data_5321 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of a SRP19 binding domain in human SRP RNA ; _BMRB_accession_number 5321 _BMRB_flat_file_name bmr5321.str _Entry_type original _Submission_date 2002-03-14 _Accession_date 2002-03-15 _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 Sakamoto T. . . 2 Morita S. . . 3 Tabata K. . . 4 Nakamura K. . . 5 Kawai G. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 164 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-05-20 original author . stop_ _Original_release_date 2002-05-20 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution Structure of a SRP19 Binding Domain in Human SRP RNA' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22148823 _PubMed_ID 12153712 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sakamoto T. . . 2 Morita S. . . 3 Tabata K. . . 4 Nakamura K. . . 5 Kawai G. . . stop_ _Journal_abbreviation 'J. Biochem. (Tokyo)' _Journal_volume 132 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 177 _Page_last 182 _Year 2002 _Details . loop_ _Keyword 'GNAR motif' 'GNRA tetraloop' 'helix 6' NMR 'RNA structure' 'signal recognition particle' tetraloop stop_ save_ ################################## # Molecular system description # ################################## save_system_helix_6_of_SRP_RNA _Saveframe_category molecular_system _Mol_system_name 'helix 6 of signal recognition particle RNA' _Abbreviation_common 'helix 6 of SRP RNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'helix 6 of SRP RNA' $helix_6_of_SRP_RNA 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_helix_6_of_SRP_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'helix 6 of signal recognition particle RNA' _Abbreviation_common 'helix 6 of SRP RNA' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GGUGACCUCCCGGGAGCGGG GGACCACCA ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 G 5 A 6 C 7 C 8 U 9 C 10 C 11 C 12 G 13 G 14 G 15 A 16 G 17 C 18 G 19 G 20 G 21 G 22 G 23 A 24 C 25 C 26 A 27 C 28 C 29 A 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 $helix_6_of_SRP_RNA 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 $helix_6_of_SRP_RNA '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 $helix_6_of_SRP_RNA 0.5 mM . 'sodium phosphate' 20 mM . NaCl 50 mM . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $helix_6_of_SRP_RNA 0.5 mM '[U-15N; U-13C]-Guanosine,Uridine' 'sodium phosphate' 20 mM . NaCl 50 mM . stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $helix_6_of_SRP_RNA 0.5 mM '[U-15N; U-13C]-Adenosine,Cytidine' 'sodium phosphate' 20 mM . NaCl 50 mM . stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $helix_6_of_SRP_RNA 0.5 mM '[U-15N; U-13C]-Guanosine,Cytidine' 'sodium phosphate' 20 mM . NaCl 50 mM . