1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Nixon, P.L. Giedroc, D.P. 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 C9 H15 N3 O8 P 1 324.204 n N3-PROTONATED 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 N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C N 86 N N N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N C N 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 R C N 120 N O N 121 R C Y 122 N N Y 123 N C Y 124 N N Y 125 N C N 126 N C N 127 N O N 128 N N N 129 N C N 130 N N N 131 N N Y 132 N C N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N O N 148 N P N 149 N O N 150 N O N 151 N O N 152 N C N 153 R C N 154 N O N 155 S C N 156 N O N 157 R C N 158 N O N 159 R C N 160 N N N 161 N C N 162 N O N 163 N N N 164 N C N 165 N O N 166 N C N 167 N C N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N doub N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing Y 137 N sing Y 138 N sing Y 139 N doub N 140 N sing Y 141 N sing N 142 N sing Y 143 N doub N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N doub N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N doub N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub N 180 N sing N 181 N sing N 182 N sing N 183 N doub N 184 N sing N 185 N doub N 186 N sing N 187 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 322 621 633 10.1016/S0022-2836(02)00779-9 12225754 Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot 2002 10.2210/pdb1kpz/pdb pdb_00001kpz 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 Pea Enation Mosaic Virus type I RNA 10640.448 P1-P2 frameshifting pseudoknot 1 syn polymer no yes GAAUUCCGGU(CH)GACUCCGGAGAAACAAAGUCAA GAAUUCCGGUCGACUCCGGAGAAACAAAGUCAA 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 n n n citation_author pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations Data collection Database references Derived calculations 1 0 2002-01-11 1 1 2008-04-27 1 2 2011-07-13 1 3 2018-01-24 1 4 2024-05-01 _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag PEMV-1 Structural Ensemble RCSB Y RCSB 2002-01-03 REL REL Naturally occuring sequence of the P1-P2 frameshifting pseudoknot from Pea Enation Mosaic Virus type I. In vitro SP6 Transcription. sample 1 2D NOESY 2D NOESY 100 mM KCl, 5 mM MgCl2 6.0 atmospheric atm 283 K 100 mM KCl, 5 mM MgCl2 6.0 atmospheric atm 298 K minimized average structure 2 mM PEMV-1 RNA 10 mM KPO4, pH 6.0, 100 mM KCl, 5 mM MgCl2 Brunger, A.T structure solution X-PLOR 3.851 Brunger, A.T refinement X-PLOR 3.851 500 Varian INOVA 600 Varian INOVA n 1 0 A n 2 1 A n 3 2 A n 4 3 A URI 4 n 5 U 4 A CYT 5 n 6 C 5 A CYT 6 n 7 C 6 A GUA 7 n 8 G 7 A GUA 8 n 9 G 8 A URI 9 n 10 U 9 A CH 10 n 11 CH 10 A GUA 11 n 12 G 11 A ADE 12 n 13 A 12 A CYT 13 n 14 C 13 A URI 14 n 15 U 14 A CYT 15 n 