0.043860 0.000000 0.000000 0.000000 0.043860 0.000000 0.000000 0.000000 0.006109 0.00000 0.00000 0.00000 Safaee, N. Noronha, A.M. Kozlov, G. Rodionov, D. Wilds, C.J. Sheldrick, G.M. Gehring, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 22.800 22.800 163.700 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer H4 N 1 18.038 AMMONIUM ION non-polymer 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 H N 40 N H N 41 N N N 42 N H N 43 N H N 44 N H N 45 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 sing N 43 N sing N 44 N sing N 45 N sing GE Angew.Chem.Int.Ed.Engl. 9999 1433-7851 52 10370 10373 10.1002/anie.201303461 23813654 Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction. 2013 10.2210/pdb4jrd/pdb pdb_00004jrd 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 100 1 100 1 100 1 FOCUSING MIRRORS CCD 2010-05-29 MARMOSAIC 300 mm CCD FOCUSING MIRRORS CCD 2010-10-21 ADSC QUANTUM 210 FOCUSING MIRRORS CCD 2010-10-21 ADSC QUANTUM 210 FOCUSING MIRRORS CCD 2010-10-21 ADSC QUANTUM 210 SI 111 DOUBLE SINGLE WAVELENGTH M x-ray 1 Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH M x-ray 1 Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH M x-ray 1 Horizontal focusing 5.05 asymmetric cut Si(111) SINGLE WAVELENGTH M x-ray 1 0.977 1.0 0.987 1.0 08ID-1 CLSI 0.977 SYNCHROTRON CLSI BEAMLINE 08ID-1 A1 CHESS 0.987 SYNCHROTRON CHESS BEAMLINE A1 A1 CHESS 0.987 SYNCHROTRON CHESS BEAMLINE A1 A1 CHESS 0.987 SYNCHROTRON CHESS BEAMLINE A1 3576.306 RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') 2 syn polymer 18.038 AMMONIUM ION 18 syn non-polymer 18.015 water 76 nat water no no AAAAAAAAAAA AAAAAAAAAAA A,B polyribonucleotide n n n n n n n n n n n 5 1.49 17.29 VAPOR DIFFUSION, SITTING DROP RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K 294 -13.408 8 2 A 2 B 1 -179.467 A_A2:A1_B 1 4.781 -6.182 -0.025 5.025 -10.282 8 2 A 3 B 2 -179.334 A_A3:A2_B 2 3.293 -6.071 -0.335 5.012 5.218 8 2 A 4 B 3 179.914 A_A4:A3_B 3 -10.155 6.228 0.020 -4.982 2.843 8 2 A 5 B 4 179.150 A_A5:A4_B 4 -11.912 6.173 0.102 -5.037 -0.083 8 2 A 6 B 5 -179.982 A_A6:A5_B 5 12.517 -6.191 0.080 5.006 3.242 8 2 A 7 B 6 -176.770 A_A7:A6_B 6 13.478 -6.156 0.057 5.094 0.631 8 2 A 8 B 7 -179.556 A_A8:A7_B 7 14.220 -6.001 -0.025 5.151 -2.264 8 2 A 9 