data_17961 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; S. cerevisiae U2/U6 snRNA complex ; _BMRB_accession_number 17961 _BMRB_flat_file_name bmr17961.str _Entry_type original _Submission_date 2011-09-26 _Accession_date 2011-09-26 _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 Burke Jordan E. . 2 Sashital Dipali G. . 3 Zuo Xiaobing . . 4 Wang Yun-Xing . . 5 Butcher Samuel E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 140 "15N chemical shifts" 54 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-04-04 update BMRB 'update entry citation' 2012-02-12 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of the yeast U2/U6 snRNA complex.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22328579 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Burke Jordan E. . 2 Sashital Dipali G. . 3 Zuo Xiaobing . . 4 Wang Yun-Xing . . 5 Butcher Samuel E. . stop_ _Journal_abbreviation RNA _Journal_name_full 'RNA (New York, N.Y.)' _Journal_volume 18 _Journal_issue 4 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 673 _Page_last 683 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name U2U6111 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label U2U6111 $U2U6111 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_U2U6111 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common U2U6111 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'pre-mRNA splicing' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 111 _Mol_residue_sequence ; GGCAAUACAGAGAUGAUCAG CAGUUCCCCUGCAUAAGGAU GAACCGUUUUACAAAGAGAU UUCUUCGGGAAUCUCUUUGC CUUUUGGCUUAGAUCAAGUG UAGUAUCUGUC ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 A 5 A 6 U 7 A 8 C 9 A 10 G 11 A 12 G 13 A 14 U 15 G 16 A 17 U 18 C 19 A 20 G 21 C 22 A 23 G 24 U 25 U 26 C 27 C 28 C 29 C 30 U 31 G 32 C 33 A 34 U 35 A 36 A 37 G 38 G 39 A 40 U 41 G 42 A 43 A 44 C 45 C 46 G 47 U 48 U 49 U 50 U 51 A 52 C 53 A 54 A 55 A 56 G 57 A 58 G 59 A 60 U 61 U 62 U 63 C 64 U 65 U 66 C 67 G 68 G 69 G 70 A 71 A 72 U 73 C 74 U 75 C 76 U 77 U 78 U 79 G 80 C 81 C 82 U 83 U 84 U 85 U 86 G 87 G 88 C 89 U 90 U 91 A 92 G 93 A 94 U 95 C 96 A 97 A 98 G 99 U 100 G 101 U 102 A 103 G 104 U 105 A 106 U 107 C 108 U 109 G 110 U 111 C 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 $U2U6111 'baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae 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 $U2U6111 'cell free synthesis' . E. "coli - cell free" . pUC19 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 $U2U6111 0.6-0.8 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $U2U6111 0.6-0.8 mM '[U-13C; U-15N]-Gua; [U-13C; U-15N]-Ura' 'potassium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $U2U6111 0.3-0.5 mM '[U-13C; U-15N]-Gua; [U-13C; U-15N]-Ura' 'potassium phosphate' 20 mM 'natural abundance' 'magnesium chloride' 2 mM 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $U2U6111 0.6-0.8 mM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' 'magnesium chloride' 2 mM 'natural abundance' stop_ save_ save_sample_5 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $U2U6111 0.3-0.5 mM '[U-13C; U-15N]-Gua; [U-13C; U-15N]-Ura' 'potassium phosphate' 20 mM 'natural abundance' 'magnesium chloride' 2 mM 'natural abundance' 'Pf1 phage' 10 mg/ml 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_MC-SYM _Saveframe_category software _Name MC-SYM _Version 4.2.2 loop_ _Vendor _Address _Electronic_address 'Parisien, Major' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.21 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Rotvieh _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ save_Telemark _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HMQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HMQC' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_3 save_ save_2D_1H-15N_HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HMQC' _Sample_label $sample_4 save_ save_2D_1H-15N_TROSY-HMQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N TROSY-HMQC' _Sample_label $sample_2 save_ save_2D_1H-15N_TROSY-HMQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N TROSY-HMQC' _Sample_label $sample_4 save_ save_2D_1H-15N_HMQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HMQC' _Sample_label $sample_5 save_ save_2D_1H-15N_TROSY-HMQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N TROSY-HMQC' _Sample_label $sample_5 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 . mM pH 7.0 . pH pressure 1 . atm temperature 283 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name U2U6111 _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 2 2 G H1 H 11.559 . 1 2 4 4 A H2 H 7.039 . 1 3 5 5 A H2 H 6.853 . 1 4 6 6 U H3 H 13.106 . 1 5 7 7 A H2 H 7.102 . 1 6 15 15 G H1 H 11.608 . 1 7 16 16 A H2 H 7.699 . 1 8 17 17 U H3 H 14.096 . 1 9 23 23 G H1 H 13.286 . 1 10 24 24 U H3 H 14.313 . 1 11 25 25 U H3 H 13.672 . 1 12 30 30 U H3 H 13.546 . 1 13 37 37 G H1 H 12.71 . 1 14 41 41 G H1 H 12.426 . 1 15 42 42 A H2 H 7.137 . 1 16 43 43 A H2 H 7.753 . 1 17 55 55 A H2 H 7.296 . 1 18 56 56 G H1 H 12.447 . 1 19 57 57 A H2 H 7.407 . 1 20 58 58 G H1 H 12.567 . 1 21 59 59 A H2 H 7.766 . 1 22 60 60 U H3 H 14.065 . 1 23 61 61 U H3 H 13.633 . 1 24 62 62 U H3 H 11.755 . 1 25 67 67 G H1 H 9.828 . 1 26 68 68 G H1 H 12.758 . 1 27 69 69 G H1 H 10.405 . 1 28 70 70 A H2 H 7.279 . 1 29 71 71 A H2 H 7.772 . 1 30 72 72 U H3 H 14.147 . 1 31 74 74 U H3 H 13.961 . 1 32 76 76 U H3 H 13.881 . 1 33 92 92 G H1 H 11.935 . 1 34 93 93 A H2 H 7.609 . 1 35 99 99 U H3 H 14.107 . 1 36 103 103 G H1 H 12.595 . 1 37 104 104 U H3 H 13.389 . 1 38 105 105 A H2 H 6.511 . 1 39 106 106 U H3 H 13.192 . 1 40 108 108 U H3 H 13.385 . 1 41 109 109 G H1 H 12.482 . 1 42 110 110 U H3 H 12.028 . 1 stop_ save_ save_assigned_chem_shift_list_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N TROSY-HMQC' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name U2U6111 _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 2 2 G H1 H 11.54 . 1 2 2 2 G N1 N 146.188 . 1 3 6 6 U H3 H 13.044 . 1 4 6 6 U N3 N 163.001 . 1 5 15 15 G H1 H 11.692 . 1 6 15 15 G N1 N 146.368 . 1 7 20 20 G H1 H 13.292 . 1 8 20 20 G N1 N 149.357 . 1 9 23 23 G H1 H 13.332 . 1 10 23 23 G N1 N 149.138 . 1 11 24 24 U H3 H 14.259 . 1 12 24 24 U N3 N 163.102 . 1 13 25 25 U H3 H 13.686 . 1 14 25 25 U N3 N 163.325 . 1 15 30 30 U H3 H 13.537 . 1 16 30 30 U N3 N 162.722 . 1 17 31 31 G H1 H 10.741 . 1 18 31 31 G N1 N 146.76 . 1 19 37 37 G H1 H 12.652 . 1 20 37 37 G N1 N 147.68 . 1 21 41 41 G H1 H 12.409 . 1 22 41 41 G N1 N 147.54 . 1 23 56 56 G N1 N 147.852 . 1 24 58 58 G H1 H 12.517 . 1 25 58 58 G N1 N 147.404 . 1 26 60 60 U H3 H 14.103 . 1 27 60 60 U N3 N 162.944 . 1 28 61 61 U H3 H 13.623 . 1 29 61 61 U N3 N 163.926 . 1 30 62 62 U H3 H 11.754 . 1 31 62 62 U N3 N 160.428 . 1 32 64 64 U H3 H 12.234 . 1 33 64 64 U N3 N 159.389 . 1 34 67 67 G H1 H 9.802 . 1 35 67 67 G N1 N 143.867 . 1 36 68 68 G H1 H 12.793 . 1 37 68 68 G N1 N 148.531 . 1 38 69 69 G H1 H 10.417 . 1 39 69 69 G N1 N 143.449 . 1 40 72 72 U H3 H 14.107 . 1 41 72 72 U N3 N 163.011 . 1 42 74 74 U H3 H 13.923 . 1 43 74 74 U N3 N 162.969 . 1 44 76 76 U H3 H 13.863 . 