 20 20 20 N 23 5.37 0.70 108.50 113.87 A A A O4' C1' N1 C C C 6 6 6 N 23 6.15 0.70 108.50 114.65 A A A O4' C1' N1 C C C 14 14 14 N 23 4.62 0.70 108.50 113.12 A A A O4' C1' N1 U U U 20 20 20 N 23 4.44 0.70 108.50 112.94 A A A O4' C1' N1 C C C 21 21 21 N 23 4.22 0.70 108.50 112.72 A A A O4' C1' N1 C C C 22 22 22 N The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 22 A N4 C 22 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 21 A N4 C 21 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 20 A N3 U 20 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 20 A O4 U 20 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 19 A N4 C 19 1_555 hydrog TYPE_8_PAIR A G 5 A N1 G 5 1_555 A A 16 A N1 A 16 1_555 hydrog TYPE_8_PAIR A G 5 A O6 G 5 1_555 A A 16 A N6 A 16 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 15 A N1 G 15 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 15 A O6 G 15 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 15 A N2 G 15 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 A C 14 A N3 C 14 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 A C 14 A O2 C 14 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 A C 14 A N4 C 14 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 13 A N1 G 13 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 13 A O6 G 13 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 13 A N2 G 13 1_555 hydrog U-G MISPAIR A U 9 A O2 U 9 1_555 A G 12 A N1 G 12 1_555 hydrog G-G MISPAIR A G 12 A N2 G 12 1_555 A G 13 A N3 G 13 1_555 RNA RNA 1OSW PDB 1 1OSW 1 23 1OSW 1 23 1OSW A 1 1 23