data_25811 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR-SAXS/WAXS Structure of the core of the U4/U6 di-snRNA ; _BMRB_accession_number 25811 _BMRB_flat_file_name bmr25811.str _Entry_type original _Submission_date 2015-09-14 _Accession_date 2015-09-14 _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 Cornilescu Gabriel . . 2 Didychuk Allison L. . 3 Rodgers Margaret L. . 4 Michael Lauren A. . 5 Burke Jordan E. . 6 Montemayor Eric J. . 7 Hoskins Aaron A. . 8 Butcher Samuel E. . 9 Tonelli Marco . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 30 "13C chemical shifts" 5 "15N chemical shifts" 25 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-07-22 update BMRB 'update entry citation' 2015-12-28 original author 'original release' stop_ _Original_release_date 2015-12-28 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural analysis of multi-helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26655855 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cornilescu Gabriel . . 2 Didychuk Allison L. . 3 Rodgers Margaret L. . 4 Michael Lauren A. . 5 Burke Jordan E. . 6 Montemayor Eric J. . 7 Hoskins Aaron A. . 8 Butcher Samuel E. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 428 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 777 _Page_last 789 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'core of the U4/U6 di-snRNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (92-MER)' $RNA_(92-MER) 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_RNA_(92-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(92-MER) _Molecular_mass 29563.637 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 92 _Mol_residue_sequence ; GGCCUUAUGCACGGGAAAUA CGCAUAUCAGUGAGGAUUCG UCCGAGAUUGUGUUUUUGCU GGUGUAAAUCAGCAGUUCCC CUGCAUAAGGCU ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 0 G 2 1 G 3 2 C 4 3 C 5 4 U 6 5 U 7 6 A 8 7 U 9 8 G 10 9 C 11 10 A 12 11 C 13 12 G 14 13 G 15 14 G 16 15 A 17 16 A 18 17 A 19 18 U 20 19 A 21 20 C 22 21 G 23 22 C 24 23 A 25 24 U 26 25 A 27 26 U 28 27 C 29 28 A 30 29 G 31 30 U 32 31 G 33 32 A 34 33 G 35 34 G 36 35 A 37 36 U 38 37 U 39 38 C 40 39 G 41 40 U 42 41 C 43 42 C 44 43 G 45 44 A 46 45 G 47 46 A 48 47 U 49 48 U 50 49 G 51 50 U 52 51 G 53 52 U 54 53 U 55 54 U 56 55 U 57 56 U 58 57 G 59 58 C 60 59 U 61 60 G 62 61 G 63 62 U 64 63 G 65 64 U 66 65 A 67 66 A 68 67 A 69 68 U 70 69 C 71 70 A 72 71 G 73 72 C 74 73 A 75 74 G 76 75 U 77 76 U 78 77 C 79 78 C 80 79 C 81 80 C 82 81 U 83 82 G 84 83 C 85 84 A 86 85 U 87 86 A 88 87 A 89 88 G 90 89 G 91 90 C 92 91 U 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 _Strain _Gene_mnemonic $RNA_(92-MER) "baker's yeast" 4932 Eukaryota Fungi Saccharomyces cerevisiae S288C 'snR14, snR6' 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 $RNA_(92-MER) 'recombinant technology' . Escherichia coli 'DH5 alpha' pUC19 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1A _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(92-MER) 0.6 mM '[U-13C; U-15N]-Gua, -Ura' 'potassium chloride' 0.02 mM 'natural abundance' 'potassium phosphate' 0.02 mM 'natural abundance' stop_ save_ save_sample_2A _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(92-MER) 0.7 mM '[U-13C; U-15N]-Ade' 'potassium chloride' 0.02 mM 'natural abundance' 'potassium phosphate' 0.02 mM 'natural abundance' stop_ save_ save_sample_1B _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(92-MER) 