1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Newby, M.I. Greenbaum, N.L. 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 US Nat.Struct.Biol. NSBIEW 2024 1072-8368 9 958 965 10.1038/nsb873 12426583 Sculpting of the Spliceosomal Branch Site Recognition Motif by a Conserved Pseudouridine 2002 10.2210/pdb1lmv/pdb pdb_00001lmv 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 unmodified U2 snRNA. Region of U2 snRNA that pairs with the intron branch site during spliceosome assembly (nucleotides 34-39 in yeast U2 snRNA). 2912.775 5'-R(*GP*GP*UP*GP*UP*AP*GP*UP*A)-3' 1 nat polymer Intron branch site sequence. Region of the pre-mRNA intron that contains the conserved branch site sequence, and pairs with U2 snRNA during spliceosome assembly. 3104.925 5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3' 1 nat polymer no no GGUGUAGUA GGUGUAGUA A polyribonucleotide no no UACUAACACC UACUAACACC B polyribonucleotide n n n n n n n n n n n n n n n n n n n baker's yeast Saccharomyces sample 4932 Saccharomyces cerevisiae baker's yeast Saccharomyces sample 4932 Saccharomyces cerevisiae -25.496 1 19 A 1 B 10 0.826 A_G1:C10_B 1 -12.442 -0.772 -0.612 -0.120 -6.382 1 19 A 2 B 9 0.803 A_G2:C9_B 2 -5.566 -0.728 0.067 -0.098 5.406 1 20 A 3 B 8 -8.241 A_U3:A8_B 3 -21.561 -0.690 -0.053 0.013 5.166 1 19 A 4 B 7 -0.983 A_G4:C7_B 4 -16.490 -0.565 0.606 -0.207 11.833 1 A 5 B 6 15.962 A_U5:A6_B 5 -25.806 -0.180 1.028 0.036 1.241 1 20 A 6 B 4 2.161 A_A6:U4_B 6 -0.033 0.274 0.047 0.002 1.594 1 19 A 7 B 3 -2.768 A_G7:C3_B 7 -14.611 -0.659 -0.093 -0.218 6.883 1 20 A 8 B 2 -2.411 A_U8:A2_B 8 -19.409 -0.487 -0.372 -0.023 1.753 1 20 A 9 B 1 3.680 A_A9:U1_B 9 -1.678 0.188 0.287 -0.039 2.739 28.186 A A 1 2 -0.174 B B 10 9 2.732 -0.085 -0.199 -0.983 AA_G1G2:C9C10_BB 1 -3.347 6.889 27.991 -2.001 -0.248 2.754 32.497 A A 2 3 6.039 B B 9 8 2.899 3.373 -0.744 -1.005 AA_G2U3:A8C9_BB 2 1.176 -2.105 32.306 -2.308 1.508 2.193 36.966 A A 3 4 22.135 B B 8 7 2.921 13.668 0.547 -1.167 AA_U3G4:C7A8_BB 3 -5.614 9.091 33.979 -3.346 -1.481 2.799 34.661 A A 4 5 2.322 B B 7 6 2.899 1.382 0.805 -1.143 AA_G4U5:A6C7_BB 4 -2.117 3.556 34.571 -2.104 -1.635 4.663 55.450 A A 5 6 2.182 B B 6 4 5.611 1.991 1.684 -1.611 AA_U5A6:U4A6_BB 5 -20.008 21.930 51.947 -1.922 -3.719 3.175 28.284 A A 6 7 0.483 B B 4 3 3.223 0.236 -0.756 -1.853 AA_A6G7:C3U4_BB 6 1.167 -2.389 28.260 -3.846 1.813 2.871 35.001 A A 7 8 1.593 B B 3 2 2.908 0.958 -0.031 -1.339 AA_G7U8:A2C3_BB 7 0.644 -1.071 34.983 -2.353 0.138 2.353 37.639 A A 8 9 21.332 B B 2 1 3.101 13.375 0.204 -1.289 AA_U8A9:U1A2_BB 8 -8.049 12.837 34.357 -3.519 -1.231 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-11-27 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine SEQUENCE Position 35 in U2 snRNA sequences from S. cerevisiae is a pseudouridine. This corresponds to position 