0.034783 0.000000 0.001744 0.000000 0.023585 0.000000 0.000000 0.000000 0.030213 0.00000 0.00000 0.00000 Berglund, J.A. Rosbash, M. Schultz, S.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 92.87 90.00 28.75 42.40 33.14 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 H2 O 18.015 WATER non-polymer 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 Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C 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 H N 110 N H N 111 N O N 112 N H N 113 N H N 114 N O N 115 N P N 116 N O N 117 N O N 118 N O N 119 N C N 120 R C N 121 N O N 122 S C N 123 N O N 124 R C N 125 N O N 126 R C N 127 N N N 128 N C N 129 N O N 130 N N N 131 N C N 132 N O N 133 N C N 134 N C 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 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 Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N doub 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 N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N doub N 145 N sing N 146 N sing N 147 N sing N 148 N doub N 149 N sing N 150 N doub N 151 N sing N 152 N sing UK RNA RNARFU 2122 1355-8382 7 682 691 10.1017/S1355838201002187 11350032 Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines. 2001 10.2210/pdb1i9x/pdb pdb_00001i9x 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.0 1 Yale mirrors IMAGE PLATE 1999-02-10 RIGAKU RAXIS IIC Yale Mirrors SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU200 BPS - U2 SNRNA DUPLEX 4126.509 5'-R(*UP*AP*CP*UP*AP*AP*CP*GP*UP*AP*GP*UP*A)-3' 2 syn polymer 18.015 water 22 nat water no no UACUAACGUAGUA UACUAACGUAGUA A,B polyribonucleotide n n n n n n n n n n n n n 1 2.44 49.68 VAPOR DIFFUSION, HANGING DROP 7.5 MPD, Spermine, Glycerol, tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP 303.0 then shifted to 287.0 MPD 1 Spermine 1 Glycerol 1 tris 1 MPD 2 4.911 1 20 A 1 B 13 7.154 A_U1:A13_B 1 -9.189 -0.365 0.356 -0.092 -1.329 1 20 A 2 B 12 3.879 A_A2:U12_B 2 -17.797 -0.184 0.528 -0.187 -2.820 1 19 A 3 B 11 6.501 A_C3:G11_B 3 -18.735 0.245 0.445 -0.155 0.270 1 20 A 4 B 10 -0.508 A_U4:A10_B 4 -16.122 0.179 0.175 -0.236 -8.766 1 20 A 6 B 9 13.839 A_A6:U9_B 5 -14.060 0.237 -0.458 -0.233 17.448 1 19 A 7 B 8 2.373 A_C7:G8_B 6 -17.470 0.168 -1.059 -0.139 -0.936 1 19 A 8 B 7 6.261 A_G8:C7_B 7 -12.536 -0.350 0.221 0.031 0.295 1 20 A 9 B 6 6.848 A_U9:A6_B 8 -11.272 -0.260 0.262 -0.346 -2.048 1 20 A 10 B 4 -0.311 A_A10:U4_B 9 -9.970 0.355 0.490 -0.225 -3.324 1 19 A 11 B 3 2.488 A_G11:C3_B 10 -16.788 -0.460 0.477 0.013 -5.864 1 20 A 12 B 2 8.348 A_U12:A2_B 11 -13.007 -0.178 0.414 0.059 -3.181 1 20 A 13 B 1 2.172 A_A13:U1_B 12 -6.283 0.286 0.420 -0.086 2.723 35.790 A A 1 2 17.580 B B 13 12 3.234 10.620 -0.458 -1.404 AA_U1A2:U12A13_BB 1 -4.709 7.794 33.911 -3.717 0.111 3.154 33.533 A A 2 3 6.854 B B 12 11 3.296 3.943 -0.438 -1.233 AA_A2C3:G11U12_BB 2 -2.201 3.826 33.236 -2.779 0.401 2.734 33.161 A A 3 4 14.937 B B 11 10 3.100 8.436 -0.600 -1.100 AA_C3U4:A10G11_BB 3 -0.201 0.356 32.098 -3.213 1.021 3.061 41.175 A A 4 6 13.053 B B 10 9 3.468 9.109 -0.633 -1.451 AA_U4A6:U9A10_BB 4 1.298 -1.860 40.178 -3.059 1.042 2.394 29.396 A A 6 7 7.259 B B 9 8 2.667 3.656 -0.563 -0.951 AA_A6C7:G8U9_BB 5 5.188 -10.301 28.717 -2.488 1.981 1.877 30.574 A A 7 8 33.605 B B 8 7 3.755 16.653 1.139 -1.821 AA_C7G8:C7G8_BB 6 -6.202 12.515 24.981 -6.599 -3.332 3.164 31.587 A A 8 9 2.324 B B 7 6 3.235 1.265 -0.358 -1.882 AA_G8U9:A6C7_BB 7 -0.495 0.910 31.559 -3.688 0.569 2.824 40.187 A A 9 10 9.880 B B 6 4 3.094 6.758 0.495 -1.516 AA_U9A10:U4A6_BB 8 1.431 -2.092 39.613 -2.906 -0.572 2.332 30.598 A A 10 11 23.893 B B 4 3 3.136 12.248 0.696 -1.541 AA_A10G11:C3U4_BB 9 3.069 -5.986 27.928 -5.044 -0.787 3.182 33.948 A A 11 12 6.912 B B 3 2 3.340 4.024 0.533 -1.420 AA_G11U12:A2C3_BB 10 2.237 -3.843 33.643 -3.078 -0.554 2.446 37.286 A A 12 13 16.271 B B 2 1 2.948 10.276 -0.238 -1.455 AA_U12A13:U1A2_BB 11 1.041 -1.649 35.876 -3.421 0.488 diffrn_source chem_comp_atom chem_comp_bond