data_17901 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Partial 1H, 13C, 15N Chemical Shift Assignments for the U6 Spliceosomal snRNA 5' Stem-Loop 30-mer Construct. ; _BMRB_accession_number 17901 _BMRB_flat_file_name bmr17901.str _Entry_type original _Submission_date 2011-08-29 _Accession_date 2011-08-29 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'This entry details partial chemical shift assignments for a 30-mer RNA construct derived from the yeast U6 spiceosomal RNA, corresponding to positions 1-29. An extra G residue was incorporated at the 5'-end to promote transcription, but is not included in the chemical shift assignments.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Butcher Samuel E. . 2 Clos Lawrence J. II stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 36 "13C chemical shifts" 17 "15N chemical shifts" 12 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-09-28 original author . stop_ _Original_release_date 2011-09-28 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title "Partial 1H, 13C, 15N Chemical Shift Assignments for the U6 Spliceosomal snRNA 5' Stem-Loop 30-mer Construct." _Citation_status 'in preparation' _Citation_type 'BMRB only' _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Clos Lawrence J. II 2 Butcher Samuel E. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . loop_ _Keyword FSL RNA Spliceosome 'U6 snRNA' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Spliceosome _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'U6 snRNA' $U6_FSL_G1-29 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_U6_FSL_G1-29 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common U6_FSL_G1-29 _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'Participates in Eukaryotic splicing' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; GGUUCGCGAAGUAACCCUUC GUGGACAUUU ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 . G 2 1 G 3 2 U 4 3 U 5 4 C 6 5 G 7 6 C 8 7 G 9 8 A 10 9 A 11 10 G 12 11 U 13 12 A 14 13 A 15 14 C 16 15 C 17 16 C 18 17 U 19 18 U 20 19 C 21 20 G 22 21 U 23 22 G 24 23 G 25 24 A 26 25 C 27 26 A 28 27 U 29 28 U 30 29 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 $U6_FSL_G1-29 '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 _Details $U6_FSL_G1-29 'enzymatic semisynthesis' . Saccharomyces cerevisiae . . 'Synthesized by in vitro transcription from short DNA template' 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 $U6_FSL_G1-29 1.5 mM '[U-13C; U-15N]' DTT 10 uM 'natural abundance' 'potassium phosphate' 15 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 750 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _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_1 save_ save_2D_1H-13C_HSQC_aliphatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 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' 15 . 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 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_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' '2D 1H-1H TOCSY' '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 'U6 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 2 G H1 H 12.713 0.003 1 2 1 2 G N1 N 147.532 0.000 1 3 2 3 U H3 H 14.283 0.003 1 4 2 3 U N3 N 162.024 0.000 1 5 3 4 U H3 H 12.184 0.002 1 6 3 4 U N3 N 158.591 0.000 1 7 4 5 C H5 H 5.719 0.005 1 8 4 5 C H6 H 7.935 0.000 1 9 4 5 C H41 H 6.943 0.001 2 10 4 5 C H42 H 8.437 0.000 2 11 4 5 C C5 C 97.517 0.000 1 12 5 6 G H1 H 10.924 0.001 1 13 5 6 G N1 N 144.020 0.000 1 14 6 7 C H5 H 5.234 0.000 1 15 6 7 C C5 C 97.215 0.000 1 16 7 8 G H1 H 11.883 0.001 1 17 7 8 G N1 N 145.800 0.000 1 18 8 9 A H2 H 7.048 0.000 1 19 8 9 A C2 C 152.657 0.000 1 20 9 10 A H2 H 7.503 0.000 1 21 9 10 A C2 C 153.170 0.000 1 22 10 11 G H1 H 13.191 0.003 1 23 10 11 G N1 N 147.850 0.000 1 24 17 18 U H3 H 14.002 0.008 1 25 17 18 U N3 N 162.236 0.000 1 26 18 19 U H1' H 5.646 0.000 1 27 18 19 U H3 H 13.854 0.002 1 28 18 19 U H5 H 5.603 0.000 1 29 18 19 U C1' C 93.490 0.000 1 30 18 19 U N3 N 162.691 0.000 1 31 19 20 C H1' H 5.498 0.000 1 32 19 20 C H5 H 5.621 0.002 1 33 19 20 C H6 H 7.809 0.004 1 34 19 20 C H41 H 6.875 0.001 2 35 19 20 C H42 H 8.177 0.000 2 36 19 20 C C1' C 93.474 0.000 1 37 19 20 C C5 C 97.561 0.000 1 38 20 21 G H1 H 12.904 0.001 1 39 20 21 G H8 H 7.450 0.000 1 40 20 21 G C8 C 136.000 0.000 1 41 20 21 G N1 N 147.226 0.000 1 42 21 22 U H3 H 11.784 0.001 1 43 21 22 U H5 H 5.372 0.000 1 44 21 22 U C5 C 103.830 0.000 1 45 21 22 U N3 N 158.313 0.000 1 46 22 23 G H1 H 12.296 0.002 1 47 22 23 G H8 H 7.870 0.000 1 48 22 23 G C8 C 137.430 0.000 1 49 22 23 G N1 N 147.421 0.000 1 50 23 24 G H1 H 10.563 0.001 1 51 23 24 G H1' H 5.710 0.000 1 52 23 24 G H8 H 7.239 0.000 1 53 23 24 G C1' C 93.463 0.000 1 54 23 24 G C8 C 137.174 0.000 1 55 23 24 G N1 N 142.588 0.000 1 56 24 25 A H2 H 7.863 0.000 1 57 24 25 A C2 C 153.989 0.000 1 58 25 26 C H5 H 5.169 0.000 1 59 25 26 C H6 H 7.279 0.000 1 60 25 26 C C5 C 97.270 0.000 1 61 25 26 C C6 C 139.833 0.000 1 62 26 27 A H2 H 7.400 0.000 1 63 26 27 A C2 C 154.205 0.000 1 64 27 28 U H5 H 5.359 0.000 1 65 27 28 U C5 C 104.169 0.000 1 stop_ save_