data_11607 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish ; _BMRB_accession_number 11607 _BMRB_flat_file_name bmr11607.str _Entry_type original _Submission_date 2016-02-03 _Accession_date 2016-03-17 _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 Otsu Maina . . 2 Norose Nao . . 3 Arai Nao . . 4 Terao Ryo . . 5 Kajikawa Masaki . . 6 Okada Norihiro . . 7 Kawai Gota . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 97 "13C chemical shifts" 33 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-02-06 original BMRB . stop_ _Original_release_date 2016-03-17 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish ; _Citation_status 'in preparation' _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 Otsu Maina . . 2 Norose Nao . . 3 Arai Nao . . 4 Terao Ryo . . 5 Kajikawa Masaki . . 6 Okada Norihiro . . 7 Kawai Gota . . stop_ _Journal_abbreviation 'Not known' _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 . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Reverse transcriptase recognition site of transcript of a LINE from Denio Renio, LS-1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (34-MER)' $RNA_(34-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_(34-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(34-MER) _Molecular_mass 10859.578 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 34 _Mol_residue_sequence ; GGCGCUUUGACACAAUCUAC AUUGUAAAAGCGCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 C 4 4 G 5 5 C 6 6 U 7 7 U 8 8 U 9 9 G 10 10 A 11 11 C 12 12 A 13 13 C 14 14 A 15 15 A 16 16 U 17 17 C 18 18 U 19 19 A 20 20 C 21 21 A 22 22 U 23 23 U 24 24 G 25 25 U 26 26 A 27 27 A 28 28 A 29 29 A 30 30 G 31 31 C 32 32 G 33 33 C 34 34 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 _Details $RNA_(34-MER) zebrafish 7955 Eukaryota Metazoa Denio Renio 'A part of transcript of a LINE, CR1-1_DR' 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 $RNA_(34-MER) 'enzymatic semisynthesis' . . . . . 'In vitro transcription with the T7 RNA polymerase' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_ZfL2-1-34_D2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(34-MER) 0.3 mM 'natural abundance' $RNA_(34-MER) 0.26 mM '[U-100% 13C; U-100% 15N]' 'sodium phosphate' 20 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' D2O 100 % [U-2H] stop_ save_ save_ZfL2-1-34_H2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(34-MER) 0.18 mM '[U-13C; U-15N]-Ade' $RNA_(34-MER) 0.19 mM '[U-13C; U-15N]-Gua' 'sodium phosphate' 20 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CNSSOLVE _Saveframe_category software _Name CNSSOLVE _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.32 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'grid search' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $ZfL2-1-34_D2O save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $ZfL2-1-34_D2O save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $ZfL2-1-34_D2O save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $ZfL2-1-34_D2O save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $ZfL2-1-34_H2O save_ save_2D_1H-13C_TROSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C TROSY' _Sample_label $ZfL2-1-34_D2O save_ save_2D_1H-13C_TROSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C TROSY' _Sample_label $ZfL2-1-34_D2O save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details '20 mM Phosphate sodium buffer, 50 mM NaCl' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 6.5 . pH pressure 1 . atm temperature 288 . 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 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0 na direct . . . 