5 on strand A, which is a uridine in 1LMV, and a pseudouridine in 1LPW. RCSB Y RCSB 2002-05-02 REL REL This structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times to assess the buildup rate of each NOE, thereby resolving some of the spectral overlap. structures with the lowest energy 300 10 2D NOESY 2D NOESY 2D TOCSY DQF-COSY 50mM sodium chloride 6.4 ambient 278 K 50mM sodium chloride 6.4 ambient 293 K torsion angle molecular dynamics, followed by congugate gradient minimization 2 lowest energy 1mM unmodified U2 snNRA - intron branch site duplex, 10mM sodium phosphate, 0.1mM EDTA 90% H2O/10% D2O 1mM unmodified U2 snNRA - intron branch site duplex, 10mM sodium phosphate, 0.1mM EDTA 100% D2O Varian, Inc. collection VNMR 5.3 T.D. Goddard and D.G. Kneller data analysis Sparky 3.69 Brunger structure solution X-PLOR 3.851 Brunger refinement X-PLOR 3.851 720 Varian UNITYPLUS G 1 n 1 G 1 A G 2 n 2 G 2 A U 3 n 3 U 3 A G 4 n 4 G 4 A U 5 n 5 U 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A U 8 n 8 U 8 A A 9 n 9 A 9 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 A 8 n 8 A 8 B C 9 n 9 C 9 B C 10 n 10 C 10 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 4.46 0.70 108.50 112.96 A A A O4' C1' N9 G G G 1 1 1 N 1 4.57 0.70 108.50 113.07 A A A O4' C1' N9 G G G 2 2 2 N 1 4.63 0.70 108.50 113.13 A A A O4' C1' N9 A A A 9 9 9 N 1 5.57 0.70 108.50 114.07 B B B O4' C1' N1 U U U 1 1 1 N 1 4.96 0.70 108.50 113.46 B B B O4' C1' N9 A A A 2 2 2 N 1 4.66 0.70 108.50 113.16 B B B O4' C1' N1 C C C 3 3 3 N 1 5.29 0.70 108.50 113.79 B B B O4' C1' N1 U U U 4 4 4 N 1 5.07 0.70 108.50 113.57 B B B O4' C1' N9 A A A 6 6 6 N 1 5.57 0.70 108.50 114.07 B B B O4' C1' N1 C C C 7 7 7 N 1 6.30 0.70 108.50 114.80 B B B O4' C1' N1 C C C 10 10 10 N 2 4.83 0.70 108.50 113.33 A A A O4' C1' N9 G G G 1 1 1 N 2 4.96 0.70 108.50 113.46 A A A O4' C1' N9 G G G 2 2 2 N 2 4.93 0.70 108.50 113.43 A A A O4' C1' N1 U U U 3 3 3 N 2 4.35 0.70 108.50 112.85 A A A O4' C1' N9 G G G 7 7 7 N 2 4.56 0.70 108.50 113.06 A A A O4' C1' N9 A A A 9 9 9 N 2 4.73 0.70 108.50 113.23 B B B O4' C1' N1 U U U 1 1 1 N 2 5.21 0.70 108.50 113.71 B B B O4' C1' N1 C C C 3 3 3 N 2 5.78 0.70 108.50 114.28 B B B O4' C1' N1 U U U 4 4 4 N 2 5.61 0.70 108.50 114.11 B B B O4' C1' N9 A A A 6 6 6 N 2 6.03 0.70 108.50 114.53 B B B O4' C1' N1 C C C 7 7 7 N 2 5.94 0.70 108.50 114.44 B B B O4' C1' N1 C C C 10 10 10 N 3 4.98 0.70 108.50 113.48 A A A O4' C1' N9 G G G 1 1 1 N 3 5.03 0.70 108.50 113.53 A A A O4' C1' N9 G G G 2 2 2 N 3 4.72 0.70 108.50 113.22 A A A O4' C1' N9 A A A 9 9 9 N 3 5.80 0.70 108.50 114.30 B B B O4' C1' N1 U U U 1 1 1 N 3 4.27 0.70 108.50 112.77 B B B O4' C1' N9 A A A 2 2 2 N 3 4.42 0.70 108.50 112.92 B B B O4' C1' N1 C C C 3 3 3 N 3 4.98 0.70 108.50 113.48 B B B O4' C1' N9 A A A 6 6 6 N 3 5.61 0.70 108.50 114.11 B B B