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.1 loop_ _Task collection stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1B loop_ _Task collection stop_ _Details . save_ save_FELIX _Saveframe_category software _Name FELIX _Version 97.0 loop_ _Task 'data analysis' stop_ _Details . save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 97.0 loop_ _Task refinement 'structure solution' stop_ _Details BIOSYM save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_HNN-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HNN-COSY' _Sample_label . save_ save_2D_half_filtered_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D half filtered NOESY' _Sample_label . save_ save_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_2D_HP-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HP-COSY' _Sample_label . save_ save_2D_TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_2D_HCCH-COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCCH-COSY' _Sample_label . save_ save_2D_HCCH-TOCSY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCCH-TOCSY' _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 HNN-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D half filtered NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HP-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCCH-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D HCCH-TOCSY' _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' 70 . mM pH 6.5 0.2 n/a pressure 1 . atm temperature 298 1 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 _Reference_correction_type H2O H 1 . ppm 4.782 internal direct . internal . 1.0 temperature 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_shifts_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 'helix 6 of SRP RNA' _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 12.09 0.02 1 2 . 1 G H8 H 8.22 0.02 1 3 . 1 G H1' H 5.95 0.02 1 4 . 1 G H2' H 4.93 0.02 1 5 . 2 G H1 H 13.10 0.02 1 6 . 2 G H8 H 7.42 0.02 1 7 . 2 G H1' H 5.82 0.02 1 8 . 2 G H2' H 4.53 0.02 1 9 . 2 G H3' H 4.69 0.02 1 10 . 3 U H3 H 13.47 0.02 1 11 . 3 U H5 H 5.10 0.02 1 12 . 3 U H6 H 7.69 0.02 1 13 . 3 U H1' H 5.56 0.02 1 14 . 3 U H2' H 4.73 0.02 1 15 . 3 U H3' H 4.53 0.02 1 16 . 4 G H1 H 12.05 0.02 1 17 . 4 G H8 H 7.68 0.02 1 18 . 4 G H1' H 5.75 0.02 1 19 . 4 G H2' H 4.60 0.02 1 20 . 4 G H3' H 4.56 0.02 1 21 . 5 A H2 H 8.10 0.02 1 22 . 5 A H8 H 8.02 0.02 1 23 . 5 A H1' H 5.95 0.02 1 24 . 5 A H2' H 4.48 0.02 1 25 . 5 A H3' H 4.54 0.02 1 26 . 6 C H5 H 5.31 0.02 1 27 . 6 C H6 H 7.76 0.02 1 28 . 6 C H1' H 5.56 0.02 1 29 . 6 C H2' H 4.46 0.02 1 30 . 6 C H3' H 4.32 0.02 1 31 . 7 C H5 H 5.59 0.02 1 32 . 7 C H6 H 7.66 0.02 1 33 . 7 C H1' H 5.65 0.02 1 34 . 7 C H2' H 4.50 0.02 1 35 . 7 C H3' H 4.45 0.02 1 36 . 8 U H3 H 11.94 0.02 1 37 . 8 U H5 H 5.73 0.02 1 38 . 8 U H6 H 7.95 0.02 1 39 . 8 U H1' H 5.61 0.02 1 40 . 8 U H2' H 4.12 0.02 1 41 . 8 U H3' H 4.59 0.02 1 42 . 9 C H5 H 5.68 0.02 1 43 . 9 C H6 H 7.98 0.02 1 44 . 9 C H1' H 5.53 0.02 1 45 . 9 C H2' H 4.36 0.02 1 46 . 9 C H3' H 4.55 0.02 1 47 . 10 C H5 H 5.50 0.02 1 48 . 10 C H6 H 7.82 0.02 1 49 . 10 C H1' H 5.45 0.02 1 50 . 10 C H2' H 4.35 0.02 1 51 . 10 C H3' H 4.42 0.02 1 52 . 11 C H5 H 5.45 0.02 1 53 . 11 C H6 H 7.78 0.02 1 54 . 11 C H1' H 5.47 0.02 1 55 . 11 C H2' H 4.48 0.02 1 56 . 11 C H3' H 4.57 0.02 1 57 . 11 C H4' H 4.40 0.02 1 58 . 