data_19081 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the P4 hairpin of the CPEB3 ribozyme ; _BMRB_accession_number 19081 _BMRB_flat_file_name bmr19081.str _Entry_type original _Submission_date 2013-03-08 _Accession_date 2013-03-08 _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 Skilandat Miriam . . 2 Rowinska-Zyrek Magdalena . . 3 Sigel Roland K.O. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 179 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-05-05 update BMRB 'update entry citation' 2014-03-31 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24652468 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Skilandat Miriam . . 2 Rowinska-Zyrek Magdalena . . 3 Sigel Roland K.O. . stop_ _Journal_abbreviation 'J. Biol. Inorg. Chem.' _Journal_name_full 'Journal of biological inorganic chemistry' _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 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name P4_CPEB3 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label P4_CPEB3 $P4_CPEB3 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_P4_CPEB3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common P4_CPEB3 _Molecular_mass 7051.259 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGCAGAUUCUGGUGAAUCUG CC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 C 4 4 A 5 5 G 6 6 A 7 7 U 8 8 U 9 9 C 10 10 U 11 11 G 12 12 G 13 13 U 14 14 G 15 15 A 16 16 A 17 17 U 18 18 C 19 19 U 20 20 G 21 21 C 22 22 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 _Gene_mnemonic $P4_CPEB3 Human 9606 Eukaryota Metazoa Homo sapiens cpeb3 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 $P4_CPEB3 'cell free synthesis' . . . . . 'The sequence was produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-Polymerase.' 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling D2O 100 % . . 'natural abundance' $P4_CPEB3 . mM 0.7 0.8 'natural abundance' KCl 50 mM . . 'natural abundance' EDTA 10 uM . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling D2O 10 % . . 'natural abundance' $P4_CPEB3 . mM 0.7 0.8 'natural abundance' H2O 90 % . . 'natural abundance' KCl 50 mM . . 'natural abundance' EDTA 10 uM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.0 _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details 'CRYO TXI inverse triple-resonance with actively shielded z-gradient coil' save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'CRYO TCI inverse triple-resonance with actively shielded z-gradient coil' save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details 'CRYO 5 mm QNP with actively shielded z-gradient coil' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_ save_1D_31P_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 31P' _Sample_label $sample_2 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' 50 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . 