1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Flinders, J.C. Dieckmann, T. 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 J.Mol.Biol. JMOBAK 0070 0022-2836 308 665 679 10.1006/jmbi.2001.4627 11350168 A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA. 2001 10.2210/pdb1hwq/pdb pdb_00001hwq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 9705.832 VS RIBOZYME SUBSTRATE RNA 1 syn polymer no no GGUGCGAAGGGCGUCGUCGCCCCGAGCGCC GGUGCGAAGGGCGUCGUCGCCCCGAGCGCC 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 -3.603 1 19 A 1 A 30 -0.955 A_G1:C30_A 1 -2.478 0.931 0.171 -0.417 1.655 1 19 A 2 A 29 -0.569 A_G2:C29_A 2 1.358 0.924 -0.120 -0.399 -0.993 1 28 A 3 A 28 5.308 A_U3:G28_A 3 -2.897 1.763 0.037 -0.319 1.854 1 19 A 4 A 27 -0.174 A_G4:C27_A 4 -2.907 0.950 -0.185 -0.418 -1.049 1 19 A 5 A 26 -2.344 A_C5:G26_A 5 -1.542 -0.991 -0.337 -0.449 3.555 6 11 A 6 A 25 1.047 A_G6:A25_A 6 -7.882 6.568 -0.095 -4.591 1.164 9 11 A 7 A 24 2.015 A_A7:G24_A 7 0.770 -6.657 0.009 -4.215 -0.703 1 A 8 A 23 -8.616 A_A8:C23_A 8 1.155 -3.775 0.067 -1.348 -5.171 1 19 A 9 A 22 -1.644 A_G9:C22_A 9 -3.057 0.875 -0.079 -0.410 3.300 1 19 A 10 A 21 -1.279 A_G10:C21_A 10 0.485 0.908 -0.110 -0.404 2.930 1 19 A 11 A 20 0.484 A_G11:C20_A 11 -0.808 0.938 -0.373 -0.481 -1.073 1 19 A 12 A 19 -1.808 A_C12:G19_A 12 4.352 -1.280 -0.925 -0.646 3.022 31.818 A A 1 2 33.631 A A 30 29 3.887 17.464 0.504 -0.478 AA_G1G2:C29C30_AA 1 0.344 -0.662 26.699 -4.558 -0.847 2.778 44.228 A A 2 3 35.076 A A 29 28 3.475 24.922 1.033 -0.423 AA_G2U3:G28C29_AA 2 5.366 -7.553 36.447 -3.030 -0.840 1.877 32.253 A A 3 4 38.262 A A 28 27 3.121 19.714 -0.249 -0.884 AA_U3G4:C27G28_AA 3 5.061 -9.822 25.153 -4.624 1.227 2.154 31.344 A A 4 5 29.948 A A 27 26 3.157 15.462 1.155 -1.483 AA_G4C5:G26C27_AA 4 3.667 -7.103 27.105 -5.293 -1.534 3.567 70.174 A A 5 6 -9.238 A A 26 25 3.647 -10.590 0.577 0.313 AA_C5G6:A25G26_AA 5 -1.006 0.877 69.466 0.688 -0.541 2.556 -20.210 A A 6 7 0.296 A A 25 24 3.215 -0.102 1.600 -1.386 AA_G6A7:G24A25_AA 6 6.307 18.271 -19.211 3.993 7.164 4.175 46.068 A A 7 8 -11.534 A A 24 23 4.014 -8.973 0.034 -1.248 AA_A7A8:C23G24_AA 7 1.311 -1.686 45.214 -0.621 0.099 3.896 51.872 A A 8 9 -10.676 A A 23 22 3.782 -9.295 -0.491 -0.986 AA_A8G9:C22C23_AA 8 -0.182 0.208 51.089 -0.388 0.547 3.167 30.832 A A 9 10 -3.717 A A 22 21 3.142 -1.973 0.431 -1.195 AA_G9G10:C21C22_AA 9 -2.448 4.612 30.675 -1.876 -1.271 2.592 33.443 A A 10 11 11.633 A A 21 20 3.038 6.648 -0.489 -1.844 AA_G10G11:C20C21_AA 10 1.946 -3.405 32.738 -4.161 1.129 3.400 30.019 A A 11 12 -4.107 A A 20 19 3.252 -2.122 0.335 -2.000 AA_G11C12:G19C20_AA 11 3.169 -6.133 29.781 -3.416 0.019 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 2001-05-16 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 2001-01-09 REL REL RNA samples were