1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Liu, H. Matsugami, A. Katahira, M. Uesugi, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H14 N5 O7 P 347.221 y ADENOSINE-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 322 955 970 10.1016/S0022-2836(02)00876-8 12367521 A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops 2002 10.2210/pdb1my9/pdb pdb_00001my9 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 K+ CATION STABILIZED 4599.764 5'-R(*GP*GP*AP*GP*GP*UP*UP*UP*UP*GP*GP*AP*GP*G)-3' 2 syn polymer no no GGAGGUUUUGGAGG GGAGGUUUUGGAGG A,B polyribonucleotide n n n n n n n n n n n n n n -26.724 6 A 11 A 14 -91.374 A_G11:G14_A 1 50.366 1.671 -1.465 2.575 -16.923 3 6 A 1 A 13 101.415 A_G1:G13_A 2 0.605 -0.529 0.328 -3.759 -0.080 A 4 B 27 18.244 A_G4:G27_B 3 34.679 -0.459 2.071 0.412 9.881 3 6 B 15 B 18 -84.126 B_G15:G18_B 4 -3.519 1.015 1.211 3.231 -18.836 6 B 25 B 28 -88.174 B_G25:G28_B 5 31.990 1.684 -1.152 3.206 8.217 6 B 19 B 16 82.301 B_G19:G16_B 6 -20.933 -2.135 -0.086 -3.322 -4.248 63.562 A A 11 1 16.935 A A 14 13 -4.341 17.480 -0.796 -1.432 AA_G11G1:G13G14_AA 1 -16.461 15.948 59.297 -0.309 1.745 -1.471 125.870 A A 1 4 0.151 A B 13 27 -1.495 0.270 -1.046 -4.148 AA_G1G4:G27G13_BA 2 -6.042 3.393 125.788 -2.328 0.610 -0.029 -172.195 A B 4 15 84.679 B B 27 18 -4.499 -164.158 -1.558 1.229 AB_G4G15:G18G27_BB 3 50.265 25.929 -40.454 -2.127 -1.244 -0.474 -176.815 B B 25 19 4.689 B B 28 16 -0.479 -9.374 0.603 3.235 BB_G25G19:G16G28_BB 4 14.810 7.408 -176.777 -1.619 0.301 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2003-10-07 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2002-10-04 REL structures with the lowest energy 1 2D NOESY 2D NOESY 2D TOCSY DQF-COSY 16 mM KCl 6.5 ambient 283 K 16 mM KCl 6.5 ambient 305.5 K simulated annealing 1 lowest energy 1.6 mM RNA, 10 mM sodium phosphate buffer (pH 6.5), 16 mM KCl 95% H2O/5% D2O 1.6 mM RNA, 10 mM sodium phosphate buffer (pH 6.5), 16 mM KCl 100% D2O Brunger structure solution X-PLOR 3.851 Brunger refinement X-PLOR 3.851 600 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 U 6 n 6 U 6 A U 7 n 7 U 7 A U 8 n 8 U 8 A U 9 n 9 U 9 A G 10 n 10 G 10 A G 11 n 11 G 11 A A 12 n 12 A 12 A G 13 n 13 G 13 A G 14 n 14 G 14 A G 15 n 1 G 15 B G 16 n 2 G 16 B A 17 n 3 A 17 B G 18 n 4 G 18 B G 19 n 5 G 19 B U 20 n 6 U 20 B U 21 n 7 U 21 B U 22 n 8 U 22 B U 23 n 9 U 23 B G 24 n 10 G 24 B G 25 n 11 G 25 B A 26 n 12 A 26 B G 27 n 13 G 27 B G 28 n 14 G 28 B author_defined_assembly 2 dimeric 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 HO2' OP2 G G 10 11 1.37 1 A B O5' H1' G G 1 18 1.53 1 A A O4' H61 G A 10 12 1.55 1 A A H1' O4' G U 5 6 1.60 1 4.31 0.50 