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 10.2210/pdb2m23/pdb pdb_00002m23 sequence 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 2197.355 RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_ IBS1 U61G, U63G 1 syn polymer no no GGAGUAUGUAUUGGCACUGAGCAUACUCC GGAGUAUGUAUUGGCACUGAGCAUACUCC A polyribonucleotide no no CAGUGUC CAGUGUC B 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 n n n -9.700 1 19 A 1 A 29 -1.057 A_G1:C29_A 1 -9.138 -0.798 0.171 -0.443 11.612 1 19 A 2 A 28 -4.093 A_G2:C28_A 2 -5.530 -0.812 0.368 -0.436 0.293 1 20 A 3 A 27 -6.436 A_A3:U27_A 3 -6.177 -0.691 0.523 -0.255 0.554 1 19 A 4 A 26 -0.488 A_G4:C26_A 4 -8.675 0.021 -0.048 -0.160 4.514 1 20 A 5 A 25 5.247 A_U5:A25_A 5 -6.690 0.903 -0.358 -0.194 3.613 1 20 A 6 A 24 10.361 A_A6:U24_A 6 -14.363 -0.803 -0.416 -0.325 2.050 1 20 A 7 A 23 -5.836 A_U7:A23_A 7 -7.103 -0.798 -0.125 -0.168 7.161 1 19 A 8 A 22 -4.319 A_G8:C22_A 8 -1.878 0.526 -0.117 0.062 -2.938 1 28 A 9 A 21 3.718 A_U9:G21_A 9 2.429 1.933 0.174 -0.261 15.659 1 20 A 11 A 20 -43.927 A_U11:A20_A 10 -31.892 -1.692 -0.047 0.268 0.420 1 19 B 59 A 19 -0.577 B_C59:G19_A 11 -5.553 -0.511 -0.068 -0.212 7.378 1 20 B 60 A 18 8.537 B_A60:U18_A 12 -9.139 -0.882 0.391 -0.348 -4.398 1 19 B 61 A 17 0.663 B_G61:C17_A 13 -10.763 0.514 -0.187 -0.241 -3.105 1 20 B 62 A 16 -11.908 B_U62:A16_A 14 -11.160 -1.193 -0.108 -0.043 2.179 1 19 B 63 A 15 -3.488 B_G63:C15_A 15 1.891 0.635 -0.240 -0.226 4.845 1 28 B 64 A 14 -8.721 B_U64:G14_A 16 -5.544 1.439 -0.991 -0.543 6.083 1 19 B 65 A 13 9.784 B_C65:G13_A 17 -12.751 -0.498 -0.354 -0.040 2.239 31.564 A A 1 2 0.852 A A 29 28 2.160 0.463 -1.366 -1.235 AA_G1G2:C28C29_AA 1 -2.458 4.523 31.468 -2.329 2.204 3.979 35.635 A A 2 3 1.746 A A 28 27 4.019 1.068 -0.279 -1.637 AA_G2A3:U27C28_AA 2 -1.758 2.875 35.578 -2.865 0.144 2.668 30.741 A A 3 4 4.088 A A 27 26 2.821 2.166 0.176 -2.151 AA_A3G4:C26U27_AA 3 0.268 -0.506 30.666 -4.413 -0.287 2.110 38.426 A A 4 5 21.261 A A 26 25 2.783 13.706 -0.207 -1.441 AA_G4U5:A25C26_AA 4 0.751 -1.165 35.977 -3.512 0.387 2.632 24.360 A A 5 6 16.139 A A 25 24 3.229 6.718 0.016 -1.720 AA_U5A6:U24A25_AA 5 1.786 -4.291 23.362 -6.003 0.475 3.957 40.110 A A 6 7 -7.379 A A 24 23 3.744 -5.036 -1.302 -0.925 AA_A6U7:A23U24_AA 6 -4.979 7.295 39.505 -0.667 1.224 2.944 34.651 A A 7 8 -0.518 A A 23 22 2.933 -0.308 0.248 -1.666 AA_U7G8:C22A23_AA 7 -0.430 0.722 34.647 -2.754 -0.476 2.548 42.121 A A 8 9 21.175 A A 22 21 3.380 14.917 -0.089 -1.851 AA_G8U9:G21C22_AA 8 0.448 -0.635 39.502 -4.020 0.167 1.336 43.647 A A 9 11 -25.909 A A 21 20 5.252 -17.049 -3.594 -0.612 AA_U9U11:A20G21_AA 9 29.017 -44.096 28.204 1.225 8.320 3.445 49.283 A B 11 59 -12.403 A A 20 19 3.502 -10.216 1.372 -1.655 AB_U11C59:G19A20_AA 10 -9.598 11.651 47.367 -1.156 -2.424 3.192 30.735 B B 59 60 -12.973 A A 19 18 