16 C 15 A CYT 16 n 17 C 16 A GUA 17 n 18 G 17 A GUA 18 n 19 G 18 A ADE 19 n 20 A 19 A GUA 20 n 21 G 20 A ADE 21 n 22 A 21 A ADE 22 n 23 A 22 A ADE 23 n 24 A 23 A CYT 24 n 25 C 24 A ADE 25 n 26 A 25 A ADE 26 n 27 A 26 A ADE 27 n 28 A 27 A GUA 28 n 29 G 28 A URI 29 n 30 U 29 A CYT 30 n 31 C 30 A ADE 31 n 32 A 31 A n 33 32 A author_defined_assembly 1 monomeric A CH 10 N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE A CH 11 C 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A G 0 A G 1 1 Y 1 A A 1 A A 2 1 Y 1 A A 2 A A 3 1 Y 1 A U 3 A U 4 1 Y 1 A A 32 A A 33 1 Y 1 A A O2 H61 C A 16 25 1.42 1 A A HO2' O4' A G 27 28 1.53 1 A A O2' O2' C A 6 22 2.15 1 A U 4 0.116 SIDE CHAIN 1 A C 5 0.098 SIDE CHAIN 1 A C 6 0.088 SIDE CHAIN 1 A G 7 0.087 SIDE CHAIN 1 A G 8 0.115 SIDE CHAIN 1 A U 9 0.114 SIDE CHAIN 1 A G 11 0.079 SIDE CHAIN 1 A A 12 0.101 SIDE CHAIN 1 A C 15 0.099 SIDE CHAIN 1 A C 16 0.098 SIDE CHAIN 1 A G 17 0.093 SIDE CHAIN 1 A G 18 0.108 SIDE CHAIN 1 A A 19 0.078 SIDE CHAIN 1 A A 21 0.210 SIDE CHAIN 1 A A 22 0.142 SIDE CHAIN 1 A A 25 0.057 SIDE CHAIN 1 A A 26 0.060 SIDE CHAIN 1 A G 28 0.090 SIDE CHAIN 1 A U 29 0.105 SIDE CHAIN 1 A C 30 0.165 SIDE CHAIN 1 5.02 0.70 108.50 113.52 A A A O4' C1' N1 U U U 4 4 4 N 1 4.29 0.70 108.50 112.79 A A A O4' C1' N1 C C C 5 5 5 N 1 -2.58 0.40 120.30 117.72 A A A C6 N1 C2 C C C 5 5 5 N 1 3.72 0.60 118.90 122.62 A A A N1 C2 O2 C C C 5 5 5 N 1 -4.71 0.70 109.70 104.99 A A A C1' O4' C4' C C C 6 6 6 N 1 -6.88 1.00 102.60 95.72 A A A C4' C3' C2' C C C 6 6 6 N 1 5.64 0.70 108.50 114.14 A A A O4' C1' N1 C C C 6 6 6 N 1 -5.26 0.70 101.30 96.04 A A A C3' C2' C1' G G G 7 7 7 N 1 7.14 0.70 108.50 115.64 A A A O4' C1' N9 G G G 7 7 7 N 1 4.91 0.50 113.10 118.01 A A A N7 C8 N9 G G G 7 7 7 N 1 -3.92 0.40 106.40 102.48 A A A C8 N9 C4 G G G 7 7 7 N 1 5.05 0.50 113.10 118.15 A A A N7 C8 N9 G G G 8 8 8 N 1 -3.60 0.40 106.40 102.80 A A A C8 N9 C4 G G G 8 8 8 N 1 5.18 0.80 101.50 106.68 A A A C3' C2' C1' U U U 9 9 9 N 1 6.69 0.70 108.50 115.19 A A A O4' C1' N9 G G G 11 11 11 N 1 5.03 0.50 113.10 118.13 A A A N7 C8 N9 G G G 11 11 11 N 1 -3.69 0.40 106.40 102.71 A A A C8 N9 C4 G G G 11 11 11 N 1 -4.40 0.70 109.70 105.30 A A A C1' O4' C4' A A A 12 12 12 N 1 -5.13 0.70 101.30 96.17 A A A C3' C2' C1' A A A 12 12 12 N 1 4.73 0.70 108.50 113.23 A A A O4' C1' N9 A A A 12 12 12 N 1 4.42 0.50 113.80 118.22 A A A N7 C8 N9 A A A 12 12 12 N 1 5.11 0.80 101.50 106.61 A A A C3' C2' C1' C C C 13 13 13 N 1 4.98 0.80 101.50 106.48 A A A C3' C2' C1' U U U 14 14 14 N 1 5.16 0.70 108.50 113.66 A A A O4' C1' N1 C C C 15 15 15 N 1 -8.33 1.20 109.10 100.77 A A A C5' C4' O4' G G G 17 17 17 N 1 9.00 0.70 108.50 117.50 A A A O4' C1' N9 G G G 17 17 17 N 1 5.03 0.50 113.10 118.13 A A A N7 C8 N9 G G G 17 17 17 N 1 -4.20 0.40 106.40 102.20 A A A