113.10 117.41 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.48 0.40 106.40 103.92 A A A C8 N9 C4 G G G 1 1 1 N 1 4.54 0.50 113.10 117.64 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.49 0.40 106.40 103.91 A A A C8 N9 C4 G G G 2 2 2 N 1 3.41 0.50 113.80 117.21 A A A N7 C8 N9 A A A 3 3 3 N 1 -2.61 0.40 105.80 103.19 A A A C8 N9 C4 A A A 3 3 3 N 1 4.35 0.50 113.10 117.45 A A A N7 C8 N9 G G G 4 4 4 N 1 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 4 4 4 N 1 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 5 5 5 N 1 -2.67 0.40 106.40 103.73 A A A C8 N9 C4 G G G 5 5 5 N 1 4.45 0.50 113.10 117.55 A A A N7 C8 N9 G G G 10 10 10 N 1 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 10 10 10 N 1 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 11 11 11 N 1 -2.60 0.40 106.40 103.80 A A A C8 N9 C4 G G G 11 11 11 N 1 3.66 0.50 113.80 117.46 A A A N7 C8 N9 A A A 12 12 12 N 1 -2.40 0.40 105.80 103.40 A A A C8 N9 C4 A A A 12 12 12 N 1 4.58 0.50 113.10 117.68 A A A N7 C8 N9 G G G 13 13 13 N 1 -2.79 0.40 106.40 103.61 A A A C8 N9 C4 G G G 13 13 13 N 1 4.56 0.50 113.10 117.66 A A A N7 C8 N9 G G G 14 14 14 N 1 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 G G G 14 14 14 N 1 4.36 0.50 113.10 117.46 B B B N7 C8 N9 G G G 15 15 15 N 1 -2.56 0.40 106.40 103.84 B B B C8 N9 C4 G G G 15 15 15 N 1 4.56 0.50 113.10 117.66 B B B N7 C8 N9 G G G 16 16 16 N 1 -2.60 0.40 106.40 103.80 B B B C8 N9 C4 G G G 16 16 16 N 1 3.46 0.50 113.80 117.26 B B B N7 C8 N9 A A A 17 17 17 N 1 -2.58 0.40 105.80 103.22 B B B C8 N9 C4 A A A 17 17 17 N 1 4.38 0.50 113.10 117.48 B B B N7 C8 N9 G G G 18 18 18 N 1 -2.59 0.40 106.40 103.81 B B B C8 N9 C4 G G G 18 18 18 N 1 4.52 0.50 113.10 117.62 B B B N7 C8 N9 G G G 19 19 19 N 1 -2.70 0.40 106.40 103.70 B B B C8 N9 C4 G G G 19 19 19 N 1 4.40 0.50 113.10 117.50 B B B N7 C8 N9 G G G 24 24 24 N 1 -2.59 0.40 106.40 103.81 B B B C8 N9 C4 G G G 24 24 24 N 1 4.49 0.50 113.10 117.59 B B B N7 C8 N9 G G G 25 25 25 N 1 -2.57 0.40 106.40 103.83 B B B C8 N9 C4 G G G 25 25 25 N 1 3.73 0.50 113.80 117.53 B B B N7 C8 N9 A A A 26 26 26 N 1 -2.43 0.40 105.80 103.37 B B B C8 N9 C4 A A A 26 26 26 N 1 4.47 0.50 113.10 117.57 B B B N7 C8 N9 G G G 27 27 27 N 1 -2.66 0.40 106.40 103.74 B B B C8 N9 C4 G G G 27 27 27 N 1 4.56 0.50 113.10 117.66 B B B N7 C8 N9 G G G 28 28 28 N 1 -2.67 0.40 106.40 103.73 B B B C8 N9 C4 G G G 28 28 28 N Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops 1 N N 1 N N hydrog TYPE_11_PAIR A G 1 A N2 G 1 1_555 A A 3 A N7 A 3 1_555 hydrog TYPE_11_PAIR A G 1 A N3 G 1 1_555 A A 3 A N6 A 3 1_555 hydrog TYPE_6_PAIR A G 1 A N1 G 1 1_555 A G 4 A O6 G 4 1_555 hydrog TYPE_6_PAIR A G 1 A N2 G 