2.855 -6.807 -0.029 -1.937 BB_C59A60:U18G19_AA 11 -3.525 6.718 29.786 -2.401 -0.594 2.196 44.922 B B 60 61 27.179 A A 18 17 3.133 20.088 -0.623 -1.380 BB_A60G61:C17U18_AA 12 2.803 -3.792 40.296 -3.378 1.034 1.889 27.659 B B 61 62 19.540 A A 17 16 2.748 9.171 -0.969 -2.200 BB_G61U62:A16C17_AA 13 -0.205 0.436 26.121 -6.226 1.990 2.519 40.566 B B 62 63 19.257 A A 16 15 3.037 13.127 0.399 -1.130 BB_U62G63:C15A16_AA 14 -1.409 2.068 38.443 -2.910 -0.712 1.786 41.009 B B 63 64 31.706 A A 15 14 3.086 21.104 -0.783 -1.416 BB_G63U64:G14C15_AA 15 7.112 -10.685 34.656 -3.896 1.750 0.610 35.986 B B 64 65 55.192 A A 14 13 2.770 29.383 0.994 -1.250 BB_U64C65:G13G14_AA 16 -0.552 1.037 21.001 -4.802 -1.661 database_2 pdbx_database_status pdbx_nmr_software pdbx_nmr_spectrometer repository Initial release Database references Database references Data collection Database references Other 1 0 2013-12-18 1 1 2014-02-26 1 2 2014-03-12 1 3 2023-06-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model 2014-04-16 SPRSDE BMRB Y RCSB 2012-12-12 REL REL REL REL 4932 Saccharomyces cerevisiae sample 34 27 36 32 28 28 33 96 747 250 348 82 structures with the lowest energy 200 20 0.2 5 0.2 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H TOCSY 2D 1H-1H NOESY 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aliphatic 2D 1H-15N HSQC 2D 1H-13C HSQC aromatic 2D 1H-13C HSQC aromatic 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aromatic 2D 1H-1H NOESY 2D 1H-1H NOESY 2D 1H-1H NOESY 2D JNN HNN COSY 1D-31P F1,2 X-filtered 1H-1H NOESY F1,2 X-filtered 1H-1H TOCSY 0.5-0.9 mM 0.5-0.9 mM 110 mM 10 uM 0.5-0.9 mM 0.5-0.9 mM 110 mM 10 uM 0.5 mM [U-100% 13C; U-100% 15N] 0.5 mM 110 mM 10 uM 0.5 mM [U-100% 13C; U-100% 15N] 0.5 mM 110 mM 10 uM 0.6 mM [3',4',5',5'',5-100% 2H] 0.6 mM 110 mM 10 uM 0.5 mM [U-100% 13C; U-100% 15N] 0.5 mM 110 mM 10 uM 25.6 mg/mL 110 6.8 ambient 298 K 110 6.8 ambient 278 K 110 6.8 ambient 293 K molecular dynamics, torsion angle dynamics 1 lowest energy 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O 100% D2O 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O 90% H2O/10% D2O 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O 100% D2O 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O 90% H2O/10% D2O 0.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O 100% D2O 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O 90% H2O/10% D2O Goddard chemical shift assignment Sparky 3.1 Goddard data analysis Sparky 3.1 Goddard peak picking Sparky 3.1 Bruker Biospin collection TopSpin 1.3, 2.0, 2.1 Bruker Biospin processing TopSpin 1.3, 2.0, 2.1 Guntert, Braun and Wuthrich data analysis DYANA 1.5 Brunger, Adams, Clore, Gros, Nilges and Read structure solution 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 C 59 n 1 C 59 B A 60 n 2 A 60 B G 61 n 3 G 61 B U 62 