data_5559 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Partial 1H and 13C assignments for 3'-stem-loop of human U4 small nuclear RNA ; _BMRB_accession_number 5559 _BMRB_flat_file_name bmr5559.str _Entry_type original _Submission_date 2002-10-15 _Accession_date 2002-10-16 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Comolli L. R. . 2 Ulyanov N. B. . 3 James T. L. . 4 Gmeiner W. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 117 "13C chemical shifts" 67 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-12-27 original author . stop_ _Original_release_date 2002-12-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title "NMR Structure of the 3' Stem-Loop from Human U4 snRNA" _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Comolli L. R. . 2 Ulyanov N. B. . 3 Soto A. M. . 4 Marky L. A. . 5 James T. L. . 6 Gmeiner W. H. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 30 _Journal_issue 20 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4371 _Page_last 4379 _Year 2002 _Details . loop_ _Keyword 'RIBONUCLEIC ACID' 'RNA OLIGONUCLEOTIDE' STEM-AND-LOOP 'U4 SMALL NUCLEAR RNA' 'UACG TETRALOOP' stop_ save_ ################################## # Molecular system description # ################################## save_system_3_SL_of_U4_snRNA _Saveframe_category molecular_system _Mol_system_name '3'-stem-loop of human U4 snRNA' _Abbreviation_common '3'SL of U4 snRNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '3'SL of U4 snRNA' $3_SL stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_3_SL _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'single chain of RNA' _Abbreviation_common RNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; GACAGUCUCUACGGAGACUG ; loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 C 4 A 5 G 6 U 7 C 8 U 9 C 10 U 11 A 12 C 13 G 14 G 15 A 16 G 17 A 18 C 19 U 20 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $3_SL Human 9606 Eukaryota Metazoa Homo sapiens stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $3_SL 'enzymatic semisynthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $3_SL 1 mM . 'sodium phosphate' 10 mM . NaCl 50 mM . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1 loop_ _Task collection stop_ _Details 'Varian Associates, Inc.' save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2.1 loop_ _Task processing stop_ _Details Delaglio save_ save_Sparky _Saveframe_category software _Name SPARKY _Version 3.0 loop_ _Task 'data analysis' stop_ _Details 'Goddard & Kneller' save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version 3.2 loop_ _Task 'iterative matrix relaxation' stop_ _Details 'Borgias et al.' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task refinement stop_ _Details Guentert save_ save_miniCarlo _Saveframe_category software _Name miniCarlo _Version n/a loop_ _Task refinement stop_ _Details 'Ulyanov et al.