0.6 mM '[U-13C; U-15N]-Gua, -Ura' 'potassium chloride' 0.02 mM 'natural abundance' 'potassium phosphate' 0.02 mM 'natural abundance' 'Pf1 phage' 5 mg/mL 'natural abundance' stop_ save_ save_sample_2B _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(92-MER) 0.7 mM '[U-13C; U-15N]-Ade' 'potassium chloride' 0.02 mM 'natural abundance' 'potassium phosphate' 0.02 mM 'natural abundance' 'Pf1 phage' 5 mg/mL 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Fleckvieh _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model INOVA _Field_strength 900 _Details . save_ save_Gelbvieh _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model INOVA _Field_strength 800 _Details . save_ save_Telemark _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ save_Dexter _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_Kerry _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1A save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1B save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2A save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2B 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' 58.5 . mM pH 7.0 . pH pressure 1 . atm temperature 273 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 58.5 . mM pH 7.0 . pH pressure 1 . atm temperature 273 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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_ _Software_label $NMRDraw stop_ loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1A $sample_2A stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (92-MER)' _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 2 G H1 H 13.232 0.01 . 2 1 2 G N1 N 149.066 0.1 . 3 4 5 U H3 H 13.659 0.01 . 4 4 5 U N3 N 162.517 0.1 . 5 5 6 U H3 H 12.788 0.01 . 6 5 6 U N3 N 162.447 0.1 . 7 7 8 U H3 H 13.129 0.01 . 8 7 8 U N3 N 162.254 0.1 . 9 8 9 G H1 H 12.160 0.01 . 10 8 9 G N1 N 147.927 0.1 . 11 10 11 A H2 H 7.094 0.01 . 12 10 11 A C2 C 153.309 0.1 . 13 12 13 G H1 H 11.960 0.01 . 14 12 13 G N1 N 147.554 0.1 . 15 13 14 G H1 H 12.205 0.01 . 16 13 14 G N1 N 147.981 0.1 . 17 14 15 G H1 H 12.075 0.01 . 18 14 15 G N1 N 147.842 0.1 . 19 15 16 A H2 H 7.152 0.01 . 20 15 16 A C2 C 153.328 0.1 . 21 21 22 G H1 H 10.748 0.01 . 22 21 22 G N1 N 144.875 0.1 . 23 23 24 A H2 H 6.880 0.01 . 24 23 24 A C2 C 153.733 0.1 . 25 33 34 G H1 H 12.275 0.01 . 26 33 34 G N1 N 147.912 0.1 . 27 34 35 G H1 H 12.013 0.01 . 28 34 35 G N1 N 147.616 0.1 . 29 39 40 G H1 H 10.169 0.01 . 30 39 40 G N1 N 144.640 0.1 . 31 40 41 U H3 H 14.431 0.01 . 32 40 41 U N3 N 164.210 0.1 . 33 49 50 G H1 H 12.736 0.01 . 34 49 50 G N1 N 148.456 0.1 . 35 50 51 U H3 H 11.562 0.01 . 36 50 51 U N3 N 159.310 0.1 . 37 51 52 G H1 H 12.704 0.01 . 38 51 52 G N1 N 148.307 0.1 . 39 60 61 G H1 H 13.085 0.01 . 40 60 61 G N1 N 149.205 0.1 . 41 61 62 G H1 H 11.240 0.01 . 42 61 62 G N1 N 145.108 0.1 . 43 62 63 U H3 H 13.723 0.01 . 44 62 63 U N3 N 161.875 0.1 . 45 63 64 G H1 H 10.198 0.01 . 46 63 64 G N1 N 146.641 0.1 . 47 67 68 A H2 H 7.973 0.01 . 48 67 68 A C2 C 153.399 0.1 . 49 68 69 U H3 H 11.761 0.01 . 50 68 69 U N3 N 159.005 0.1 . 51 76 77 U H3 H 13.080 0.01 . 52 76 77 U N3 N 162.170 0.1 . 53 85 86 U H3 H 12.983 0.01 . 54 85 86 U N3 N 162.083 0.1 . 55 87 88 A H2 H 7.287 0.01 . 56 87 88 A C2 C 153.545 0.1 . 57 88 89 G H1 H 12.662 0.01 . 58 88 89 G N1 N 147.925 0.1 . 59 89 90 G H1 H 13.099 0.01 . 60 89 90 G N1 N 148.524 0.1 . stop_ save_