1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kruschel, D. Skilandat, M. Sigel, R.K.O. 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 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 Rna RNARFU 2122 1355-8382 20 295 307 10.1261/rna.041137.113 24448450 NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition. 2014 the sequence was produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-polymerase 9301.547 RNA (29-MER) d3'EBS1 A15C, A17C 1 syn polymer no no GGAGUAUGUAUUGGCACUGAGCAUACUCC GGAGUAUGUAUUGGCACUGAGCAUACUCC 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 -4.707 1 19 A 1 A 29 -2.165 A_G1:C29_A 1 -3.708 -0.746 0.131 -0.380 1.735 1 19 A 2 A 28 0.549 A_G2:C28_A 2 -3.898 -0.773 0.108 -0.328 -7.020 1 20 A 3 A 27 -4.030 A_A3:U27_A 3 1.023 -0.834 -0.218 -0.122 -5.668 1 19 A 4 A 26 0.185 A_G4:C26_A 4 -10.373 0.530 -0.288 -0.213 0.345 1 20 A 5 A 25 12.374 A_U5:A25_A 5 -5.698 0.519 -0.217 -0.320 -0.636 1 20 A 6 A 24 15.510 A_A6:U24_A 6 -14.543 -0.544 -0.298 -0.315 1.034 1 20 A 7 A 23 10.706 A_U7:A23_A 7 -9.337 0.116 -0.483 -0.402 0.601 1 19 A 8 A 22 -6.640 A_G8:C22_A 8 -1.392 0.780 -0.427 -0.189 3.928 1 28 A 9 A 21 -8.674 A_U9:G21_A 9 3.395 1.646 -0.292 -0.160 7.845 1 A 10 A 20 -52.005 A_A10:A20_A 10 -3.090 1.841 -2.450 -0.398 3.368 32.532 A A 1 2 1.792 A A 29 28 3.363 1.004 -0.931 -0.709 AA_G1G2:C28C29_AA 1 -1.031 1.842 32.501 -1.446 1.477 4.651 37.906 A A 2 3 -18.098 A A 28 27 4.595 -11.576 -0.162 -0.934 AA_G2A3:U27C28_AA 2 2.058 -3.217 36.100 0.712 0.632 2.006 32.035 A A 3 4 20.895 A A 27 26 2.751 11.296 0.070 -1.675 AA_A3G4:C26U27_AA 3 0.063 -0.117 30.026 -4.567 -0.117 2.240 35.173 A A 4 5 22.667 A A 26 25 2.868 13.370 -0.167 -1.158 AA_G4U5:A25C26_AA 4 -1.258 2.132 32.584 -3.538 0.124 1.964 37.195 A A 5 6 36.053 A A 25 24 2.986 21.627 -0.143 -0.852 AA_U5A6:U24A25_AA 5 1.763 -2.939 30.393 -3.754 0.421 3.468 39.814 A A 6 7 2.828 A A 24 23 3.516 1.925 -0.120 -0.977 AA_A6U7:A23U24_AA 6 -0.644 0.946 39.765 -1.672 0.097 2.213 35.661 A A 7 8 19.534 A A 23 22 2.992 11.742 -1.008 -1.688 AA_U7G8:C22A23_AA 7 2.686 -4.469 33.627 -4.153 1.966 2.313 35.029 A A 8 9 25.574 A A 22 21 3.287 14.908 -0.525 -1.488 AA_G8U9:G21C22_AA 8 3.175 -5.446 31.633 -4.498 1.303 2.940 32.935 A A 9 10 -18.153 A A 21 20 3.929 -9.959 -2.570 -0.640 AA_U9A10:A20G21_AA 9 10.475 -19.092 29.673 0.752 6.513 repository Initial release Database references Database references 1 0 2013-12-18 1 1 2014-02-26 1 2 2014-03-12 2014-04-16 SPRSDE BMRB Y RCSB 2012-12-12 REL REL REL 4932 Saccharomyces cerevisiae sample 28 16 29 16 16 16 27 48 511 176 250 45 structures with the lowest energy 200 20 0.2 5 0.2 2D 1H-1H NOESY 2D 1H-1H TOCSY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aromatic 2D 1H-15N HSQC 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aromatic 2D JNN HNN COSY 2D 1H-1H NOESY 2D 1H-1H NOESY 1D 31P 2D 1H-1H NOESY 2D 1H-13C HSQC 0.4-1.2 mM 10 mM 10 uM 0.4-1.2 mM 10 mM 10 uM 0.7 mM [U-100% 13C; U-100% 15N] 10 mM 10 uM 0.7 mM [U-100% 13C; U-100% 15N] 10 mM 10 uM 25.6 mg/mL 0.7 mM [U-100% 13C; U-100% 15N] 10 mM 10 uM 0.6 mM [3',4',5',5'',5, 100% 2H] 10 mM 10 uM 10 6.8 ambient 293 K 10 6.8 ambient 278 K 10 6.8 ambient 298 K 10 6.8 ambient 283 K molecular dynamics, torsion angle dynamics 1 lowest energy 0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O 100% D2O 0.4-1.2 mM RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O 90% H2O/10% D2O 0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O 90% H2O/10% D2O 0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O 90% H2O/10% D2O 0.7 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O 100% D2O 0.6 mM [3',4',5',5'',5, 100% 2H] RNA (29-MER), 10 mM potassium chloride, 10 uM EDTA, 100% D2O 100% D2O Bruker Biospin collection TOPSPIN 1.3, 2.0, 2.1 Bruker Biospin processing TOPSPIN 1.3, 2.0, 2.1 Goddard chemical shift assignment SPARKY 3.1 Goddard data analysis SPARKY 