n 4 U 62 B G 63 n 5 G 63 B U 64 n 6 U 64 B C 65 n 7 C 65 B author_and_software_defined_assembly PISA 2 dimeric 894 -2.8 6209 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 B O2 HO5' U C 12 59 1.52 1 A A H2' O4' C C 28 29 1.57 2 A A H2' O4' C C 28 29 1.54 3 A A H2' O4' C C 28 29 1.51 3 A B O2 HO5' U C 12 59 1.56 4 A A H2' O4' C C 28 29 1.55 5 A A H2' O4' C C 28 29 1.58 6 A A H2' O4' C C 28 29 1.54 7 A A H2' O4' C C 28 29 1.57 9 A A H2' O4' C C 28 29 1.59 10 A A H2' O4' C C 28 29 1.53 11 A A H2' O4' C C 28 29 1.54 13 A A H2' O4' C C 28 29 1.58 13 A B H1' O5' U C 12 59 1.60 14 A A H2' O4' C C 28 29 1.57 15 A A H2' O4' C C 28 29 1.53 16 A B H1' O5' U C 12 59 1.56 16 A B O2 HO5' U C 12 59 1.56 16 A A H2' O4' C C 28 29 1.60 17 A B O2 HO5' U C 12 59 1.49 17 A A H2' O4' C C 28 29 1.56 17 A B H1' O5' U C 12 59 1.57 19 A A H2' O4' C C 28 29 1.58 20 A A H2' O4' C C 28 29 1.56 lowest energy, model 1 NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1 1 N N 2 N N hydrog G-C PAIR A G 1 A O6 G 1 1_555 A C 28 A N4 C 28 1_555 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 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 N6 A 10 1_555 A A 20 A N1 A 20 1_555 hydrog WATSON-CRICK A U 11 A N3 U 11 1_555 A A 20 A N1 A 20 1_555 hydrog WATSON-CRICK A U 11 A O4 U 11 1_555 A A 20 A N6 A 20 1_555 hydrog U-A PAIR A U 12 A O4 U 12 1_555 B A 60 B N6 A 2 1_555 hydrog WATSON-CRICK A G 13 A N1 G 13 1_555 B C 65 B N3 C 7 1_555 hydrog WATSON-CRICK A G 13 A N2 G 13 1_555 B C 65 B O2 C 7 1_555 hydrog WATSON-CRICK A G 13 A O6 G 13 1_555 B C 65 B N4 C 7 1_555 hydrog TYPE_28_PAIR A G 14 A N1 G 14 1_555 B U 64 B O2 U 6 1_555 hydrog TYPE_28_PAIR A G 14 A O6 G 14 1_555 B U 64 B N3 U 6 1_555 hydrog G-C PAIR A G 14 A N1 G 14 1_555 B C 65 B O2 C 7 1_555 hydrog WATSON-CRICK A C 15 A N3 C 15 1_555 B G 63 B N1 G 5 1_555 hydrog WATSON-CRICK A C 15 A N4 C 15 1_555 B G 63 B O6 G 5 1_555 hydrog WATSON-CRICK A C 15 A O2 C 15 1_555 B G 63 B N2 G 5 1_555 hydrog WATSON-CRICK A A 16 A N1 A 16 1_555 B U 62 B N3 U 4 1_555 hydrog WATSON-CRICK A A 16 A N6 A 16 1_555 B U 62 B O4 U 4 1_555 hydrog WATSON-CRICK A C 17 A N3 C 17 1_555 B G 61 B N1 G 3 1_555 hydrog WATSON-CRICK A C 17 A N4 C 17 1_555 B G 61 B O6 G 3 1_555 hydrog WATSON-CRICK A C 17 A O2 C 17 1_555 B G 61 B N2 G 3 1_555 hydrog WATSON-CRICK A U 18 A N3 U 18 1_555 B A 60 B N1 A 2 1_555 hydrog WATSON-CRICK A U 18 A O4 U 18 1_555 B A 60 B N6 A 2 1_555 hydrog WATSON-CRICK A G 19 A N1 G 19 1_555 B C 59 B N3 C 1 1_555 hydrog WATSON-CRICK A G 19 A N2 G 19 1_555 B C 59 B O2 C 1 1_555 hydrog WATSON-CRICK A G 19 A O6 G 19 1_555 B C 59 B N4 C 1 1_555 RNA group II intron, ribozyme, hairpin, EBS1, IBS1, splicing, 5'-splice site, RNA 2M23 PDB 1 2M23 GGAGUAUGUAUUGGCACUGAGCAUACUCC 2M23 PDB 2 2M23 CAGUGUC 1 29 2M23 1 29 2M23 A 1 1 29 59 65 2M23 59 65 2M23 B 2 1 7