transcribed from synthetic DNA templates using T7 RNA polymerase. sample structures with the lowest energy 200 20 2D NOESY 2D NOESY 3D_13C-separated_NOESY DQF-COSY 5 mM NaCl 6.0 ambient 274 K 5 mM NaCl 6.0 ambient 298 K 5 mM NaCl 6.0 ambient 298 K These structures were calculated using a total of 568 restraints; including 335 NOE-derived distance constraints, 158 dihedral angle restraints, 12 planarity restraints, and 63 H-bond distance restraints. simulated annealing 1 lowest energy 1.5 mM VS RNA 90% H2O/10% D2O 1.5 mM VS RNA 100% D2O 1.5 mM VS RNA, 13C, 15N labeled 100% D2O Bruker collection XwinNMR 2.6 Bruker processing XwinNMR 2.6 Bartels, C. data analysis XEASY 1.3.13 Brunger, A. structure solution CNS 1.0 Brunger, A. refinement CNS 1.0 600 Bruker DRX G 1 n 1 G 1 A G 2 n 2 G 2 A U 3 n 3 U 3 A G 4 n 4 G 4 A C 5 n 5 C 5 A G 6 n 6 G 6 A A 7 n 7 A 7 A A 8 n 8 A 8 A G 9 n 9 G 9 A G 10 n 10 G 10 A G 11 n 11 G 11 A C 12 n 12 C 12 A G 13 n 13 G 13 A U 14 n 14 U 14 A C 15 n 15 C 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 C 21 n 21 C 21 A C 22 n 22 C 22 A C 23 n 23 C 23 A G 24 n 24 G 24 A A 25 n 25 A 25 A G 26 n 26 G 26 A C 27 n 27 C 27 A G 28 n 28 G 28 A C 29 n 29 C 29 A C 30 n 30 C 30 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 H61 O2 A C 8 23 1.34 1 A A HO2' O5' C C 22 23 1.43 1 A A HO2' O5' G U 13 14 1.44 1 A A O2' H5' C G 18 19 1.47 1 A A HO2' O5' U C 14 15 1.50 1 A A N3 H21 C G 12 19 1.53 2 A A HO2' O5' G G 9 10 1.35 2 A A H61 O2 A C 8 23 1.36 2 A A HO2' O5' G C 26 27 1.48 2 A A O2' H61 G A 6 25 1.53 2 A A H2' O4' C U 15 17 1.56 2 A A H21 N3 G C 4 27 1.58 2 A A H2' O4' C G 5 6 1.60 3 A A HO2' O5' U C 17 18 1.36 3 A A H61 O2 A C 8 23 1.38 3 A A HO2' O2 U C 14 15 1.51 3 A A N3 H21 C G 12 19 1.51 3 A A O2' H5' C G 18 19 1.52 4 A A H61 O2 A C 8 23 1.32 4 A A O2' H5' C G 18 19 1.46 4 A A O2 H2' U C 17 18 1.48 4 A A HO2' O5' C G 23 24 1.52 4 A A O3' H8 C G 15 16 1.58 5 A A H61 O2 A C 8 23 1.34 5 A A HO2' O2 U C 14 15 1.43 5 A A O2' H5' C G 18 19 1.49 5 A A N3 H21 C G 12 19 1.52 5 A A O2' H5' G G 9 10 1.54 5 A A HO2' O5' C G 23 24 1.56 6 A A H61 O2 A C 8 23 1.31 6 A A HO2' O5' G A 6 7 1.43 6 A A O2' H5' C G 18 19 1.50 6 A A O2' H8 U G 17 19 1.53 6 A A HO2' O5' G U 13 14 1.54 6 A A HO2' O5' G C 26 27 1.57 6 A A HO2' O5' C G 5 6 1.57 6 A A N3 H21 C G 12 19 1.58 6 A A O2' H3' U C 17 18 1.59 6 A A H21 N3 G C 4 27 1.59 7 A A H61 O2 A C 8 23 1.37 7 A A O2' H5' C G 18 19 1.55 7 A A N3 H21 C G 12 19 1.58 8 A A H61 O2 A C 8 23 1.38 8 A A HO2' O5' C G 15 16 1.39 8 A A O2' H3' C G 15 16 1.44 8 A A O2' H8 C G 18 19 1.57 9 A A HO2' O5' G A 6 7 1.31 9 A A H61 O2 A C 8 23 1.34 9 A A HO2' O5' U C 17 18 1.39 9 A A HO2' O2 U C 14 15 1.40 9 A A N3 H21 C G 12 19 1.51 9 A A HO2' O5' G C 26 27 1.58 9 A A H21 N3 G C 4 27 1.59 10 A A H61 O2 A C 8 23 1.33 10 A A