O4' C1' N1 C C C 7 7 7 N 3 4.31 0.70 108.50 112.81 B B B O4' C1' N1 C C C 9 9 9 N 3 6.19 0.70 108.50 114.69 B B B O4' C1' N1 C C C 10 10 10 N 4 4.52 0.70 108.50 113.02 A A A O4' C1' N9 A A A 9 9 9 N 4 5.55 0.70 108.50 114.05 B B B O4' C1' N1 U U U 1 1 1 N 4 5.10 0.70 108.50 113.60 B B B O4' C1' N1 C C C 3 3 3 N 4 5.91 0.70 108.50 114.41 B B B O4' C1' N1 U U U 4 4 4 N 4 4.74 0.70 108.50 113.24 B B B O4' C1' N9 A A A 5 5 5 N 4 5.21 0.70 108.50 113.71 B B B O4' C1' N9 A A A 6 6 6 N 4 4.53 0.70 108.50 113.03 B B B O4' C1' N1 C C C 7 7 7 N 4 6.09 0.70 108.50 114.59 B B B O4' C1' N1 C C C 10 10 10 N 5 4.37 0.70 108.50 112.87 A A A O4' C1' N9 G G G 1 1 1 N 5 4.99 0.70 108.50 113.49 A A A O4' C1' N9 G G G 2 2 2 N 5 4.24 0.70 108.50 112.74 A A A O4' C1' N1 U U U 3 3 3 N 5 -4.47 0.70 101.30 96.83 A A A C3' C2' C1' A A A 6 6 6 N 5 4.99 0.70 108.50 113.49 A A A O4' C1' N9 A A A 9 9 9 N 5 5.68 0.70 108.50 114.18 B B B O4' C1' N1 U U U 1 1 1 N 5 4.76 0.70 108.50 113.26 B B B O4' C1' N1 U U U 4 4 4 N 5 5.01 0.70 108.50 113.51 B B B O4' C1' N9 A A A 6 6 6 N 5 5.71 0.70 108.50 114.21 B B B O4' C1' N1 C C C 7 7 7 N 5 4.36 0.70 108.50 112.86 B B B O4' C1' N9 A A A 8 8 8 N 5 5.77 0.70 108.50 114.27 B B B O4' C1' N1 C C C 10 10 10 N 6 4.29 0.70 108.50 112.79 A A A O4' C1' N9 G G G 1 1 1 N 6 4.29 0.70 108.50 112.79 A A A O4' C1' N9 G G G 2 2 2 N 6 4.71 0.70 108.50 113.21 A A A O4' C1' N9 G G G 7 7 7 N 6 4.56 0.70 108.50 113.06 A A A O4' C1' N9 A A A 9 9 9 N 6 5.64 0.70 108.50 114.14 B B B O4' C1' N1 U U U 1 1 1 N 6 4.32 0.70 108.50 112.82 B B B O4' C1' N1 C C C 3 3 3 N 6 5.15 0.70 108.50 113.65 B B B O4' C1' N1 U U U 4 4 4 N 6 5.13 0.70 108.50 113.63 B B B O4' C1' N9 A A A 6 6 6 N 6 5.47 0.70 108.50 113.97 B B B O4' C1' N1 C C C 7 7 7 N 6 5.70 0.70 108.50 114.20 B B B O4' C1' N1 C C C 10 10 10 N 7 4.23 0.70 108.50 112.73 A A A O4' C1' N9 G G G 2 2 2 N 7 4.30 0.70 108.50 112.80 A A A O4' C1' N1 U U U 3 3 3 N 7 4.53 0.70 108.50 113.03 A A A O4' C1' N9 A A A 9 9 9 N 7 5.53 0.70 108.50 114.03 B B B O4' C1' N1 U U U 1 1 1 N 7 4.40 0.70 108.50 112.90 B B B O4' C1' N1 C C C 3 3 3 N 7 6.00 0.70 108.50 114.50 B B B O4' C1' N1 U U U 4 4 4 N 7 5.00 0.70 108.50 113.50 B B B O4' C1' N9 A A A 6 6 6 N 7 5.81 0.70 108.50 114.31 B B B O4' C1' N1 C C C 7 7 7 N 7 4.72 0.70 108.50 113.22 B B B O4' C1' N9 A A A 8 8 8 N 7 5.41 0.70 108.50 113.91 B B B O4' C1' N1 C C C 10 10 10 N 8 4.42 0.70 108.50 112.92 A A A O4' C1' N9 G G G 1 1 1 N 8 5.21 0.70 108.50 113.71 A A A O4' C1' N9 A A A 9 9 9 N 8 5.56 0.70 108.50 114.06 B B B O4' C1' N1 U U U 1 1 1 N 8 4.95 0.70 108.50 113.45 B B B O4' C1' N9 A A A 2 2 2 N 8 5.66 0.70 108.50 114.16 B B B O4' C1' N1 C C C 3 3 3 N 8 5.72 0.70 108.50 114.22 B B B O4' C1' N1 U U U 4 4 4 N 8 4.26 0.70 108.50 112.76 B B B O4' C1' N1 C C C 7 7 7 N 8 4.20 0.70 108.50 112.70 B B B O4' C1' N1 C C