1 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' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $ZfL2-1-34_D2O stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (34-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 1 G H1' H 5.85 0.01 1 2 1 1 G H2' H 4.98 0.01 1 3 1 1 G H8 H 8.19 0.01 1 4 1 1 G C8 C 136.42 0.16 1 5 2 2 G H1' H 5.96 0.01 1 6 2 2 G H8 H 7.68 0.01 1 7 2 2 G C8 C 133.95 0.16 1 8 3 3 C H1' H 5.59 0.01 1 9 3 3 C H5 H 5.28 0.01 1 10 3 3 C H6 H 7.70 0.01 1 11 4 4 G H1' H 5.76 0.01 1 12 4 4 G H8 H 7.58 0.01 1 13 4 4 G C8 C 133.17 0.16 1 14 5 5 C H1' H 5.52 0.01 1 15 5 5 C H5 H 5.25 0.01 1 16 5 5 C H6 H 7.72 0.01 1 17 6 6 U H1' H 5.54 0.01 1 18 6 6 U H5 H 5.44 0.01 1 19 6 6 U H6 H 7.90 0.01 1 20 6 6 U C5 C 100.51 0.16 1 21 7 7 U H1' H 5.64 0.01 1 22 7 7 U H5 H 5.59 0.01 1 23 7 7 U H6 H 8.02 0.01 1 24 8 8 U H1' H 5.62 0.01 1 25 8 8 U H5 H 5.54 0.01 1 26 8 8 U H6 H 7.83 0.01 1 27 9 9 G H1' H 5.43 0.01 1 28 9 9 G H8 H 7.68 0.01 1 29 9 9 G C8 C 135.12 0.16 1 30 10 10 A H2 H 7.49 0.01 1 31 10 10 A H8 H 7.77 0.01 1 32 10 10 A C2 C 151.61 0.16 1 33 10 10 A C8 C 137.44 0.16 1 34 11 11 C H1' H 6.05 0.01 1 35 11 11 C H5 H 5.81 0.01 1 36 11 11 C H6 H 7.82 0.01 1 37 12 12 A H1' H 5.90 0.01 1 38 12 12 A H2 H 7.33 0.01 1 39 12 12 A H8 H 8.39 0.01 1 40 12 12 A C2 C 150.45 0.16 1 41 12 12 A C8 C 138.05 0.16 1 42 13 13 C H1' H 5.41 0.01 1 43 13 13 C H5 H 5.23 0.01 1 44 13 13 C H6 H 7.58 0.01 1 45 14 14 A H1' H 5.87 0.01 1 46 14 14 A H2 H 6.75 0.01 1 47 14 14 A H8 H 7.95 0.01 1 48 14 14 A C2 C 149.33 0.16 1 49 14 14 A C8 C 136.71 0.16 1 50 15 15 A H1' H 5.91 0.01 1 51 15 15 A H2 H 7.79 0.01 1 52 15 15 A H8 H 7.76 0.01 1 53 15 15 A C2 C 151.16 0.16 1 54 15 15 A C8 C 136.25 0.16 1 55 16 16 U H1' H 5.56 0.01 1 56 16 16 U H5 H 5.03 0.01 1 57 16 16 U H6 H 7.34 0.01 1 58 17 17 C H1' H 5.69 0.01 1 59 17 17 C H2' H 4.24 0.01 1 60 17 17 C H3' H 4.48 0.01 1 61 17 17 C H5 H 5.91 0.01 1 62 17 17 C H6 H 7.76 0.01 1 63 17 17 C C6 C 140.09 0.16 1 64 18 18 U H1' H 5.65 0.01 1 65 18 18 U H5 H 5.77 0.01 1 66 18 18 U H6 H 7.66 0.01 1 67 18 18 U C5 C 102.59 0.16 1 68 18 18 U C6 C 140.58 0.16 1 69 19 19 A H1' H 5.63 0.01 1 70 19 19 A H2 H 7.95 0.01 1 71 19 19 A H8 H 8.00 0.01 1 72 19 19 A C2 C 152.19 0.16 1 73 19 19 A C8 C 138.52 0.16 1 74 20 20 C H1' H 5.94 0.01 1 75 20 20 C H5 H 5.88 0.01 1 76 20 20 C H6 H 7.81 0.01 1 77 21 21 A H1' H 5.79 0.01 1 78 21 21 A H2 H 7.87 0.01 1 79 21 21 A H8 H 8.30 0.01 1 80 21 21 A C2 C 151.11 0.16 1 81 21 21 A C8 C 138.08 0.16 1 82 22 22 U H1' H 5.59 0.01 1 83 22 22 U H5 H 5.13 0.01 1 84 22 22 U H6 H 7.68 0.01 1 85 23 23 U H1' H 5.69 0.01 1 86 23 23 U H5 H 5.57 0.01 1 87 23 23 U H6 H 7.96 0.01 1 88 24 24 G H1' H 5.76 0.01 1 89 24 24 G H8 H 7.72 0.01 1 90 24 24 G C8 C 133.54 0.16 1 91 25 25 U H1' H 5.57 0.01 1 92 25 25 U H5 H 5.07 0.01 1 93 25 25 U H6 H 7.56 0.01 1 94 26 26 A H1' H 5.81 0.01 1 95 26 26 A H2 H 7.32 0.01 1 96 26 26 A H2' H 4.56 0.01 1 97 26 26 A H3' H 4.72 0.01 1 98 26 26 A H8 H 8.08 0.01 1 99 26 26 A C2 C 151.59 0.16 1 100 26 26 A C8 C 138.07 0.16 1 101 27 27 A H1' H 5.61 0.01 1 102 27 27 A H2 H 6.95 0.01 1 103 27 27 A H8 H 8.21 0.01 1 104 27 27 A C2 C 149.82 0.16 1 105 28 28 A H1' H 5.83 0.01 1 106 28 28 A H2 H 7.11 0.01 1 107 28 28 A H8 H 7.83 0.01 1 108 28 28 A C2 C 149.89 0.16 1 109 28 28 A C8 C 136.99 0.16 1 110 29 29 A H1' H 5.85 0.01 1 111 29 29 A H2 H 7.40 0.01 1 112 29 29 A H8 H 7.71 0.01 1 113 29 29 A C2 C 150.32 0.16 1 114 29 29 A C8 C 136.04 0.16 1 115 30 30 G H1' H 5.56 0.01 1 116 30 30 G H8 H 7.15 0.01 1 117 30 30 G C8 C 132.63 0.16 1 118 31 31 C H1' H 5.50 0.01 1 119 31 31 C H5 H 5.17 0.01 1 120 31 31 C H6 H 7.54 0.01 1 121 31 31 C C5 C 94.68 0.16 1 122 31 31 C C6 C 137.35 0.16 1 123 32 32 G H8 H 7.60 0.01 1 124 32 32 G C8 C 133.65 0.16 1 125 33 33 C H1' H 5.55 0.01 1 126 33 33 C H5 H 5.24 0.01 1 127 33 33 C H6 H 7.73 0.01 1 128 34 34 C H5 H 5.55 0.01 1 129 34 34 C H6 H 7.70 0.01 1 130 34 34 C C5 C 95.33 0.16 1 stop_ save_