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_SS-NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D SS-NOESY' _Sample_label . save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label . save_ save_2D_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_natural_abundance_13C-HMQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'natural abundance 13C-HMQC' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D SS-NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'natural abundance 13C-HMQC' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 60 . mM pH 6.4 0.1 n/a pressure 1 . atm temperature 303 0.5 K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 60 . mM pH 6.4 0.1 n/a pressure 1 . atm temperature 293 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio TSP C 13 'methyl protons' ppm 0.00 internal indirect cylindrical internal parallel 0.2514495 TSP H 1 'methyl protons' ppm 0.00 internal direct cylindrical internal parallel 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '3'SL of U4 snRNA' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 G H1' H 5.700 0.005 1 2 . 1 G H2' H 4.738 0.002 1 3 . 1 G H8 H 8.007 0.013 1 4 . 2 A C1' C 90.952 0.1 1 5 . 2 A C2 C 155.208 0.1 1 6 . 2 A H1' H 5.985 0.010 1 7 . 2 A H2 H 8.014 0.005 1 8 . 2 A H2' H 4.776 0.009 1 9 . 2 A H8 H 8.259 0.010 1 10 . 3 C C1' C 93.152 0.1 1 11 . 3 C C5 C 98.527 0.1 1 12 . 3 C H1' H 5.412 0.011 1 13 . 3 C H2' H 4.523 0.004 1 14 . 3 C H5 H 5.699 0.014 1 15 . 3 C H6 H 7.791 0.011 1 16 . 4 A C1' C 92.733 0.1 1 17 . 4 A C2 C 152.827 0.1 1 18 . 4 A H1' H 5.969 0.002 1 19 . 4 A H2 H 7.293 0.003 1 20 . 4 A H2' H 4.766 0.002 1 21 . 4 A H5' H 4.274 0.002 1 22 . 4 A H8 H 8.143 0.004 1 23 . 5 G C1' C 92.870 0.1 1 24 . 5 G C2' C 75.441 0.1 1 25 . 5 G C8 C 136.063 0.1 1 26 . 5 G H1' H 5.632 0.001 1 27 . 5 G H2' H 4.416 0.002 1 28 . 5 G H3' H 4.499 0.004 1 29 . 5 G H4' H 4.565 0.003 1 30 . 5 G H5'' H 4.452 0.002 1 31 . 5 G H5' H 4.130 0.001 1 32 . 5 G H8 H 7.278 0.001 1 33 . 6 U C2' C 75.468 0.1 1 34 . 6 U C5 C 102.709 0.1 1 35 . 6 U H1' H 5.586 0.001 1 36 . 6 U H2' H 4.524 0.002 1 37 . 6 U H5 H 5.078 0.003 1 38 . 6 U H5' H 4.110 0.003 1 39 . 6 U H6 H 7.763 0.004 1 40 . 7 C C1' C 94.218 0.1 1 41 . 7 C C2' C 75.649 0.1 1 42 . 7 C C5 C 97.841 0.1 1 43 . 7 C H1' H 5.620 0.001 1 44 . 7 C H2' H 4.366 0.002 1 45 . 7 C H3' H 4.485 0.003 1 46 . 7 C H5 H 5.694 0.002 1 47 . 7 C H5' H 4.130 0.001 1 48 . 7 C H6 H 7.893 0.003 1 49 . 8 U C1' C 93.794 0.1 1 50 . 8 U C2' C 75.334 0.1 1 51 . 8 U C5 C 103.412 0.1 1 52 . 8 U C6 C 142.374 0.1 1 53 . 8 U H1' H 5.543 0.001 1 54 . 8 U H2' H 4.550 0.002 1 55 . 8 U H5 H 5.431 0.002 1 56 . 8 U H5'' H 4.602 0.005 1 57 . 8 U H5' H 4.124 0.003 1 58 . 8 U H6 H 7.940 0.003 1 59 . 9 C C1' C 94.002 0.1 1 60 . 9 C C2' C 75.634 0.1 1 61 . 9 C C3' C 72.089 0.1 1 62 . 9 C C5 C 97.573 0.1 1 63 . 9 C H1' H 5.560 0.003 1 64 . 9 C H2' H 4.453 0.002 1 65 . 9 C H3' H 4.328 0.004 1 66 . 9 C H5 H 5.636 0.002 1 67 . 9 C H6 H 7.776 0.003 1 68 . 10 U C1' C 94.443 0.1 1 69 . 10 U C2' C 76.032 0.1 1 70 . 10 U C5 C 105.102 0.1 1 71 . 10 U H1' H 5.555 0.001 1 72 . 10 U H2' H 3.811 0.001 1 73 . 10 U H3' H 4.597 0.004 1 74 . 10 U H4' H 4.555 0.002 1 75 . 10 U H5 H 5.757 0.002 1 76 . 10 U H5'' H 4.545 0.001 1 77 . 10 U H5' H 4.139 0.005 1 78 . 10 U H6 H 7.790 0.001 1 79 . 11 A C1' C 88.350 0.1 1 80 . 11 A C2 C 155.829 0.1 1 81 . 11 A C2' C 75.542 0.1 1 82 . 