3.1 Goddard peak picking SPARKY 3.1 Guntert, Braun and Wuthrich data analysis DYANA 1.5 Brunger, Adams, Clore, Gros, Nilges and Read structure solution CNSSOLVE 1.2 Brunger, Adams, Clore, Gros, Nilges and Read refinement CNSSOLVE 1.2 Schwieters, Kuszewski, Tjandra and Clore structure solution X-PLOR_NIH 2.24 Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR_NIH 2.24 700 Bruker Avance Bruker Avance 600 Bruker Avance Bruker Avance 500 Bruker Avance Bruker Avance 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 U 5 n 5 U 5 A A 6 n 6 A 6 A U 7 n 7 U 7 A G 8 n 8 G 8 A U 9 n 9 U 9 A A 10 n 10 A 10 A U 11 n 11 U 11 A U 12 n 12 U 12 A G 13 n 13 G 13 A G 14 n 14 G 14 A C 15 n 15 C 15 A A 16 n 16 A 16 A C 17 n 17 C 17 A U 18 n 18 U 18 A G 19 n 19 G 19 A A 20 n 20 A 20 A G 21 n 21 G 21 A C 22 n 22 C 22 A A 23 n 23 A 23 A U 24 n 24 U 24 A A 25 n 25 A 25 A C 26 n 26 C 26 A U 27 n 27 U 27 A C 28 n 28 C 28 A C 29 n 29 C 29 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 H3 N1 U A 7 23 1.56 2 A A O2' H6 A U 10 11 1.45 2 A A O2' H6 U U 11 12 1.51 4 A A O2' H6 A U 10 11 1.45 5 A A H4' O4' U G 18 19 1.51 5 A A H3 N1 U A 7 23 1.58 6 A A O2' H6 U U 11 12 1.44 6 A A HO2' O5' U U 11 12 1.51 7 A A O2' H6 U U 11 12 1.51 8 A A H3 N1 U A 7 23 1.57 8 A A O2' H6 A U 10 11 1.59 9 A A O4 H61 U A 11 20 1.35 9 A A H3 N1 U A 7 23 1.57 10 A A H1 O2' G G 13 19 1.41 10 A A O2' H6 A U 10 11 1.45 10 A A H3 N1 U A 11 20 1.59 11 A A O2' H6 U U 11 12 1.47 11 A A O2' H5' G A 19 20 1.49 12 A A HO2' O5' C A 15 16 1.39 12 A A O2' H6 U U 11 12 1.54 12 A A H3 N1 U A 7 23 1.56 12 A A HO2' O5' U U 11 12 1.59 13 A A O2' H6 A U 10 11 1.45 13 A A O2' H6 U U 11 12 1.50 13 A A H3 N1 U A 7 23 1.56 14 A A HO2' O5' A U 10 11 1.56 14 A A O3' H8 U G 18 19 1.57 15 A A O2' H6 A U 10 11 1.44 15 A A O2' H6 U U 11 12 1.54 16 A A O4 H61 U A 11 20 1.46 16 A A H3 N1 U A 11 20 1.50 16 A A O2' H6 A U 10 11 1.59 17 A A O3' H8 U G 18 19 1.52 18 A A O2' H6 A U 10 11 1.45 19 A A HO2' O5' A U 10 11 1.40 19 A A O2' H6 A U 10 11 1.49 19 A A H3 N1 U A 7 23 1.56 19 A A H4' O4' C A 15 16 1.57 20 A A HO2' O5' A U 10 11 1.41 20 A A O2' H6 U U 11 12 1.50 20 A A H3 N1 U A 7 23 1.55 29-MER lowest energy, model1 NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 29 A N3 C 29 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 29 A O2 C 29 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 29 A N4 C 29 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 28 A N3 C 28 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 28 A O2 C 28 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 28 A N4 C 28 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 27 A N3 U 27 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 27 A O4 U 27 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 26 A N3 C 26 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 26 A O2 C 26 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 26 A N4 C 26 1_555 hydrog G-U MISPAIR A G 4 A N2 G 4 1_555 A U 27 A O2 U 27 1_555 hydrog WATSON-CRICK A U 5 A N3 U 5 1_555 A A 25 A N1 A 25 1_555 hydrog WATSON-CRICK A U 5 A O4 U 5 1_555 A A 25 A N6 A 25 1_555 hydrog WATSON-CRICK A A 6 A N1 A 6 1_555 A U 24 A N3 U 24 1_555 hydrog WATSON-CRICK A A 6 A N6 A 6 1_555 A U 24 A O4 U 24 1_555 hydrog WATSON-CRICK A U 7 A N3 U 7 1_555 A A 23 A N1 A 23 1_555 hydrog WATSON-CRICK A U 7 A O4 U 7 1_555 A A 23 A N6 A 23 1_555 hydrog WATSON-CRICK A G 8 A N1 G 8 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 8 A N2 G 8 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 8 A O6 G 8 1_555 A C 22 A N4 C 22 1_555 hydrog TYPE_28_PAIR A U 9 A N3 U 9 1_555 A G 21 A O6 G 21 1_555 hydrog TYPE_28_PAIR A U 9 A O2 U 9 1_555 A G 21 A N1 G 21 1_555 hydrog A-A MISPAIR A A 10 A N1 A 10 1_555 A A 20 A N6 A 20 1_555 RNA group II intron, ribozyme, splicing, EBS1, hairpin, RNA 2M24 PDB 1 2M24 GGAGUAUGUAUUGGCACUGAGCAUACUCC 1 29 2M24 1 29 2M24 A 1 1 29