1 1_555 A G 4 A N7 G 4 1_555 hydrog TYPE_6_PAIR A G 1 A N7 G 1 1_555 A G 13 A N2 G 13 1_555 hydrog TYPE_6_PAIR A G 1 A O6 G 1 1_555 A G 13 A N1 G 13 1_555 hydrog TYPE_6_PAIR A G 2 A N1 G 2 1_555 A G 5 A O6 G 5 1_555 hydrog TYPE_6_PAIR A G 2 A N2 G 2 1_555 A G 5 A N7 G 5 1_555 hydrog TYPE_6_PAIR A G 2 A N7 G 2 1_555 A G 14 A N2 G 14 1_555 hydrog TYPE_6_PAIR A G 2 A O6 G 2 1_555 A G 14 A N1 G 14 1_555 hydrog TYPE_6_PAIR A G 4 A N1 G 4 1_555 A G 10 A O6 G 10 1_555 hydrog TYPE_6_PAIR A G 4 A N2 G 4 1_555 A G 10 A N7 G 10 1_555 hydrog G-G MISPAIR A G 4 A O6 G 4 1_555 B G 27 B N1 G 13 1_555 hydrog TYPE_6_PAIR A G 5 A N1 G 5 1_555 A G 11 A O6 G 11 1_555 hydrog TYPE_6_PAIR A G 5 A N2 G 5 1_555 A G 11 A N7 G 11 1_555 hydrog TYPE_11_PAIR A G 10 A N2 G 10 1_555 A A 12 A N7 A 12 1_555 hydrog TYPE_11_PAIR A G 10 A N3 G 10 1_555 A A 12 A N6 A 12 1_555 hydrog TYPE_6_PAIR A G 10 A N1 G 10 1_555 A G 13 A O6 G 13 1_555 hydrog TYPE_6_PAIR A G 10 A N2 G 10 1_555 A G 13 A N7 G 13 1_555 hydrog TYPE_6_PAIR A G 11 A N1 G 11 1_555 A G 14 A O6 G 14 1_555 hydrog TYPE_6_PAIR A G 11 A N2 G 11 1_555 A G 14 A N7 G 14 1_555 hydrog A-G MISPAIR A A 12 A N6 A 12 1_555 B G 27 B N7 G 13 1_555 hydrog G-A MISPAIR A G 13 A N7 G 13 1_555 B A 26 B N6 A 12 1_555 hydrog TYPE_11_PAIR B G 15 B N2 G 1 1_555 B A 17 B N7 A 3 1_555 hydrog TYPE_11_PAIR B G 15 B N3 G 1 1_555 B A 17 B N6 A 3 1_555 hydrog TYPE_6_PAIR B G 15 B N1 G 1 1_555 B G 18 B O6 G 4 1_555 hydrog TYPE_6_PAIR B G 15 B N2 G 1 1_555 B G 18 B N7 G 4 1_555 hydrog TYPE_6_PAIR B G 15 B N7 G 1 1_555 B G 27 B N2 G 13 1_555 hydrog TYPE_6_PAIR B G 15 B O6 G 1 1_555 B G 27 B N1 G 13 1_555 hydrog TYPE_6_PAIR B G 16 B N1 G 2 1_555 B G 19 B O6 G 5 1_555 hydrog TYPE_6_PAIR B G 16 B N2 G 2 1_555 B G 19 B N7 G 5 1_555 hydrog TYPE_6_PAIR B G 16 B N7 G 2 1_555 B G 28 B N2 G 14 1_555 hydrog TYPE_6_PAIR B G 16 B O6 G 2 1_555 B G 28 B N1 G 14 1_555 hydrog TYPE_6_PAIR B G 18 B N1 G 4 1_555 B G 24 B O6 G 10 1_555 hydrog TYPE_6_PAIR B G 18 B N2 G 4 1_555 B G 24 B N7 G 10 1_555 hydrog TYPE_6_PAIR B G 19 B N1 G 5 1_555 B G 25 B O6 G 11 1_555 hydrog TYPE_6_PAIR B G 19 B N2 G 5 1_555 B G 25 B N7 G 11 1_555 hydrog TYPE_11_PAIR B G 24 B N2 G 10 1_555 B A 26 B N7 A 12 1_555 hydrog TYPE_11_PAIR B G 24 B N3 G 10 1_555 B A 26 B N6 A 12 1_555 hydrog TYPE_6_PAIR B G 24 B N1 G 10 1_555 B G 27 B O6 G 13 1_555 hydrog TYPE_6_PAIR B G 24 B N2 G 10 1_555 B G 27 B N7 G 13 1_555 hydrog TYPE_6_PAIR B G 25 B N1 G 11 1_555 B G 28 B O6 G 14 1_555 hydrog TYPE_6_PAIR B G 25 B N2 G 11 1_555 B G 28 B N7 G 14 1_555 RNA Parallel RNA quadruplex with a loop, Dimer of two quadruplexes, RNA 1MY9 PDB 1 1MY9 1 14 1MY9 1 14 1MY9 A 1 1 14 15 28 1MY9 15 28 1MY9 B 1 1 14