C8 N9 C4 G G G 17 17 17 N 1 7.99 0.70 108.50 116.49 A A A O4' C1' N9 G G G 18 18 18 N 1 5.51 0.50 113.10 118.61 A A A N7 C8 N9 G G G 18 18 18 N 1 -5.17 0.40 106.40 101.23 A A A C8 N9 C4 G G G 18 18 18 N 1 -11.12 1.20 109.10 97.98 A A A C5' C4' O4' A A A 19 19 19 N 1 9.24 0.70 108.50 117.74 A A A O4' C1' N9 A A A 19 19 19 N 1 6.34 0.50 113.80 120.14 A A A N7 C8 N9 A A A 19 19 19 N 1 -4.76 0.40 105.80 101.04 A A A C8 N9 C4 A A A 19 19 19 N 1 4.71 0.50 113.10 117.81 A A A N7 C8 N9 G G G 20 20 20 N 1 -3.11 0.40 106.40 103.29 A A A C8 N9 C4 G G G 20 20 20 N 1 4.65 0.70 126.80 131.45 A A A N3 C4 C5 A A A 21 21 21 N 1 -4.70 0.50 103.90 99.20 A A A C5 N7 C8 A A A 21 21 21 N 1 4.27 0.50 113.80 118.07 A A A N7 C8 N9 A A A 21 21 21 N 1 -3.04 0.40 105.80 102.76 A A A C8 N9 C4 A A A 21 21 21 N 1 3.57 0.40 105.80 109.37 A A A N9 C4 C5 A A A 21 21 21 N 1 -8.28 0.80 127.40 119.12 A A A N3 C4 N9 A A A 21 21 21 N 1 -5.70 0.80 108.20 102.50 A A A O4' C1' N9 A A A 22 22 22 N 1 3.82 0.50 113.80 117.62 A A A N7 C8 N9 A A A 22 22 22 N 1 -3.22 0.40 105.80 102.58 A A A C8 N9 C4 A A A 22 22 22 N 1 3.53 0.50 113.80 117.33 A A A N7 C8 N9 A A A 23 23 23 N 1 4.96 0.80 101.50 106.46 A A A C3' C2' C1' C C C 24 24 24 N 1 5.62 0.70 108.50 114.12 A A A O4' C1' N9 A A A 25 25 25 N 1 3.11 0.50 113.80 116.91 A A A N7 C8 N9 A A A 25 25 25 N 1 4.91 0.80 101.50 106.41 A A A C3' C2' C1' A A A 26 26 26 N 1 3.72 0.50 113.80 117.52 A A A N7 C8 N9 A A A 26 26 26 N 1 3.17 0.50 113.80 116.97 A A A N7 C8 N9 A A A 27 27 27 N 1 -7.24 1.20 109.10 101.86 A A A C5' C4' O4' G G G 28 28 28 N 1 -4.94 0.70 101.30 96.36 A A A C3' C2' C1' G G G 28 28 28 N 1 7.93 0.70 108.50 116.43 A A A O4' C1' N9 G G G 28 28 28 N 1 4.96 0.50 113.10 118.06 A A A N7 C8 N9 G G G 28 28 28 N 1 -4.14 0.40 106.40 102.26 A A A C8 N9 C4 G G G 28 28 28 N 1 -8.27 1.00 102.60 94.33 A A A C4' C3' C2' U U U 29 29 29 N 1 11.77 1.30 114.00 125.77 A A A N1 C1' C2' C C C 30 30 30 N 1 4.80 0.80 101.50 106.30 A A A C3' C2' C1' A A A 31 31 31 N 1 3.69 0.50 113.80 117.49 A A A N7 C8 N9 A A A 31 31 31 N 1 A A C2' C1' U U 4 4 -0.106 0.008 1.526 1.420 N 1 A A C2' C1' C C 5 5 -0.111 0.008 1.526 1.415 N 1 A A C2' C1' G G 7 7 -0.130 0.008 1.526 1.396 N 1 A A C2' C1' G G 8 8 -0.142 0.008 1.526 1.384 N 1 A A C2' C1' G G 11 11 -0.128 0.008 1.526 1.398 N 1 A A C2' C1' A A 12 12 -0.130 0.008 1.526 1.396 N 1 A A C2' C1' C C 15 15 -0.123 0.008 1.526 1.403 N 1 A A C2' C1' C C 16 16 -0.097 0.008 1.526 1.429 N 1 A A C2' C1' G G 17 17 -0.136 0.008 1.526 1.390 N 1 A A C5' C4' G G 18 18 -0.045 0.007 1.508 1.463 N 1 A A C2' C1' G G 18 18 -0.101 0.008 1.526 1.425 N 1 A A C2' C1' A A 19 19 -0.148 0.008 1.526 1.378 N 1 A A C8 N9 A A 19 19 -0.049 0.008 1.373 1.324 N 1 A A C2 N3 A A 21 21 -0.096 0.009 1.331 1.235 N 1 A A N3 C4 A A 21 21 -0.061 0.006 1.344 