11 C H5' H 4.37 0.02 2 59 . 11 C H5'' H 4.10 0.02 2 60 . 12 G H1 H 12.25 0.02 1 61 . 12 G H8 H 7.48 0.02 1 62 . 12 G H1' H 5.69 0.02 1 63 . 12 G H2' H 4.62 0.02 1 64 . 12 G H3' H 4.45 0.02 1 65 . 12 G H4' H 4.12 0.02 1 66 . 12 G H5' H 4.09 0.02 2 67 . 13 G H21 H 6.25 0.02 2 68 . 13 G H8 H 7.24 0.02 1 69 . 13 G H1' H 5.61 0.02 1 70 . 13 G H2' H 4.34 0.02 1 71 . 13 G H3' H 4.59 0.02 1 72 . 13 G H4' H 4.45 0.02 1 73 . 14 G H8 H 7.81 0.02 1 74 . 14 G H1' H 5.56 0.02 1 75 . 14 G H2' H 4.72 0.02 1 76 . 14 G H3' H 4.57 0.02 1 77 . 14 G H4' H 4.29 0.02 1 78 . 14 G H5' H 4.00 0.02 2 79 . 14 G H5'' H 4.20 0.02 2 80 . 15 A H2 H 8.00 0.02 1 81 . 15 A H8 H 8.16 0.02 1 82 . 15 A H1' H 5.90 0.02 1 83 . 15 A H2' H 4.59 0.02 1 84 . 15 A H3' H 4.72 0.02 1 85 . 15 A H4' H 4.42 0.02 1 86 . 15 A H5' H 4.01 0.02 2 87 . 15 A H5'' H 4.41 0.02 2 88 . 16 G H8 H 7.78 0.02 1 89 . 16 G H1' H 5.92 0.02 1 90 . 16 G H2' H 4.73 0.02 1 91 . 16 G H3' H 4.85 0.02 1 92 . 16 G H4' H 4.53 0.02 1 93 . 16 G H5' H 4.24 0.02 2 94 . 16 G H5'' H 4.41 0.02 2 95 . 17 C H5 H 6.00 0.02 1 96 . 17 C H6 H 7.90 0.02 1 97 . 17 C H1' H 5.05 0.02 1 98 . 17 C H2' H 4.59 0.02 1 99 . 17 C H3' H 4.41 0.02 1 100 . 17 C H4' H 4.30 0.02 1 101 . 17 C H5' H 4.28 0.02 2 102 . 18 G H1 H 12.25 0.02 1 103 . 18 G H8 H 7.66 0.02 1 104 . 18 G H1' H 5.73 0.02 1 105 . 18 G H2' H 4.63 0.02 1 106 . 18 G H3' H 4.59 0.02 1 107 . 18 G H4' H 4.47 0.02 1 108 . 19 G H1 H 12.66 0.02 1 109 . 19 G H8 H 7.25 0.02 1 110 . 19 G H1' H 5.75 0.02 1 111 . 19 G H2' H 4.53 0.02 1 112 . 19 G H3' H 4.48 0.02 1 113 . 20 G H1 H 12.49 0.02 1 114 . 20 G H8 H 7.22 0.02 1 115 . 20 G H1' H 5.81 0.02 1 116 . 20 G H2' H 4.55 0.02 1 117 . 20 G H3' H 4.52 0.02 1 118 . 21 G H1 H 10.78 0.02 1 119 . 21 G H8 H 7.06 0.02 1 120 . 21 G H1' H 5.75 0.02 1 121 . 21 G H2' H 4.80 0.02 1 122 . 21 G H3' H 4.29 0.02 1 123 . 22 G H1 H 12.69 0.02 1 124 . 22 G H8 H 7.27 0.02 1 125 . 22 G H1' H 5.77 0.02 1 126 . 22 G H2' H 4.66 0.02 1 127 . 22 G H3' H 4.61 0.02 1 128 . 23 A H2 H 8.23 0.02 1 129 . 23 A H8 H 8.02 0.02 1 130 . 23 A H1' H 5.98 0.02 1 131 . 23 A H2' H 4.30 0.02 1 132 . 23 A H3' H 4.55 0.02 1 133 . 24 C H5 H 5.40 0.02 1 134 . 24 C H6 H 7.77 0.02 1 135 . 24 C H1' H 5.54 0.02 1 136 . 24 C H2' H 4.13 0.02 1 137 . 24 C H3' H 4.56 0.02 1 138 . 25 C H5 H 5.64 0.02 1 139 . 25 C H6 H 7.81 0.02 1 140 . 25 C H1' H 5.63 0.02 1 141 . 25 C H2' H 4.38 0.02 1 142 . 25 C H3' H 4.59 0.02 1 143 . 25 C H4' H 4.14 0.02 1 144 . 26 A H2 H 7.38 0.02 1 145 . 26 A H8 H 8.12 0.02 1 146 . 26 A H1' H 5.86 0.02 1 147 . 26 A H2' H 4.49 0.02 1 148 . 26 A H3' H 4.67 0.02 1 149 . 26 A H4' H 4.38 0.02 1 150 . 27 C H5 H 5.18 0.02 1 151 . 27 C H6 H 7.59 0.02 1 152 . 27 C H1' H 5.42 0.02 1 153 . 27 C H2' H 4.38 0.02 1 154 . 27 C H3' H 4.50 0.02 1 155 . 27 C H4' H 4.21 0.02 1 156 . 28 C H5 H 5.38 0.02 1 157 . 28 C H6 H 7.61 0.02 1 158 . 28 C H1' H 5.47 0.02 1 159 . 28 C H2' H 4.40 0.02 1 160 . 28 C H3' H 4.45 0.02 1 161 . 29 A H2 H 7.36 0.02 1 162 . 29 A H8 H 8.02 0.02 1 163 . 29 A H1' H 5.98 0.02 1 164 . 29 A H2' H 4.05 0.02 1 stop_ save_