C 9 9 9 N 8 5.77 0.70 108.50 114.27 B B B O4' C1' N1 C C C 10 10 10 N 9 4.75 0.70 108.50 113.25 A A A O4' C1' N9 G G G 1 1 1 N 9 4.63 0.70 108.50 113.13 A A A O4' C1' N9 G G G 2 2 2 N 9 4.21 0.70 108.50 112.71 A A A O4' C1' N1 U U U 8 8 8 N 9 4.63 0.70 108.50 113.13 A A A O4' C1' N9 A A A 9 9 9 N 9 4.60 0.70 108.50 113.10 B B B O4' C1' N1 U U U 1 1 1 N 9 4.28 0.70 108.50 112.78 B B B O4' C1' N1 C C C 3 3 3 N 9 5.10 0.70 108.50 113.60 B B B O4' C1' N1 U U U 4 4 4 N 9 4.48 0.70 108.50 112.98 B B B O4' C1' N9 A A A 6 6 6 N 9 5.87 0.70 108.50 114.37 B B B O4' C1' N1 C C C 7 7 7 N 9 5.63 0.70 108.50 114.13 B B B O4' C1' N1 C C C 10 10 10 N 10 4.74 0.70 108.50 113.24 A A A O4' C1' N9 A A A 9 9 9 N 10 5.68 0.70 108.50 114.18 B B B O4' C1' N1 U U U 1 1 1 N 10 5.44 0.70 108.50 113.94 B B B O4' C1' N1 C C C 3 3 3 N 10 5.23 0.70 108.50 113.73 B B B O4' C1' N1 U U U 4 4 4 N 10 5.77 0.70 108.50 114.27 B B B O4' C1' N9 A A A 6 6 6 N 10 5.15 0.70 108.50 113.65 B B B O4' C1' N1 C C C 7 7 7 N 10 4.59 0.70 108.50 113.09 B B B O4' C1' N1 C C C 9 9 9 N 10 5.54 0.70 108.50 114.04 B B B O4' C1' N1 C C C 10 10 10 N Solution structure of the unmodified U2 snRNA-intron branch site helix from S. cerevisiae 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 10 B N3 C 10 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 10 B O2 C 10 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 10 B N4 C 10 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 9 B N3 C 9 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 9 B O2 C 9 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 9 B N4 C 9 1_555 hydrog WATSON-CRICK A U 3 A N3 U 3 1_555 B A 8 B N1 A 8 1_555 hydrog WATSON-CRICK A U 3 A O4 U 3 1_555 B A 8 B N6 A 8 1_555 hydrog G-A MISPAIR A G 4 A O6 G 4 1_555 B A 6 B N6 A 6 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B C 7 B N3 C 7 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B C 7 B O2 C 7 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B C 7 B N4 C 7 1_555 hydrog U-A PAIR A U 5 A O4 U 5 1_555 B A 5 B N6 A 5 1_555 hydrog U-A PAIR A U 5 A N3 U 5 1_555 B A 6 B N1 A 6 1_555 hydrog WATSON-CRICK A A 6 A N1 A 6 1_555 B U 4 B N3 U 4 1_555 hydrog WATSON-CRICK A A 6 A N6 A 6 1_555 B U 4 B O4 U 4 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 3 B N3 C 3 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 3 B O2 C 3 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 3 B N4 C 3 1_555 hydrog WATSON-CRICK A U 8 A N3 U 8 1_555 B A 2 B N1 A 2 1_555 hydrog WATSON-CRICK A U 8 A O4 U 8 1_555 B A 2 B N6 A 2 1_555 hydrog WATSON-CRICK A A 9 A N1 A 9 1_555 B U 1 B N3 U 1 1_555 hydrog WATSON-CRICK A A 9 A N6 A 9 1_555 B U 1 B O4 U 1 1_555 RNA U2 snRNA, branch site, solution structure, A-form helix, RNA 1LMV PDB 1 1LMV 1LMV PDB 2 1LMV 1 9 1LMV 1 9 1LMV A 1 1 9 1 10 1LMV 1 10 1LMV B 2 1 10