1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Comolli, L.R. Ulyanov, N.B. James, T.L. Gmeiner, W.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 Nucleic Acids Res. NARHAD 0389 0305-1048 30 4371 4379 10.1093/nar/gkf560 12384583 NMR Structure of the 3' Stem-Loop from Human U4 snRNA 2002 10.2210/pdb1mfj/pdb pdb_00001mfj 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3'stem-loop of human U4 snRNA 6422.879 5'-R(*GP*AP*CP*AP*GP*UP*CP*UP*CP*UP*AP*CP*GP*GP*AP*GP*AP*CP*UP*G)-3' 1 syn polymer no no GACAGUCUCUACGGAGACUG GACAGUCUCUACGGAGACUG A polyribonucleotide n n n n n n n n n n n n n n n n n n n n 46.208 A 2 A 1 -8.191 A_A2:G1_A 1 -31.163 -6.578 -1.033 -2.936 -17.006 1 19 A 3 A 20 -1.520 A_C3:G20_A 2 -0.918 -0.060 0.234 -0.113 -4.413 1 20 A 4 A 19 -4.577 A_A4:U19_A 3 -13.184 -0.021 0.090 -0.124 -6.629 1 19 A 5 A 18 -0.990 A_G5:C18_A 4 -19.337 0.053 0.040 -0.162 3.197 1 20 A 6 A 17 -4.386 A_U6:A17_A 5 -14.657 0.060 0.065 -0.134 12.561 1 19 A 7 A 16 -1.075 A_C7:G16_A 6 -13.527 -0.111 -0.158 -0.118 12.678 1 20 A 8 A 15 -1.356 A_U8:A15_A 7 -13.419 0.064 -0.457 -0.131 5.190 1 19 A 9 A 14 -4.391 A_C9:G14_A 8 20.834 0.043 -0.592 -0.276 7.233 2 A 10 A 13 -99.591 A_U10:G13_A 9 -13.174 0.898 -0.748 -5.524 -0.856 42.763 A A 2 3 -14.048 A A 1 20 2.952 -8.703 -3.683 -2.495 AA_A2C3:G20G1_AA 1 35.121 -56.692 23.183 -3.050 6.552 2.613 29.609 A A 3 4 14.012 A A 20 19 3.025 7.094 -0.416 -1.387 AA_C3A4:U19G20_AA 2 0.189 -0.374 28.764 -4.026 0.849 2.759 33.626 A A 4 5 19.438 A A 19 18 3.387 11.047 0.076 -1.407 AA_A4G5:C18U19_AA 3 0.306 -0.539 31.807 -4.179 -0.083 2.839 31.438 A A 5 6 8.424 A A 18 17 3.040 4.548 -0.213 -1.254 AA_G5U6:A17C18_AA 4 -1.250 2.315 31.091 -3.084 0.181 2.856 30.389 A A 6 7 7.258 A A 17 16 3.039 3.794 0.323 -1.394 AA_U6C7:G16A17_AA 5 1.044 -1.996 30.139 -3.349 -0.426 2.917 32.743 A A 7 8 13.535 A A 16 15 3.329 7.562 0.097 -1.455 AA_C7U8:A15G16_AA 6 1.543 -2.761 31.845 -3.844 0.086 2.390 34.539 A A 8 9 30.045 A A 15 14 3.725 17.080 -0.449 -1.848 AA_U8C9:G14A15_AA 7 -2.502 4.401 30.030 -5.769 0.367 2.595 90.132 A A 9 10 7.383 A A 14 13 2.822 10.353 -0.671 0.047 AA_C9U10:G13G14_AA 8 24.934 -17.781 86.836 -0.145 0.904 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2002-11-06 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2002-08-11 REL REL This sequence is part of human U4 snRNA. sample This structure was determined using standard 2D homonuclear techniques and complete relaxation matrix analysis of NOE intensities. Lowest total energy (a weighted sum of conformational energy and restraint energy). 15 10 2D NOESY 2D NOESY DQF-COSY 2D TOCSY natural abundance 13C-HMQC 10 mM sodium phosphate & 50 mM NaCl 6.4 ambient 303 K 10 mM sodium phosphate & 50 mM NaCl 6.4 ambient 293 K Structures are based on 200 distance restraints, of which 140 are quantitative bounds for nonexchangeable protons calculated with MARDIGRAS, 56 are upper bounds for exchangeable protons, and 4 are hydrogen bond restraints. complete relaxation matrix; random error analysis of NOE; torsion angle dynamics; simulated annealing using Metropolis Monte Carlo; restrained minimization 1 lowest total energy 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride D2O 1 mM RNA; 10 mM sodium phosphate buffer; 50 mM sodium chloride 90% H2O/10% D2O Varian Associates, Inc. collection VNMR 6.1 Delaglio processing NMRPipe 2.1 Goddard & Kneller data analysis Sparky 3.0 Borgias et al. iterative matrix relaxation MARDIGRAS 3.2 Guentert refinement DYANA 1.5 Ulyanov et al. refinement miniCarlo 600 Varian INOVA G 1 n 1 G 1 A A 2 n 2 A 2 A C 3 n 3 C 3 A A 4 n 4 A 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A C 7 n 7 C 7 A U 8 n 8 U 8 A C 9 n 9 C 9 A U 10 n 10 U 10 A A 11 n 11 A 11 A C 12 n 12 C 12 A G 13 n 13 G 13 A G 14 n 14 G 14 A A 15 n 15 A 15 A G 16 n 16 G 16 A A 17 n 17 A 17 A C 18 n 18 C 18 A U 19 n 19 U 19 A G 20 n 20 G 20 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 7 5.61 0.80 101.50 107.11 A A A C3' C2' C1' A A A 15 15 15 N 3' Stem-Loop from Human U4 SNRNA 1 N N hydrog G-A MISPAIR A G 1 A N2 G 1 1_555 A A 2 A N7 A 2 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 20 A N1 G 20 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 20 A O6 G 20 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 20 A N2 G 20 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 19 A N3 U 19 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 19 A O4 U 19 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 18 A N3 C 18 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 18 A O2 C 18 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 18 A N4 C 18 1_555 hydrog WATSON-CRICK A U 6 A N3 U 6 1_555 A A 17 A N1 A 17 1_555 hydrog WATSON-CRICK A U 6 A O4 U 6 1_555 A A 17 A N6 A 17 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 A G 16 A N2 G 16 1_555 hydrog WATSON-CRICK A U 8 A N3 U 8 1_555 A A 15 A N1 A 15 1_555 hydrog WATSON-CRICK A U 8 A O4 U 8 1_555 A A 15 A N6 A 15 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 A G 14 A N1 G 14 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 A G 14 A O6 G 14 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 A G 14 A N2 G 14 1_555 hydrog U-G MISPAIR A U 10 A O2 U 10 1_555 A G 13 A N1 G 13 1_555 hydrog TYPE_28_PAIR A U 10 A N3 U 10 1_555 A G 14 A O6 G 14 1_555 hydrog TYPE_28_PAIR A U 10 A O2 U 10 1_555 A G 14 A N1 G 14 1_555 RNA RIBONUCLEIC ACID, RNA OLIGONUCLEOTIDE, STEM-AND-LOOP, U4 SMALL NUCLEAR RNA, UACG TETRALOOP, RNA 1MFJ PDB 1 1MFJ 1 20 1MFJ 1 20 1MFJ A 1 1 20 1 P 1