B 8 179.228 A_A9:A8_B 8 -15.216 6.110 -0.051 -5.056 4.937 8 2 A 10 B 9 -179.243 A_A10:A9_B 9 13.390 -6.191 -0.033 4.996 0.116 8 2 A 11 B 10 -178.911 A_A11:A10_B 10 5.294 -6.148 0.102 5.017 3.191 33.652 A A 2 3 7.702 B B 1 2 3.491 4.432 -0.079 -1.754 AA_A2A3:A2A1_BB 1 4.899 -8.514 33.016 -3.776 0.961 3.812 -138.988 A A 3 4 1.934 B B 2 3 3.817 -3.624 0.025 -0.462 AA_A3A4:A3A2_BB 2 0.081 0.043 -138.966 0.271 0.014 3.735 41.604 A A 4 5 2.128 B B 3 4 3.750 1.511 0.165 -0.403 AA_A4A5:A4A3_BB 3 0.341 -0.480 41.576 -0.751 -0.191 3.783 -136.306 A A 5 6 -0.716 B B 4 5 3.780 1.330 0.287 -0.515 AA_A5A6:A5A4_BB 4 -1.113 -0.599 -136.301 0.268 0.146 3.761 41.129 A A 6 7 0.271 B B 5 6 3.764 0.191 0.238 -0.441 AA_A6A7:A6A5_BB 5 -0.199 0.283 41.128 -0.651 -0.364 3.807 45.127 A A 7 8 0.967 B B 6 7 3.811 0.742 -0.151 0.078 AA_A7A8:A7A6_BB 6 1.084 -1.413 45.108 0.025 0.310 3.828 -139.077 A A 8 9 0.141 B B 7 8 3.827 -0.264 -0.224 -0.024 AA_A8A9:A8A7_BB 7 0.426 0.227 -139.076 0.014 -0.117 3.778 -138.297 A A 9 10 -0.371 B B 8 9 3.778 0.693 -0.362 0.231 AA_A9A10:A9A8_BB 8 0.234 0.125 -138.296 -0.128 -0.192 3.565 40.074 A A 10 11 -1.667 B B 9 10 3.563 -1.142 -0.134 -0.036 AA_A10A11:A10A9_BB 9 -0.878 1.282 40.050 0.089 0.086 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Database references Data collection Database references Derived calculations 1 0 2013-06-05 1 1 2015-08-12 1 2 2024-02-28 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2013-03-21 REL REL NH4 AMMONIUM ION HOH water NH4 101 2 NH4 NH4 101 A NH4 102 2 NH4 NH4 102 A NH4 103 2 NH4 NH4 103 A NH4 104 2 NH4 NH4 104 A NH4 105 2 NH4 NH4 105 A NH4 106 2 NH4 NH4 106 A NH4 107 2 NH4 NH4 107 A NH4 108 2 NH4 NH4 108 A NH4 109 2 NH4 NH4 109 A NH4 110 2 NH4 NH4 110 A NH4 111 2 NH4 NH4 111 A NH4 101 2 NH4 NH4 101 B NH4 102 2 NH4 NH4 102 B NH4 103 2 NH4 NH4 103 B NH4 104 2 NH4 NH4 104 B NH4 105 2 NH4 NH4 105 B NH4 106 2 NH4 NH4 106 B NH4 107 2 NH4 NH4 107 B HOH 201 3 HOH HOH 201 A HOH 202 3 HOH HOH 202 A HOH 203 3 HOH HOH 203 A HOH 204 3 HOH HOH 204 A HOH 205 3 HOH HOH 205 A HOH 206 3 HOH HOH 206 A HOH 207 3 HOH HOH 207 A HOH 208 3 HOH HOH 208 A HOH 209 3 HOH HOH 209 A HOH 210 3 HOH HOH 210 A HOH 211 3 HOH HOH 211 A HOH 212 3 HOH HOH 212 A HOH 213 3 HOH HOH 213 A HOH 214 3 HOH HOH 214 A HOH 215 3 HOH