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' 50 . mM pH 6.8 . pH pressure 1 . atm temperature 278 . 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 external direct . 'separate tube (no insert) similar to the experimental sample tube' . 1.0 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_2 $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name P4_CPEB3 _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 12.863 0.005 1 2 1 1 G H1' H 5.809 0.005 1 3 1 1 G H2' H 4.939 0.005 1 4 1 1 G H3' H 4.728 0.005 1 5 1 1 G H4' H 4.530 0.005 1 6 1 1 G H5' H 4.297 0.005 1 7 1 1 G H5'' H 4.159 0.005 1 8 1 1 G H8 H 8.114 0.005 1 9 2 2 G H1 H 13.348 0.005 1 10 2 2 G H1' H 5.905 0.005 1 11 2 2 G H2' H 4.568 0.005 1 12 2 2 G H3' H 4.534 0.005 1 13 2 2 G H4' H 4.592 0.005 1 14 2 2 G H5' H 4.241 0.005 1 15 2 2 G H8 H 7.584 0.005 1 16 2 2 G H22 H 5.735 0.005 1 17 3 3 C H1' H 5.520 0.005 1 18 3 3 C H2' H 4.562 0.005 1 19 3 3 C H3' H 4.548 0.005 1 20 3 3 C H4' H 4.444 0.005 1 21 3 3 C H5 H 5.274 0.005 1 22 3 3 C H5'' H 4.130 0.005 1 23 3 3 C H6 H 7.658 0.005 1 24 3 3 C H41 H 8.504 0.005 1 25 3 3 C H42 H 6.982 0.005 1 26 4 4 A H1' H 5.958 0.005 1 27 4 4 A H2 H 6.969 0.005 1 28 4 4 A H2' H 4.721 0.005 1 29 4 4 A H3' H 4.681 0.005 1 30 4 4 A H4' H 4.514 0.005 1 31 4 4 A H5'' H 4.164 0.005 1 32 4 4 A H8 H 7.966 0.005 1 33 4 4 A H61 H 7.803 0.005 1 34 4 4 A H62 H 6.346 0.005 1 35 5 5 G H1 H 12.599 0.005 1 36 5 5 G H1' H 5.539 0.005 1 37 5 5 G H2' H 4.560 0.005 1 38 5 5 G H3' H 4.451 0.005 1 39 5 5 G H4' H 4.478 0.005 1 40 5 5 G H5'' H 4.079 0.005 1 41 5 5 G H8 H 7.124 0.005 1 42 5 5 G H21 H 8.037 0.005 1 43 5 5 G H22 H 6.073 0.005 1 44 6 6 A H1' H 5.942 0.005 1 45 6 6 A H2 H 7.767 0.005 1 46 6 6 A H2' H 4.529 0.005 1 47 6 6 A H3' H 4.574 0.005 1 48 6 6 A H5'' H 4.110 0.005 1 49 6 6 A H8 H 7.730 0.005 1 50 6 6 A H61 H 8.003 0.005 1 51 6 6 A H62 H 6.789 0.005 1 52 7 7 U H1' H 5.505 0.005 1 53 7 7 U H2' H 4.319 0.005 1 54 7 7 U H3 H 14.178 0.005 1 55 7 7 U H3' H 4.433 0.005 1 56 7 7 U H5 H 5.002 0.005 1 57 7 7 U H5'' H 4.068 0.005 1 58 7 7 U H6 H 7.614 0.005 1 59 8 8 U H1' H 5.682 0.005 1 60 8 8 U H2' H 4.346 0.005 1 61 8 8 U H3 H 13.790 0.005 1 62 8 8 U H3' H 4.514 0.005 1 63 8 8 U H4' H 4.291 0.005 1 64 8 8 U H5 H 5.510 0.005 1 65 8 8 U H5'' H 4.098 0.005 1 66 8 8 U H6 H 7.961 0.005 1 67 9 9 C H1' H 5.662 0.005 1 68 9 9 C H2' H 4.484 0.005 1 69 9 9 C H3' H 4.368 0.005 1 70 9 9 C H4' H 4.209 0.005 1 71 9 9 C H5 H 5.534 0.005 1 72 9 9 C H5' H 4.071 0.005 1 73 9 9 C H5'' H 4.017 0.005 1 74 9 9 C H6 H 7.737 0.005 1 75 9 9 C H41 H 8.272 0.005 1 76 9 9 C H42 H 7.014 0.005 1 77 10 10 U H1' H 5.273 0.005 1 78 10 10 U H2' H 4.337 0.005 1 79 10 10 U H3' H 4.306 0.005 1 80 10 10 U H4' H 4.134 0.005 1 81 10 10 U H5 H 5.566 0.005 1 82 10 10 U H5'' H 3.967 0.005 1 83 10 10 U H6 H 7.567 0.005 1 84 11 11 G H1' H 5.412 0.005 1 85 11 11 G H2' H 4.584 0.005 1 86 11 11 G H3' H 4.461 0.005 1 87 11 11 G H4' H 3.774 0.005 1 88 11 11 G H5' H 