H2' O4' A A 7 8 1.57 10 A A H21 N3 G C 4 27 1.57 10 A A N3 H21 C G 12 19 1.60 11 A A H61 O2 A C 8 23 1.30 11 A A H1' O5' U C 17 18 1.56 11 A A HO2' O5' G C 26 27 1.59 12 A A H61 O2 A C 8 23 1.32 12 A A HO2' O2 U C 14 15 1.36 12 A A O2' H5' C G 18 19 1.48 12 A A N3 H21 C G 12 19 1.51 13 A A H61 O2 A C 8 23 1.29 13 A A O2 H2' U C 17 18 1.39 13 A A O2' H5' C G 18 19 1.55 13 A A N3 H21 C G 12 19 1.58 14 A A HO2' O5' U C 17 18 1.33 14 A A H61 O2 A C 8 23 1.36 14 A A O2' H5' C G 18 19 1.52 14 A A N3 H21 C G 12 19 1.52 15 A A HO2' N3 U C 14 15 1.32 15 A A H61 O2 A C 8 23 1.33 15 A A O2' H5' C G 18 19 1.50 15 A A N3 H21 C G 12 19 1.59 16 A A H61 O2 A C 8 23 1.34 16 A A HO2' O5' C U 15 17 1.54 16 A A O2' H8 C G 15 16 1.54 16 A A O2' H8 C G 18 19 1.56 17 A A H61 O2 A C 8 23 1.34 17 A A HO2' O5' U C 17 18 1.39 17 A A O2' H61 G A 6 25 1.48 17 A A N3 H21 C G 12 19 1.50 17 A A HO2' O5' C G 23 24 1.51 17 A A HO2' O5' G U 13 14 1.58 18 A A H61 O2 A C 8 23 1.36 18 A A HO2' O5' C U 15 17 1.41 18 A A O2' H8 C G 18 19 1.44 18 A A O2' H8 C G 15 16 1.52 18 A A H21 N3 G C 4 27 1.58 19 A A H61 O2 A C 8 23 1.32 19 A A O2' H5' C G 18 19 1.51 20 A A H61 O2 A C 8 23 1.34 20 A A HO2' O5' G G 9 10 1.48 20 A A O2' H2' U C 17 18 1.52 SOLUTION STRUCTURE OF THE VS RIBOZYME SUBSTRATE STEM-LOOP 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 30 A N3 C 30 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 30 A O2 C 30 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 30 A N4 C 30 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 29 A N3 C 29 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 29 A O2 C 29 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 29 A N4 C 29 1_555 hydrog TYPE_28_PAIR A U 3 A N3 U 3 1_555 A G 28 A O6 G 28 1_555 hydrog TYPE_28_PAIR A U 3 A O2 U 3 1_555 A G 28 A N1 G 28 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A C 5 A N3 C 5 1_555 A G 26 A N1 G 26 1_555 hydrog WATSON-CRICK A C 5 A N4 C 5 1_555 A G 26 A O6 G 26 1_555 hydrog WATSON-CRICK A C 5 A O2 C 5 1_555 A G 26 A N2 G 26 1_555 hydrog TYPE_11_PAIR A G 6 A N2 G 6 1_555 A A 25 A N7 A 25 1_555 hydrog TYPE_11_PAIR A G 6 A N3 G 6 1_555 A A 25 A N6 A 25 1_555 hydrog TYPE_11_PAIR A A 7 A N6 A 7 1_555 A G 24 A N3 G 24 1_555 hydrog TYPE_11_PAIR A A 7 A N7 A 7 1_555 A G 24 A N2 G 24 1_555 hydrog A-C MISPAIR A A 8 A N6 A 8 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 22 A N4 C 22 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 A C 21 A N4 C 21 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 A C 20 A N4 C 20 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 A G 19 A O6 G 19 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 A G 19 A N2 G 19 1_555 RNA VS RIBOZYME, STEM-LOOP, TANDEM GA, PROTONATED ADENINE, A+C BASE PAIR, RNA 1HWQ PDB 1 1HWQ 1 30 1HWQ 1 30 1HWQ A 1 1 30 1 P 1