HOH 215 A HOH 216 3 HOH HOH 216 A HOH 217 3 HOH HOH 217 A HOH 218 3 HOH HOH 218 A HOH 219 3 HOH HOH 219 A HOH 220 3 HOH HOH 220 A HOH 221 3 HOH HOH 221 A HOH 222 3 HOH HOH 222 A HOH 223 3 HOH HOH 223 A HOH 224 3 HOH HOH 224 A HOH 225 3 HOH HOH 225 A HOH 226 3 HOH HOH 226 A HOH 227 3 HOH HOH 227 A HOH 228 3 HOH HOH 228 A HOH 229 3 HOH HOH 229 A HOH 230 3 HOH HOH 230 A HOH 231 3 HOH HOH 231 A HOH 232 3 HOH HOH 232 A HOH 233 3 HOH HOH 233 A HOH 234 3 HOH HOH 234 A HOH 201 3 HOH HOH 201 B HOH 202 3 HOH HOH 202 B HOH 203 3 HOH HOH 203 B HOH 204 3 HOH HOH 204 B HOH 205 3 HOH HOH 205 B HOH 206 3 HOH HOH 206 B HOH 207 3 HOH HOH 207 B HOH 208 3 HOH HOH 208 B HOH 209 3 HOH HOH 209 B HOH 210 3 HOH HOH 210 B HOH 211 3 HOH HOH 211 B HOH 212 3 HOH HOH 212 B HOH 213 3 HOH HOH 213 B HOH 214 3 HOH HOH 214 B HOH 215 3 HOH HOH 215 B HOH 216 3 HOH HOH 216 B HOH 217 3 HOH HOH 217 B HOH 218 3 HOH HOH 218 B HOH 219 3 HOH HOH 219 B HOH 220 3 HOH HOH 220 B HOH 221 3 HOH HOH 221 B HOH 222 3 HOH HOH 222 B HOH 223 3 HOH HOH 223 B HOH 224 3 HOH HOH 224 B HOH 225 3 HOH HOH 225 B HOH 226 3 HOH HOH 226 B HOH 227 3 HOH HOH 227 B HOH 228 3 HOH HOH 228 B HOH 229 3 HOH HOH 229 B HOH 230 3 HOH HOH 230 B HOH 231 3 HOH HOH 231 B HOH 232 3 HOH HOH 232 B HOH 233 3 HOH HOH 233 B HOH 234 3 HOH HOH 234 B HOH 235 3 HOH HOH 235 B HOH 236 3 HOH HOH 236 B HOH 237 3 HOH HOH 237 B HOH 238 3 HOH HOH 238 B HOH 239 3 HOH HOH 239 B HOH 240 3 HOH HOH 240 B HOH 241 3 HOH HOH 241 B HOH 242 3 HOH HOH 242 B A 1 n 1 A 1 A A 2 n 2 A 2 A A 3 n 3 A 3 A A 4 n 4 A 4 A A 5 n 5 A 5 A A 6 n 6 A 6 A A 7 n 7 A 7 A A 8 n 8 A 8 A A 9 n 9 A 9 A A 10 n 10 A 10 A A 11 n 11 A 11 A A 1 n 1 A 1 B A 2 n 2 A 2 B A 3 n 3 A 3 B A 4 n 4 A 4 B A 5 n 5 A 5 B A 6 n 6 A 6 B A 7 n 7 A 7 B A 8 n 8 A 8 B A 9 n 9 A 9 B A 10 n 10 A 10 B A 11 n 11 A 11 B 0.120 0.128 0.118 0.126 0.151 0.158 986 1152 5.260 5.010 18730 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 HOH 225 U HOH 1 B HOH 217 V HOH 1 A A 1 0.079 SIDE CHAIN 1 A A 3 0.067 SIDE CHAIN 1 A A 4 0.055 SIDE CHAIN 1 A A 7 0.053 SIDE CHAIN 1 A A 9 0.055 SIDE CHAIN 1 B A 4 0.084 SIDE CHAIN 1 B A 11 0.056 SIDE CHAIN 1 4.90 0.50 129.30 134.20 A A A N1 C2 N3 A A A 3 3 3 N 0.158 0.118 0.126 1.00 41.00 5165 1152 23042 22972 6773 5.010 92.6 RANDOM 1,2,3,4 FREE R 1.000 AB INITIO