1.283 N 1 A A C4 C5 A A 21 21 -0.061 0.007 1.383 1.322 N 1 A A C8 N9 A A 21 21 -0.059 0.008 1.373 1.314 N 1 A A N9 C4 A A 21 21 -0.072 0.006 1.374 1.302 N 1 A A N1 C6 C C 24 24 0.046 0.006 1.367 1.413 N 1 A A C2' C1' G G 28 28 -0.132 0.008 1.526 1.394 N 1 A A C2' C1' U U 29 29 -0.068 0.008 1.526 1.458 N 1 A A C2' C1' C C 30 30 -0.069 0.008 1.526 1.457 N minimized average PEMV-1 P1-P2 Frameshifting Pseudoknot Regularized Average Structure 1 N N covale 1.610 both A U 9 A O3' U 10 1_555 A CH 10 A P CH 11 1_555 covale 1.652 both A CH 10 A O3' CH 11 1_555 A G 11 A P G 12 1_555 hydrog WATSON-CRICK A U 4 A N3 U 5 1_555 A A 19 A N1 A 20 1_555 hydrog WATSON-CRICK A U 4 A O4 U 5 1_555 A A 19 A N6 A 20 1_555 hydrog U-A PAIR A U 4 A O2 U 5 1_555 A A 21 A N6 A 22 1_555 hydrog WATSON-CRICK A C 5 A N3 C 6 1_555 A G 18 A N1 G 19 1_555 hydrog WATSON-CRICK A C 5 A N4 C 6 1_555 A G 18 A O6 G 19 1_555 hydrog WATSON-CRICK A C 5 A O2 C 6 1_555 A G 18 A N2 G 19 1_555 hydrog WATSON-CRICK A C 6 A N3 C 7 1_555 A G 17 A N1 G 18 1_555 hydrog WATSON-CRICK A C 6 A N4 C 7 1_555 A G 17 A O6 G 18 1_555 hydrog WATSON-CRICK A C 6 A O2 C 7 1_555 A G 17 A N2 G 18 1_555 hydrog WATSON-CRICK A G 7 A N1 G 8 1_555 A C 16 A N3 C 17 1_555 hydrog WATSON-CRICK A G 7 A N2 G 8 1_555 A C 16 A O2 C 17 1_555 hydrog WATSON-CRICK A G 7 A O6 G 8 1_555 A C 16 A N4 C 17 1_555 hydrog WATSON-CRICK A G 8 A N1 G 9 1_555 A C 15 A N3 C 16 1_555 hydrog WATSON-CRICK A G 8 A N2 G 9 1_555 A C 15 A O2 C 16 1_555 hydrog WATSON-CRICK A G 8 A O6 G 9 1_555 A C 15 A N4 C 16 1_555 hydrog TYPE_10_PAIR A G 8 A N2 G 9 1_555 A A 26 A N1 A 27 1_555 hydrog TYPE_10_PAIR A G 8 A N3 G 9 1_555 A A 26 A N6 A 27 1_555 hydrog HOOGSTEEN A U 9 A N3 U 10 1_555 A A 27 A N7 A 28 1_555 hydrog HOOGSTEEN A U 9 A O4 U 10 1_555 A A 27 A N6 A 28 1_555 hydrog CH-A MISPAIR A CH 10 A O2 CH 11 1_555 A A 12 A N6 A 13 1_555 hydrog CH-G PAIR A CH 10 A N4 CH 11 1_555 A G 28 A N7 G 29 1_555 hydrog WATSON-CRICK A G 11 A N1 G 12 1_555 A C 30 A N3 C 31 1_555 hydrog WATSON-CRICK A G 11 A N2 G 12 1_555 A C 30 A O2 C 31 1_555 hydrog WATSON-CRICK A G 11 A O6 G 12 1_555 A C 30 A N4 C 31 1_555 hydrog A-G MISPAIR A A 12 A N6 A 13 1_555 A G 28 A O6 G 29 1_555 hydrog WATSON-CRICK A A 12 A N1 A 13 1_555 A U 29 A N3 U 30 1_555 hydrog WATSON-CRICK A A 12 A N6 A 13 1_555 A U 29 A O4 U 30 1_555 hydrog WATSON-CRICK A C 13 A N3 C 14 1_555 A G 28 A N1 G 29 1_555 hydrog WATSON-CRICK A C 13 A N4 C 14 1_555 A G 28 A O6 G 29 1_555 hydrog WATSON-CRICK A C 13 A O2 C 14 1_555 A G 28 A N2 G 29 1_555 hydrog C-A MISPAIR A C 16 A O2 C 17 1_555 A A 25 A N6 A 26 1_555 hydrog G-A MISPAIR A G 18 A N2 G 19 1_555 A A 22 A N3 A 23 1_555 RNA Pseudoknot, Frameshifting, Luteovirus, Triple Helix, Protonated Cytidine, Ribonucleic Acid, RNA 1KPZ PDB 1 1KPZ 0 32 1KPZ 0 32 1KPZ A 1 1 33