3.965 0.005 1 89 11 11 G H5'' H 3.866 0.005 1 90 11 11 G H8 H 7.669 0.005 1 91 12 12 G H1' H 5.819 0.005 1 92 12 12 G H2' H 5.038 0.005 1 93 12 12 G H3' H 5.119 0.005 1 94 12 12 G H4' H 4.364 0.005 1 95 12 12 G H5' H 4.097 0.005 1 96 12 12 G H5'' H 4.024 0.005 1 97 12 12 G H8 H 7.856 0.005 1 98 13 13 U H1' H 6.065 0.005 1 99 13 13 U H2' H 4.579 0.005 1 100 13 13 U H3' H 4.688 0.005 1 101 13 13 U H4' H 4.569 0.005 1 102 13 13 U H5 H 5.935 0.005 1 103 13 13 U H5' H 4.311 0.005 1 104 13 13 U H5'' H 4.150 0.005 1 105 13 13 U H6 H 7.911 0.005 1 106 14 14 G H1 H 12.154 0.005 1 107 14 14 G H1' H 5.155 0.005 1 108 14 14 G H2' H 4.697 0.005 1 109 14 14 G H3' H 4.560 0.005 1 110 14 14 G H4' H 4.405 0.005 1 111 14 14 G H5' H 4.369 0.005 1 112 14 14 G H5'' H 4.243 0.005 1 113 14 14 G H8 H 7.959 0.005 1 114 14 14 G H21 H 7.898 0.005 1 115 14 14 G H22 H 5.981 0.005 1 116 15 15 A H1' H 5.964 0.005 1 117 15 15 A H2 H 7.268 0.005 1 118 15 15 A H2' H 4.686 0.005 1 119 15 15 A H3' H 4.656 0.005 1 120 15 15 A H4' H 4.569 0.005 1 121 15 15 A H5'' H 4.244 0.005 1 122 15 15 A H8 H 7.859 0.005 1 123 15 15 A H61 H 8.001 0.005 1 124 15 15 A H62 H 6.728 0.005 1 125 16 16 A H1' H 5.909 0.005 1 126 16 16 A H2 H 7.775 0.005 1 127 16 16 A H2' H 4.448 0.005 1 128 16 16 A H3' H 4.572 0.005 1 129 16 16 A H4' H 4.534 0.005 1 130 16 16 A H5'' H 4.143 0.005 1 131 16 16 A H8 H 7.798 0.005 1 132 16 16 A H61 H 8.169 0.005 1 133 16 16 A H62 H 6.926 0.005 1 134 17 17 U H1' H 5.464 0.005 1 135 17 17 U H2' H 4.409 0.005 1 136 17 17 U H3 H 14.193 0.005 1 137 17 17 U H5 H 5.028 0.005 1 138 17 17 U H5'' H 4.066 0.005 1 139 17 17 U H6 H 7.570 0.005 1 140 18 18 C H1' H 5.550 0.005 1 141 18 18 C H2' H 4.345 0.005 1 142 18 18 C H3' H 4.440 0.005 1 143 18 18 C H4' H 4.441 0.005 1 144 18 18 C H5 H 5.609 0.005 1 145 18 18 C H5'' H 4.078 0.005 1 146 18 18 C H6 H 7.782 0.005 1 147 18 18 C H41 H 8.433 0.005 1 148 18 18 C H42 H 7.031 0.005 1 149 19 19 U H1' H 5.487 0.005 1 150 19 19 U H2' H 4.605 0.005 1 151 19 19 U H3 H 13.421 0.005 1 152 19 19 U H5 H 5.389 0.005 1 153 19 19 U H5'' H 4.105 0.005 1 154 19 19 U H6 H 7.831 0.005 1 155 20 20 G H1 H 12.561 0.005 1 156 20 20 G H1' H 5.789 0.005 1 157 20 20 G H2' H 4.487 0.005 1 158 20 20 G H3' H 4.442 0.005 1 159 20 20 G H5'' H 4.149 0.005 1 160 20 20 G H8 H 7.776 0.005 1 161 20 20 G H21 H 8.155 0.005 1 162 20 20 G H22 H 5.971 0.005 1 163 21 21 C H1' H 5.480 0.005 1 164 21 21 C H2' H 4.221 0.005 1 165 21 21 C H3' H 4.445 0.005 1 166 21 21 C H4' H 4.393 0.005 1 167 21 21 C H5 H 5.212 0.005 1 168 21 21 C H5'' H 4.053 0.005 1 169 21 21 C H6 H 7.684 0.005 1 170 21 21 C H41 H 8.575 0.005 1 171 21 21 C H42 H 6.966 0.005 1 172 22 22 C H1' H 5.745 0.005 1 173 22 22 C H2' H 3.999 0.005 1 174 22 22 C H3' H 4.162 0.005 1 175 22 22 C H4' H 4.164 0.005 1 176 22 22 C H5 H 5.490 0.005 1 177 22 22 C H6 H 7.658 0.005 1 178 22 22 C H41 H 8.441 0.005 1 179 22 22 C H42 H 7.032 0.005 1 stop_ save_