PHASING BABINET 0 242.00 571.00 1.00 41.00 76 572 18 478 0 0.007 0.021 0.038 0.021 0.005 0.015 0.100 1.000 41.000 4JRD 23042 22972 4 -3.000 0.09440 1,2,3,4 34.3500 2.730 92.6 0.14190 1.00 1.10 4.720 1,2,3,4 1.20 73.1 data collection MxDC phasing SHELXD refinement SHELXL data reduction HKL-2000 data scaling HKL-2000 Crystal structure of the parallel double-stranded helix of poly(A) RNA 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N hydrog TYPE_2_PAIR A A 2 A N6 A 2 1_555 B A 1 B N7 A 1 1_555 hydrog TYPE_2_PAIR A A 2 A N7 A 2 1_555 B A 1 B N6 A 1 1_555 hydrog TYPE_2_PAIR A A 3 A N6 A 3 1_555 B A 2 B N7 A 2 1_555 hydrog TYPE_2_PAIR A A 3 A N7 A 3 1_555 B A 2 B N6 A 2 1_555 hydrog TYPE_2_PAIR A A 4 A N6 A 4 1_555 B A 3 B N7 A 3 1_555 hydrog TYPE_2_PAIR A A 4 A N7 A 4 1_555 B A 3 B N6 A 3 1_555 hydrog TYPE_2_PAIR A A 5 A N6 A 5 1_555 B A 4 B N7 A 4 1_555 hydrog TYPE_2_PAIR A A 5 A N7 A 5 1_555 B A 4 B N6 A 4 1_555 hydrog TYPE_2_PAIR A A 6 A N6 A 6 1_555 B A 5 B N7 A 5 1_555 hydrog TYPE_2_PAIR A A 6 A N7 A 6 1_555 B A 5 B N6 A 5 1_555 hydrog TYPE_2_PAIR A A 7 A N6 A 7 1_555 B A 6 B N7 A 6 1_555 hydrog TYPE_2_PAIR A A 7 A N7 A 7 1_555 B A 6 B N6 A 6 1_555 hydrog TYPE_2_PAIR A A 8 A N6 A 8 1_555 B A 7 B N7 A 7 1_555 hydrog TYPE_2_PAIR A A 8 A N7 A 8 1_555 B A 7 B N6 A 7 1_555 hydrog TYPE_2_PAIR A A 9 A N6 A 9 1_555 B A 8 B N7 A 8 1_555 hydrog TYPE_2_PAIR A A 9 A N7 A 9 1_555 B A 8 B N6 A 8 1_555 hydrog TYPE_2_PAIR A A 10 A N6 A 10 1_555 B A 9 B N7 A 9 1_555 hydrog TYPE_2_PAIR A A 10 A N7 A 10 1_555 B A 9 B N6 A 9 1_555 hydrog TYPE_2_PAIR A A 11 A N6 A 11 1_555 B A 10 B N7 A 10 1_555 hydrog TYPE_2_PAIR A A 11 A N7 A 11 1_555 B A 10 B N6 A 10 1_555 RNA PARALLEL DOUBLE HELIX, POLY(A), MRNA, PABP, Poly(A) motif, RNA 4JRD PDB 1 4JRD 1 11 4JRD 1 11 4JRD A 1 1 11 1 11 4JRD 1 11 4JRD B 1 1 11 BINDING SITE FOR RESIDUE NH4 A 101 A NH4 101 Software 3 BINDING SITE FOR RESIDUE NH4 A 102 A NH4 102 Software 4 BINDING SITE FOR RESIDUE NH4 A 103 A NH4 103 Software 4 BINDING SITE FOR RESIDUE NH4 A 104 A NH4 104 Software 6 BINDING SITE FOR RESIDUE NH4 A 105 A NH4 105 Software 4 BINDING SITE FOR RESIDUE NH4 A 106 A NH4 106 Software 1 BINDING SITE FOR RESIDUE NH4 A 107 A NH4 107 Software 5 BINDING SITE FOR RESIDUE NH4 A 108 A NH4 108 Software 5 BINDING