11 A C3' C 78.227 0.1 1 83 . 11 A C4' C 87.418 0.1 1 84 . 11 A C8 C 143.175 0.1 1 85 . 11 A H1' H 6.143 0.003 1 86 . 11 A H2 H 8.300 0.003 1 87 . 11 A H2' H 5.118 0.002 1 88 . 11 A H3' H 4.143 0.002 1 89 . 11 A H4' H 4.590 0.002 1 90 . 11 A H5'' H 4.074 0.002 1 91 . 11 A H5' H 4.210 0.003 1 92 . 11 A H8 H 8.779 0.002 1 93 . 12 C C1' C 89.173 0.1 1 94 . 12 C C2' C 77.612 0.1 1 95 . 12 C C3' C 80.220 0.1 1 96 . 12 C C4' C 84.548 0.1 1 97 . 12 C C5 C 98.736 0.1 1 98 . 12 C C5' C 67.486 0.1 1 99 . 12 C C6 C 142.927 0.1 1 100 . 12 C H1' H 5.966 0.002 1 101 . 12 C H2' H 4.126 0.003 1 102 . 12 C H3' H 4.515 0.002 1 103 . 12 C H4' H 3.817 0.002 1 104 . 12 C H5 H 6.180 0.001 1 105 . 12 C H5'' H 3.650 0.002 1 106 . 12 C H5' H 2.787 0.002 1 107 . 12 C H6 H 7.709 0.002 1 108 . 13 G C1' C 94.540 0.1 1 109 . 13 G C2' C 77.339 0.1 1 110 . 13 G C3' C 75.993 0.1 1 111 . 13 G C5' C 69.057 0.1 1 112 . 13 G H1' H 5.960 0.002 1 113 . 13 G H2' H 4.838 0.002 1 114 . 13 G H3' H 5.633 0.001 1 115 . 13 G H4' H 4.421 0.002 1 116 . 13 G H5'' H 4.422 0.002 1 117 . 13 G H5' H 4.209 0.002 1 118 . 13 G H8 H 7.828 0.001 1 119 . 14 G C1' C 93.152 0.1 1 120 . 14 G C2' C 75.204 0.1 1 121 . 14 G C3' C 74.686 0.1 1 122 . 14 G C5' C 69.751 0.1 1 123 . 14 G H1' H 4.437 0.004 1 124 . 14 G H2' H 4.533 0.002 1 125 . 14 G H3' H 4.353 0.004 1 126 . 14 G H4' H 4.414 0.010 1 127 . 14 G H5'' H 4.537 0.001 1 128 . 14 G H5' H 4.307 0.001 1 129 . 14 G H8 H 8.298 0.002 1 130 . 15 A C1' C 93.041 0.1 1 131 . 15 A C2 C 153.414 0.1 1 132 . 15 A C2' C 75.818 0.1 1 133 . 15 A H1' H 5.985 0.003 1 134 . 15 A H2 H 7.469 0.002 1 135 . 15 A H2' H 4.714 0.003 1 136 . 15 A H3' H 4.686 0.004 1 137 . 15 A H8 H 7.761 0.001 1 138 . 16 G C1' C 92.789 0.1 1 139 . 16 G C2' C 75.566 0.1 1 140 . 16 G C5' C 66.117 0.1 1 141 . 16 G C8 C 135.999 0.1 1 142 . 16 G H1' H 5.614 0.002 1 143 . 16 G H2' H 4.554 0.001 1 144 . 16 G H5'' H 4.461 0.001 1 145 . 16 G H5' H 4.079 0.001 1 146 . 16 G H8 H 7.117 0.003 1 147 . 17 A C1' C 93.041 0.1 1 148 . 17 A C2 C 154.212 0.1 1 149 . 17 A C2' C 75.674 0.1 1 150 . 17 A H1' H 5.985 0.003 1 151 . 17 A H2 H 7.838 0.002 1 152 . 17 A H2' H 4.614 0.002 1 153 . 17 A H5' H 4.141 0.001 1 154 . 17 A H8 H 7.800 0.002 1 155 . 18 C C1' C 94.073 0.1 1 156 . 18 C C2' C 75.656 0.1 1 157 . 18 C C3' C 72.611 0.1 1 158 . 18 C C5 C 97.454 0.1 1 159 . 18 C C5' C 65.013 0.1 1 160 . 18 C H1' H 5.392 0.002 1 161 . 18 C H2' H 4.284 0.002 1 162 . 18 C H3' H 4.337 0.003 1 163 . 18 C H4' H 4.427 0.003 1 164 . 18 C H5 H 5.244 0.002 1 165 . 18 C H5'' H 4.506 0.004 1 166 . 18 C H5' H 4.059 0.002 1 167 . 18 C H6 H 7.431 0.003 1 168 . 19 U C2' C 75.505 0.1 1 169 . 19 U C5 C 103.965 0.1 1 170 . 19 U H1' H 5.586 0.001 1 171 . 19 U H2' H 4.388 0.003 1 172 . 19 U H5 H 5.390 0.002 1 173 . 19 U H6 H 7.801 0.001 1 174 . 20 G C1' C 90.882 0.1 1 175 . 20 G C2' C 78.050 0.1 1 176 . 20 G C3' C 71.047 0.1 1 177 . 20 G C4' C 84.474 0.1 1 178 . 20 G H1' H 5.918 0.002 1 179 . 20 G H2' H 4.211 0.003 1 180 . 20 G H3' H 4.397 0.005 1 181 . 20 G H4' H 4.301 0.002 1 182 . 20 G H5'' H 4.482 0.010 1 183 . 20 G H5' H 4.106 0.002 1 184 . 20 G H8 H 7.784 0.003 1 stop_ save_