database_2 repository Initial release Version format compliance Version format compliance Data collection Data collection Database references 1 0 2001-09-05 1 1 2008-04-27 1 2 2011-07-13 1 3 2018-04-04 1 4 2024-02-07 _diffrn_source.type _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2001-03-21 REL REL HOH water The UACUAAC is the conserved branchpoint sequence in budding yeast and the GUAGUA is conserved in the U2 snRNP particle. sample HOH 25 2 HOH HOH 25 A HOH 26 2 HOH HOH 26 A HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 29 2 HOH HOH 29 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 40 2 HOH HOH 40 A HOH 41 2 HOH HOH 41 A HOH 21 2 HOH HOH 21 B HOH 22 2 HOH HOH 22 B HOH 23 2 HOH HOH 23 B HOH 24 2 HOH HOH 24 B HOH 30 2 HOH HOH 30 B HOH 31 2 HOH HOH 31 B HOH 32 2 HOH HOH 32 B HOH 33 2 HOH HOH 33 B HOH 37 2 HOH HOH 37 B HOH 38 2 HOH HOH 38 B HOH 39 2 HOH HOH 39 B HOH 42 2 HOH HOH 42 B U 1 n 1 U 1 A A 2 n 2 A 2 A C 3 n 3 C 3 A U 4 n 4 U 4 A A 5 n 5 A 5 A A 6 n 6 A 6 A C 7 n 7 C 7 A G 8 n 8 G 8 A U 9 n 9 U 9 A A 10 n 10 A 10 A G 11 n 11 G 11 A U 12 n 12 U 12 A A 13 n 13 A 13 A U 1 n 1 U 1 B A 2 n 2 A 2 B C 3 n 3 C 3 B U 4 n 4 U 4 B A 5 n 5 A 5 B A 6 n 6 A 6 B C 7 n 7 C 7 B G 8 n 8 G 8 B U 9 n 9 U 9 B A 10 n 10 A 10 B G 11 n 11 G 11 B U 12 n 12 U 12 B A 13 n 13 A 13 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 58 22.18 0.00 12.48 -15.43 0.00 -6.75 Bulk solvent was not used in the refinement. 0.2760000 0.2530000 2.18 8.0 410 4145 3980 96.0 Random 1 Anistropic THROUGHOUT 0.0 0.0 MIR G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996). 0.47 0.36 5.0 0.56 0.54 2.18 8.0 22 568 0 546 0 0.005 1.2 12.7 1.49 0.4570000 0.055 0.4270000 2.31 69 93.2 41.4 2.0 30.0 1I9X 4369 4125 0.0 0.0 0.0480000 4.7000000 1 30.1 4.9 96.0 0.3840000 2.18 2.26 2.6 440 27.7000000 4.1 94.0 phasing MLPHARE refinement CNS data reduction DENZO data scaling SCALEPACK CRYSTAL STRUCTURE OF BPS-U2 SNRNA DUPLEX 1 N N 1 N N 2 N N 2 N N hydrog WATSON-CRICK A U 1 A N3 U 1 1_555 B A 13 B N1 A 13 1_555 hydrog WATSON-CRICK A U 1 A O4 U 1 1_555 B A 13 B N6 A 13 1_555 hydrog WATSON-CRICK A A 2 A N1 A 2 1_555 B U 12 B N3 U 12 1_555 hydrog WATSON-CRICK A A 2 A N6 A 2 1_555 B U 12 B O4 U 12 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B G 11 B N1 G 11 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B G 11 B O6 G 11 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B G 11 B N2 G 11 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 B A 10 B N1 A 10 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 B A 10 B N6 A 10 1_555 hydrog WATSON-CRICK A A 6 A N1 A 6 1_555 B U 9 B N3 U 9 1_555 hydrog WATSON-CRICK A A 6 A N6 A 6 1_555 B U 9 B O4 U 9 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 B G 8 B N1 G 8 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 B G 8 B O6 G 8 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 B G 8 B N2 G 8 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 B C 7 B N3 C 7 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 B C 7 B O2 C 7 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 B C 7 B N4 C 7 1_555 hydrog WATSON-CRICK A U 9 A N3 U 9 1_555 B A 6 B N1 A 6 1_555 hydrog WATSON-CRICK A U 9 A O4 U 9 1_555 B A 6 B N6 A 6 1_555 hydrog WATSON-CRICK A A 10 A N1 A 10 1_555 B U 4 B N3 U 4 1_555 hydrog WATSON-CRICK A A 10 A N6 A 10 1_555 B U 4 B O4 U 4 1_555 hydrog WATSON-CRICK A G 11 A N1 G 11 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A G 11 A N2 G 11 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A G 11 A O6 G 11 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A U 12 A N3 U 12 1_555 B A 2 B N1 A 2 1_555 hydrog WATSON-CRICK A U 12 A O4 U 12 1_555 B A 2 B N6 A 2 1_555 hydrog WATSON-CRICK A A 13 A N1 A 13 1_555 B U 1 B N3 U 1 1_555 hydrog WATSON-CRICK A A 13 A N6 A 13 1_555 B U 1 B O4 U 1 1_555 RNA pre-mRNA splicing, bulged adenosine, three helix junction, RNA 1I9X PDB 1 1I9X 1 13 1I9X 1 13 1I9X A 1 1 13 1 13 1I9X 1 13 1I9X B 1 1 13 4 P 1 21 1