SITE FOR RESIDUE NH4 A 109 A NH4 109 Software 5 BINDING SITE FOR RESIDUE NH4 A 110 A NH4 110 Software 5 BINDING SITE FOR RESIDUE NH4 A 111 A NH4 111 Software 4 BINDING SITE FOR RESIDUE NH4 B 101 B NH4 101 Software 4 BINDING SITE FOR RESIDUE NH4 B 102 B NH4 102 Software 5 BINDING SITE FOR RESIDUE NH4 B 103 B NH4 103 Software 6 BINDING SITE FOR RESIDUE NH4 B 104 B NH4 104 Software 6 BINDING SITE FOR RESIDUE NH4 B 105 B NH4 105 Software 5 BINDING SITE FOR RESIDUE NH4 B 106 B NH4 106 Software 5 BINDING SITE FOR RESIDUE NH4 B 107 B NH4 107 Software 5 A A 2 A A 2 3 1_555 A A 3 A A 3 3 1_555 B A 2 B A 2 3 1_555 A A 3 A A 3 4 1_555 A A 4 A A 4 4 1_555 A A 11 A A 11 4 7_645 B A 3 B A 3 4 1_555 A A 6 A A 6 4 1_555 A A 7 A A 7 4 1_555 A HOH 216 U HOH 4 7_655 B A 6 B A 6 4 1_555 A A 5 A A 5 6 7_545 A A 9 A A 9 6 1_555 A A 10 A A 10 6 1_555 B A 9 B A 9 6 1_555 B A 10 B A 10 6 1_555 B NH4 103 P NH4 6 7_545 A A 4 A A 4 4 7_545 A A 10 A A 10 4 1_555 A A 11 A A 11 4 1_555 B A 10 B A 10 4 1_555 A A 11 A A 11 1 1_555 A A 7 A A 7 5 1_555 A A 8 A A 8 5 1_555 A HOH 213 U HOH 5 7_555 B A 7 B A 7 5 1_555 B A 8 B A 8 5 1_555 A A 8 A A 8 5 1_555 A A 9 A A 9 5 1_555 A HOH 233 U HOH 5 1_555 B A 8 B A 8 5 1_555 B A 9 B A 9 5 1_555 A A 4 A A 4 5 1_555 A A 5 A A 5 5 1_555 A HOH 234 U HOH 5 1_555 B A 4 B A 4 5 1_555 B A 5 B A 5 5 1_555 A A 7 A A 7 5 1_555 A A 8 A A 8 5 1_555 A HOH 227 U HOH 5 1_555 B A 5 B A 5 5 1_555 B A 6 B A 6 5 1_555 A A 10 A A 10 4 1_555 A A 11 A A 11 4 1_555 B A 8 B A 8 4 1_555 B A 9 B A 9 4 1_555 A A 1 A A 1 4 3_645 A A 11 A A 11 4 1_555 B A 9 B A 9 4 1_555 B A 10 B A 10 4 1_555 A A 3 A A 3 5 1_555 A A 4 A A 4 5 1_555 B A 1 B A 1 5 1_555 B A 2 B A 2 5 1_555 B HOH 201 V HOH 5 1_555 A A 5 A A 5 6 1_555 A A 6 A A 6 6 1_555 A A 9 A A 9 6 7_655 A NH4 104 F NH4 6 7_655 B A 5 B A 5 6 1_555 B A 6 B A 6 6 1_555 A A 9 A A 9 6 1_555 A A 10 A A 10 6 1_555 B A 5 B A 5 6 7_645 B A 7 B A 7 6 1_555 B A 8 B A 8 6 1_555 B HOH 213 V HOH 6 7_645 A A 4 A A 4 5 1_555 A A 5 A A 5 5 1_555 B A 2 B A 2 5 1_555 B A 3 B A 3 5 1_555 B HOH 204 V HOH 5 7_555 A A 6 A A 6 5 1_555 A A 7 A A 7 5 1_555 B A 4 B A 4 5 1_555 B A 5 B A 5 5 1_555 B HOH 210 V HOH 5 7_545 A A 5 A A 5 5 1_555 A A 6 A A 6 5 1_555 B A 3 B A 3 5 1_555 B A 4 B A 4 5 1_555 B HOH 214 V HOH 5 1_555 92 P 41 21 2