1 45 76 76 U N3 N 162.849 . 1 46 87 87 G H1 H 13.425 . 1 47 87 87 G N1 N 148.915 . 1 48 103 103 G H1 H 12.555 . 1 49 103 103 G N1 N 148.511 . 1 50 104 104 U H3 H 13.366 . 1 51 104 104 U N3 N 162.403 . 1 52 106 106 U H3 H 13.175 . 1 53 106 106 U N3 N 163.29 . 1 54 108 108 U H3 H 13.345 . 1 55 108 108 U N3 N 161.428 . 1 56 110 110 U H3 H 11.931 . 1 57 110 110 U N3 N 159.108 . 1 stop_ save_ save_assigned_chem_shift_list_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_3 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name U2U6111 _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 2 2 G H1 H 11.594 0.042 1 2 4 4 A H2 H 7.1 0.061 1 3 5 5 A H2 H 6.924 0.071 1 4 6 6 U H3 H 13.433 0.232 1 5 7 7 A H2 H 7.389 0.286 1 6 15 15 G H1 H 11.711 0.103 1 7 16 16 A H2 H 7.699 0 1 8 17 17 U H3 H 14.105 0.018 1 9 23 23 G H1 H 13.356 0.049 1 10 24 24 U H3 H 14.375 0.063 1 11 25 25 U H3 H 13.75 0.078 1 12 30 30 U H3 H 13.783 0.167 1 13 36 36 A H2 H 7.717 0 1 14 37 37 G H1 H 12.794 0.061 1 15 38 38 G H1 H 12.562 0 1 16 41 41 G H1 H 12.49 0.064 1 17 42 42 A H2 H 7.189 0.052 1 18 43 43 A H2 H 7.793 0.039 1 19 55 55 A H2 H 7.296 0 1 20 56 56 G H1 H 12.521 0.074 1 21 57 57 A H2 H 7.456 0.049 1 22 58 58 G H1 H 12.629 0.063 1 23 59 59 A H2 H 7.819 0.052 1 24 60 60 U H3 H 14.115 0.051 1 25 61 61 U H3 H 13.706 0.073 1 26 62 62 U H3 H 11.82 0.065 1 27 67 67 G H1 H 9.874 0.046 1 28 68 68 G H1 H 12.831 0.073 1 29 69 69 G H1 H 10.455 0.05 1 30 70 70 A H2 H 7.322 0.043 1 31 71 71 A H2 H 7.818 0.046 1 32 72 72 U H3 H 14.192 0.046 1 33 74 74 U H3 H 14.029 0.068 1 34 76 76 U H3 H 13.925 0.065 1 35 87 87 G H1 H 12.425 0 1 36 92 92 G H1 H 11.935 0 1 37 93 93 A H2 H 7.678 0.07 1 38 94 94 U H3 H 14.121 0.021 1 39 103 103 G H1 H 12.666 0.07 1 40 104 104 U H3 H 13.477 0.097 1 41 105 105 A H2 H 6.834 0.323 1 42 106 106 U H3 H 13.243 0.044 1 43 108 108 U H3 H 13.443 0.061 1 44 109 109 G H1 H 12.537 0.06 1 45 110 110 U H3 H 12.046 0.02 1 stop_ save_ save_assigned_chem_shift_list_4 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N TROSY-HMQC' stop_ loop_ _Sample_label $sample_4 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name U2U6111 _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 2 2 G H1 H 11.564 . 1 2 2 2 G N1 N 145.956 . 1 3 6 6 U H3 H 13.19 . 1 4 6 6 U N3 N 161.622 . 1 5 15 15 G H1 H 11.681 . 1 6 15 15 G N1 N 146.629 . 1 7 23 23 G H1 H 13.426 . 1 8 23 23 G N1 N 148.956 . 1 9 24 24 U H3 H 14.373 . 1 10 24 24 U N3 N 163.121 . 1 11 25 25 U H3 H 13.73 . 1 12 25 25 U N3 N 163.069 . 1 13 30 30 U H3 H 13.884 . 1 14 30 30 U N3 N 162.771 . 1 15 37 37 G H1 H 12.791 . 1 16 37 37 G N1 N 147.557 . 1 17 41 41 G H1 H 12.457 . 1 18 41 41 G N1 N 147.775 . 1 19 56 56 G H1 H 12.514 . 1 20 56 56 G N1 N 147.258 . 1 21 58 58 G H1 H 12.598 . 1 22 58 58 G N1 N 147.29 . 1 23 60 60 U H3 H 14.105 . 1 24 60 60 U N3 N 163.026 . 1 25 61 61 U H3 H 13.684 . 1 26 61 61 U N3 N 162.671 . 1 27 62 62 U H3 H 11.784 . 1 28 62 62 U N3 N 160.541 . 1 29 64 64 U H3 H 12.144 . 1 30 64 64 U N3 N 159.29 . 1 31 67 67 G H1 H 9.821 . 1 32 67 67 G N1 N 143.939 . 1 33 68 68 G H1 H 12.854 . 1 34 68 68 G N1 N 148.552 . 1 35 69 69 G H1 H 10.419 . 1 36 69 69 G N1 N 143.456 . 1 37 72 72 U H3 H 14.153 . 1 38 72 72 U N3 N 163.109 . 1 39 74 74 U H3 H 14.055 . 1 40 74 74 U N3 N 162.97 . 1 41 76 76 U H3 H 14.015 . 1 42 76 76 U N3 N 163.055 . 1 43 103 103 G H1 H 12.698 . 1 44 103 103 G N1 N 148.518 . 1 45 106 106 U H3 H 13.205 . 1 46 106 106 U N3 N 163.389 . 1 47 108 108 U H3 H 13.383 . 1 48 108 108 U N3 N 162.439 . 1 49 110 110 U H3 H 11.896 . 1 50 110 110 U N3 N 159.111 . 1 stop_ save_